omic/digital-trial
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Digital Trials pipeline configured for WES

Browse Source 
Source-only snapshot of the cluster branch for WES execution. Large
reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are
omitted: they are baked into the container images at build time and
mounted from the dreamdock-data PVC at runtime, and exceed the Gitea
request size limit.

Pipeline entry point is main.nf, which orchestrates the biotransformer,
conplex and tissue modules as a single workflow. Ligand inputs are read
from the eureka workspace; protein_zarr and chembl_db come from the
dreamdock-data PVC.
This commit is contained in:
Olamide Isreal
2026-07-27 21:59:52 +01:00
commit 9e75f44f1a
86 changed files with 10142 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
.gitignore vendored Normal file
View File

@@ -0,0 +1,12 @@
work
.nextflow
*.ignored
ncbiproteins_seq*
/input/
# Large STRING-DB reference files (baked into Docker image, not needed in git)
app_network/9606.protein.aliases.v12.0.txt
app_network/9606.protein.enrichment.terms.v12.0.txt
app_network/9606.protein.links.detailed.v12.0.txt
app_network/9606.protein.links.v12.0.txt

79
.nextflow.log Normal file
View File

@@ -0,0 +1,79 @@
Apr-03 17:30:46.267 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test_string_only.nf -params-file /data/runs/R01-caline-nac_similar/J15-string/params.json
Apr-03 17:30:46.687 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Apr-03 17:30:46.758 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Apr-03 17:30:46.876 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Apr-03 17:30:46.878 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Apr-03 17:30:46.882 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Apr-03 17:30:46.898 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Apr-03 17:30:46.926 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Apr-03 17:30:46.930 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Apr-03 17:30:46.985 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Apr-03 17:30:46.991 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Apr-03 17:30:47.022 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Apr-03 17:30:47.826 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Apr-03 17:30:47.850 [main] DEBUG nextflow.cli.CmdRun - Launching `test_string_only.nf` [deadly_faggin] DSL2 - revision: 8e3db5067a
Apr-03 17:30:47.852 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Apr-03 17:30:47.853 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Apr-03 17:30:47.855 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Apr-03 17:30:47.877 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Apr-03 17:30:47.877 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Apr-03 17:30:47.962 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Apr-03 17:30:48.062 [main] DEBUG nextflow.Session - Session UUID: 4c59e728-8373-423d-b172-5781faf18d0f
Apr-03 17:30:48.062 [main] DEBUG nextflow.Session - Run name: deadly_faggin
Apr-03 17:30:48.063 [main] DEBUG nextflow.Session - Executor pool size: 80
Apr-03 17:30:48.073 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Apr-03 17:30:48.081 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Apr-03 17:30:48.208 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 2896370@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (184.8 GB) - Swap: 0 (0)
Apr-03 17:30:48.264 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Apr-03 17:30:48.265 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Apr-03 17:30:48.294 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Apr-03 17:30:48.318 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Apr-03 17:30:48.323 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Apr-03 17:30:48.325 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Apr-03 17:30:48.355 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Apr-03 17:30:48.372 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Apr-03 17:30:48.619 [main] DEBUG nextflow.Session - Session start
Apr-03 17:30:48.966 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Apr-03 17:30:49.582 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Apr-03 17:30:49.583 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Apr-03 17:30:49.590 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Apr-03 17:30:49.601 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Apr-03 17:30:49.604 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Apr-03 17:30:49.637 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Apr-03 17:30:49.680 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: CONPLEX, MERGE_DRUG, MERGE_INTERACTIONS, NETWORK_ENRICHMENT, PREPROCESS_PROTEIN
Apr-03 17:30:49.682 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
Apr-03 17:30:49.684 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Apr-03 17:30:49.685 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_98e4d45ae72cf7d4: /data/bugra/digital_trials/test_string_only.nf
Script_158116c0b930c4dd: /data/bugra/digital_trials/main_conplex.nf
Apr-03 17:30:49.685 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Apr-03 17:30:49.685 [main] DEBUG nextflow.Session - Session await
Apr-03 17:30:49.974 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Apr-03 17:30:49.979 [Task submitter] INFO nextflow.Session - [eb/7f494f] Submitted process > NETWORK_ENRICHMENT (1)
Apr-03 17:30:49.996 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Apr-03 17:30:49.997 [Task submitter] INFO nextflow.Session - [e9/27e18e] Submitted process > NETWORK_ENRICHMENT (2)
Apr-03 17:30:50.004 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Apr-03 17:30:50.004 [Task submitter] INFO nextflow.Session - [d2/7834f1] Submitted process > NETWORK_ENRICHMENT (3)
Apr-03 17:31:00.726 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NETWORK_ENRICHMENT (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d2/7834f119d9556ee05e00daf44d874b]
Apr-03 17:31:00.728 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Apr-03 17:31:00.850 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Apr-03 17:31:02.158 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NETWORK_ENRICHMENT (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e9/27e18e08e53e0c4d45c5407deebea2]
Apr-03 17:31:02.185 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/eb/7f494fae594fe3be1f36cd54af9382]
Apr-03 17:31:02.198 [main] DEBUG nextflow.Session - Session await > all processes finished
Apr-03 17:31:02.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Apr-03 17:31:02.288 [main] DEBUG nextflow.Session - Session await > all barriers passed
Apr-03 17:31:02.291 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Apr-03 17:31:02.292 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Apr-03 17:31:02.307 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=35s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=3; peakMemory=3 GB; ]
Apr-03 17:31:02.512 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Apr-03 17:31:02.595 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Apr-03 17:31:02.595 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Apr-03 17:31:02.597 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Apr-03 17:31:02.597 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

757
.nextflow.log.1 Normal file
View File

@@ -0,0 +1,757 @@
Mar-23 12:31:42.184 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/runs/R01-caline-nac_similar/J02-digtrial/params.json
Mar-23 12:31:42.570 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Mar-23 12:31:42.599 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Mar-23 12:31:42.635 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-23 12:31:42.636 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-23 12:31:42.639 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Mar-23 12:31:42.653 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-23 12:31:42.679 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Mar-23 12:31:42.682 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Mar-23 12:31:42.722 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Mar-23 12:31:42.727 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Mar-23 12:31:42.756 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-23 12:31:43.516 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Mar-23 12:31:43.541 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [distraught_dijkstra] DSL2 - revision: 0e14afbd94
Mar-23 12:31:43.543 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-23 12:31:43.544 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Mar-23 12:31:43.547 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Mar-23 12:31:43.560 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Mar-23 12:31:43.561 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Mar-23 12:31:43.580 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Mar-23 12:31:43.662 [main] DEBUG nextflow.Session - Session UUID: df1066b0-f8aa-4422-8387-039b7127dc16
Mar-23 12:31:43.663 [main] DEBUG nextflow.Session - Run name: distraught_dijkstra
Mar-23 12:31:43.664 [main] DEBUG nextflow.Session - Executor pool size: 80
Mar-23 12:31:43.677 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Mar-23 12:31:43.686 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-23 12:31:43.723 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3209064@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (174.9 GB) - Swap: 0 (0)
Mar-23 12:31:43.756 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Mar-23 12:31:43.757 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Mar-23 12:31:43.773 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-23 12:31:43.789 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-23 12:31:43.795 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Mar-23 12:31:43.798 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Mar-23 12:31:43.832 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-23 12:31:43.844 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Mar-23 12:31:44.024 [main] DEBUG nextflow.Session - Session start
Mar-23 12:31:44.500 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-23 12:31:45.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.371 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.378 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-23 12:31:45.388 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Mar-23 12:31:45.391 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Mar-23 12:31:45.425 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Mar-23 12:31:45.535 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.536 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.538 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Mar-23 12:31:45.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Mar-23 12:31:45.556 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.556 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.558 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Mar-23 12:31:45.616 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.616 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.617 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Mar-23 12:31:45.648 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.648 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.649 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Mar-23 12:31:45.657 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.657 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.658 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Mar-23 12:31:45.669 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-23 12:31:45.669 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-23 12:31:45.670 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Mar-23 12:31:45.673 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Mar-23 12:31:45.676 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Mar-23 12:31:45.683 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Mar-23 12:31:45.684 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Mar-23 12:31:45.685 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Mar-23 12:31:45.686 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Mar-23 12:31:45.686 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/runs/R01-caline-nac_similar/input/ligands/; pattern: *.csv; options: [:]
Mar-23 12:31:45.686 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Mar-23 12:31:45.687 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Mar-23 12:31:45.687 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Mar-23 12:31:45.688 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Mar-23 12:31:45.689 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec2c89c0dbf76553: /data/bugra/digital_trials/test.nf
Script_e613579b607a4f34: /data/bugra/digital_trials/main_biotransformer.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Mar-23 12:31:45.689 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Mar-23 12:31:45.689 [main] DEBUG nextflow.Session - Session await
Mar-23 12:31:45.997 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.000 [Task submitter] INFO nextflow.Session - [11/907b6d] Submitted process > HUMAN_TRANSFORMER (27)
Mar-23 12:31:46.011 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.012 [Task submitter] INFO nextflow.Session - [dc/09507c] Submitted process > HUMAN_TRANSFORMER (20)
Mar-23 12:31:46.018 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.019 [Task submitter] INFO nextflow.Session - [20/1a7d4d] Submitted process > HUMAN_TRANSFORMER (17)
Mar-23 12:31:46.025 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.025 [Task submitter] INFO nextflow.Session - [ae/d4edcb] Submitted process > HUMAN_TRANSFORMER (21)
Mar-23 12:31:46.030 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.031 [Task submitter] INFO nextflow.Session - [66/85b2c7] Submitted process > HUMAN_TRANSFORMER (23)
Mar-23 12:31:46.037 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.037 [Task submitter] INFO nextflow.Session - [f7/f16540] Submitted process > HUMAN_TRANSFORMER (2)
Mar-23 12:31:46.042 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.042 [Task submitter] INFO nextflow.Session - [f1/b1e309] Submitted process > HUMAN_TRANSFORMER (16)
Mar-23 12:31:46.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.048 [Task submitter] INFO nextflow.Session - [1e/26e912] Submitted process > HUMAN_TRANSFORMER (14)
Mar-23 12:31:46.053 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.053 [Task submitter] INFO nextflow.Session - [f3/2167e6] Submitted process > HUMAN_TRANSFORMER (4)
Mar-23 12:31:46.058 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.059 [Task submitter] INFO nextflow.Session - [c2/2ce2ac] Submitted process > HUMAN_TRANSFORMER (1)
Mar-23 12:31:46.065 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.065 [Task submitter] INFO nextflow.Session - [9c/107234] Submitted process > HUMAN_TRANSFORMER (22)
Mar-23 12:31:46.070 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.071 [Task submitter] INFO nextflow.Session - [02/506940] Submitted process > HUMAN_TRANSFORMER (8)
Mar-23 12:31:46.076 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.076 [Task submitter] INFO nextflow.Session - [35/b8dc93] Submitted process > HUMAN_TRANSFORMER (9)
Mar-23 12:31:46.081 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.081 [Task submitter] INFO nextflow.Session - [8f/b72148] Submitted process > HUMAN_TRANSFORMER (5)
Mar-23 12:31:46.085 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.086 [Task submitter] INFO nextflow.Session - [9e/68d27c] Submitted process > HUMAN_TRANSFORMER (19)
Mar-23 12:31:46.090 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.090 [Task submitter] INFO nextflow.Session - [ce/eac613] Submitted process > HUMAN_TRANSFORMER (7)
Mar-23 12:31:46.095 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.096 [Task submitter] INFO nextflow.Session - [88/d6f61a] Submitted process > HUMAN_TRANSFORMER (11)
Mar-23 12:31:46.100 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.100 [Task submitter] INFO nextflow.Session - [de/d2b3da] Submitted process > HUMAN_TRANSFORMER (10)
Mar-23 12:31:46.105 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.106 [Task submitter] INFO nextflow.Session - [85/3e7894] Submitted process > HUMAN_TRANSFORMER (13)
Mar-23 12:31:46.128 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.129 [Task submitter] INFO nextflow.Session - [58/5a1016] Submitted process > HUMAN_TRANSFORMER (32)
Mar-23 12:31:46.135 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.136 [Task submitter] INFO nextflow.Session - [d7/93d38d] Submitted process > HUMAN_TRANSFORMER (29)
Mar-23 12:31:46.142 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.143 [Task submitter] INFO nextflow.Session - [d6/937a35] Submitted process > HUMAN_TRANSFORMER (12)
Mar-23 12:31:46.149 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.150 [Task submitter] INFO nextflow.Session - [e1/2d650b] Submitted process > HUMAN_TRANSFORMER (25)
Mar-23 12:31:46.154 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.155 [Task submitter] INFO nextflow.Session - [8c/614048] Submitted process > HUMAN_TRANSFORMER (28)
Mar-23 12:31:46.160 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.161 [Task submitter] INFO nextflow.Session - [a7/55cb6c] Submitted process > HUMAN_TRANSFORMER (31)
Mar-23 12:31:46.166 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.167 [Task submitter] INFO nextflow.Session - [7f/fffcfc] Submitted process > HUMAN_TRANSFORMER (6)
Mar-23 12:31:46.182 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.185 [Task submitter] INFO nextflow.Session - [1d/701bd0] Submitted process > HUMAN_TRANSFORMER (26)
Mar-23 12:31:46.191 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.192 [Task submitter] INFO nextflow.Session - [9d/1c6085] Submitted process > HUMAN_TRANSFORMER (24)
Mar-23 12:31:46.196 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.196 [Task submitter] INFO nextflow.Session - [ba/11e874] Submitted process > HUMAN_TRANSFORMER (30)
Mar-23 12:31:46.200 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.201 [Task submitter] INFO nextflow.Session - [30/24835f] Submitted process > HUMAN_TRANSFORMER (18)
Mar-23 12:31:46.206 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.206 [Task submitter] INFO nextflow.Session - [4f/522cdb] Submitted process > HUMAN_TRANSFORMER (15)
Mar-23 12:31:46.213 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:31:46.214 [Task submitter] INFO nextflow.Session - [f8/10a61c] Submitted process > HUMAN_TRANSFORMER (3)
Mar-23 12:32:26.204 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: HUMAN_TRANSFORMER (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/dc/09507c87b781fe02fdebde1b1c949d]
Mar-23 12:32:26.207 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-23 12:32:26.290 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-23 12:32:26.374 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:26.375 [Task submitter] INFO nextflow.Session - [a9/6c5151] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Mar-23 12:32:39.876 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c2/2ce2acf8a3662f1dc112d6f0f05ff9]
Mar-23 12:32:39.893 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:39.894 [Task submitter] INFO nextflow.Session - [57/fc4060] Submitted process > GET_FINAL_METABOLITES_STATIC (2)
Mar-23 12:32:44.956 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a9/6c51514dff4ffe92722c7cf24245b5]
Mar-23 12:32:45.061 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:45.062 [Task submitter] INFO nextflow.Session - [a5/23b628] Submitted process > CONPLEX_ALL (1)
Mar-23 12:32:49.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: GET_FINAL_METABOLITES_STATIC (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/57/fc4060cde07e37c3f0d31dfa56f1c7]
Mar-23 12:32:49.510 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:49.510 [Task submitter] INFO nextflow.Session - [69/3bf75d] Submitted process > CONPLEX_ALL (2)
Mar-23 12:32:54.794 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: HUMAN_TRANSFORMER (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9d/1c60859d50538fe14819139778987b]
Mar-23 12:32:54.826 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:54.828 [Task submitter] INFO nextflow.Session - [ac/7afb43] Submitted process > GET_FINAL_METABOLITES_STATIC (3)
Mar-23 12:32:58.839 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: HUMAN_TRANSFORMER (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/58/5a101692f7278fc7c1d861dc268944]
Mar-23 12:32:58.855 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:32:58.856 [Task submitter] INFO nextflow.Session - [b9/353957] Submitted process > GET_FINAL_METABOLITES_STATIC (4)
Mar-23 12:33:05.887 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: HUMAN_TRANSFORMER (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/66/85b2c748f0247fecfb2a6144d0ea85]
Mar-23 12:33:05.888 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: HUMAN_TRANSFORMER (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/88/d6f61a8ea069829d5d3b8d2d6ed3d2]
Mar-23 12:33:05.909 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:05.911 [Task submitter] INFO nextflow.Session - [8c/87d858] Submitted process > GET_FINAL_METABOLITES_STATIC (6)
Mar-23 12:33:05.923 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:05.924 [Task submitter] INFO nextflow.Session - [8d/b292b1] Submitted process > GET_FINAL_METABOLITES_STATIC (5)
Mar-23 12:33:07.951 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: HUMAN_TRANSFORMER (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ae/d4edcb9c1c862ea8272f42f2bd999d]
Mar-23 12:33:07.967 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:07.968 [Task submitter] INFO nextflow.Session - [fa/28ee3d] Submitted process > GET_FINAL_METABOLITES_STATIC (7)
Mar-23 12:33:09.241 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: GET_FINAL_METABOLITES_STATIC (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ac/7afb4318418e08d8f973b9ffbbcea5]
Mar-23 12:33:09.263 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:09.264 [Task submitter] INFO nextflow.Session - [47/e3689c] Submitted process > CONPLEX_ALL (3)
Mar-23 12:33:21.678 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: HUMAN_TRANSFORMER (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a7/55cb6cfd3954144d267fc883e9f71e]
Mar-23 12:33:21.702 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:21.703 [Task submitter] INFO nextflow.Session - [33/e9e7e8] Submitted process > GET_FINAL_METABOLITES_STATIC (8)
Mar-23 12:33:23.614 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: HUMAN_TRANSFORMER (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9e/68d27c8d1ee060a4836f615f8bc8b7]
Mar-23 12:33:23.627 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:23.627 [Task submitter] INFO nextflow.Session - [aa/87ad5d] Submitted process > GET_FINAL_METABOLITES_STATIC (9)
Mar-23 12:33:26.271 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: GET_FINAL_METABOLITES_STATIC (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b9/35395791cb206f27e75128b0d43acf]
Mar-23 12:33:26.286 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:26.286 [Task submitter] INFO nextflow.Session - [2b/1f832e] Submitted process > CONPLEX_ALL (4)
Mar-23 12:33:28.739 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: HUMAN_TRANSFORMER (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8c/614048724953cdaf85576db432cb71]
Mar-23 12:33:28.979 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:28.981 [Task submitter] INFO nextflow.Session - [e8/674830] Submitted process > GET_FINAL_METABOLITES_STATIC (10)
Mar-23 12:33:30.718 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: GET_FINAL_METABOLITES_STATIC (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8c/87d858d63310846892df016cab7a7c]
Mar-23 12:33:30.808 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:30.809 [Task submitter] INFO nextflow.Session - [11/41fa41] Submitted process > CONPLEX_ALL (5)
Mar-23 12:33:34.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: HUMAN_TRANSFORMER (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4f/522cdbd6c71ca2b84a5c7c40c75be8]
Mar-23 12:33:34.222 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:34.224 [Task submitter] INFO nextflow.Session - [07/e85ae9] Submitted process > GET_FINAL_METABOLITES_STATIC (11)
Mar-23 12:33:34.335 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: GET_FINAL_METABOLITES_STATIC (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/fa/28ee3dc5d2854cb6ec7a06b2b077cd]
Mar-23 12:33:34.349 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:34.350 [Task submitter] INFO nextflow.Session - [8a/d96785] Submitted process > CONPLEX_ALL (6)
Mar-23 12:33:35.976 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: GET_FINAL_METABOLITES_STATIC (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8d/b292b16c812d7dfd6914291c9ea916]
Mar-23 12:33:36.036 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:36.048 [Task submitter] INFO nextflow.Session - [dd/50d730] Submitted process > CONPLEX_ALL (7)
Mar-23 12:33:50.315 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: HUMAN_TRANSFORMER (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/1d/701bd014e2b99ea7030776393f4d5e]
Mar-23 12:33:50.355 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:50.356 [Task submitter] INFO nextflow.Session - [83/b74538] Submitted process > GET_FINAL_METABOLITES_STATIC (12)
Mar-23 12:33:51.575 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: HUMAN_TRANSFORMER (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e1/2d650bd0b461beee593bbcf4146cd9]
Mar-23 12:33:51.596 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:51.598 [Task submitter] INFO nextflow.Session - [33/3c10fd] Submitted process > GET_FINAL_METABOLITES_STATIC (13)
Mar-23 12:33:54.414 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: HUMAN_TRANSFORMER (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/11/907b6d28da29bbd89e5d2ccfae4efa]
Mar-23 12:33:54.429 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:54.430 [Task submitter] INFO nextflow.Session - [fc/8331ce] Submitted process > GET_FINAL_METABOLITES_STATIC (14)
Mar-23 12:33:55.766 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: HUMAN_TRANSFORMER (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/85/3e7894d128f1a7ca4e512265de5963]
Mar-23 12:33:55.787 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:55.789 [Task submitter] INFO nextflow.Session - [57/5023ee] Submitted process > GET_FINAL_METABOLITES_STATIC (15)
Mar-23 12:33:56.685 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: GET_FINAL_METABOLITES_STATIC (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/33/e9e7e8904fe466f69f4df57cce2c64]
Mar-23 12:33:56.708 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:33:56.709 [Task submitter] INFO nextflow.Session - [9a/2fecc9] Submitted process > CONPLEX_ALL (8)
Mar-23 12:34:00.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: GET_FINAL_METABOLITES_STATIC (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/aa/87ad5d6b5867590135e05f76c3bb54]
Mar-23 12:34:00.299 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:00.299 [Task submitter] INFO nextflow.Session - [f1/5e18e2] Submitted process > CONPLEX_ALL (9)
Mar-23 12:34:01.320 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: GET_FINAL_METABOLITES_STATIC (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e8/67483098b1e320bd4b8f1a79daaa0d]
Mar-23 12:34:01.339 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:01.554 [Task submitter] INFO nextflow.Session - [31/8a1dcd] Submitted process > CONPLEX_ALL (10)
Mar-23 12:34:04.378 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: GET_FINAL_METABOLITES_STATIC (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/07/e85ae96b214083751ee72ad0a6bfb7]
Mar-23 12:34:04.396 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:04.398 [Task submitter] INFO nextflow.Session - [de/729b43] Submitted process > CONPLEX_ALL (11)
Mar-23 12:34:11.898 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: HUMAN_TRANSFORMER (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/1e/26e9125254af1d3a5deaa84c7d3811]
Mar-23 12:34:11.920 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:11.921 [Task submitter] INFO nextflow.Session - [0e/b1ba67] Submitted process > GET_FINAL_METABOLITES_STATIC (16)
Mar-23 12:34:19.892 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: GET_FINAL_METABOLITES_STATIC (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/fc/8331ce93639011dd35f13ae21ff3f7]
Mar-23 12:34:19.907 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:19.908 [Task submitter] INFO nextflow.Session - [89/e57fd5] Submitted process > CONPLEX_ALL (12)
Mar-23 12:34:19.959 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: GET_FINAL_METABOLITES_STATIC (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/83/b745382ed20b6665e5054177cdf014]
Mar-23 12:34:20.422 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:20.423 [Task submitter] INFO nextflow.Session - [6b/d6191a] Submitted process > CONPLEX_ALL (13)
Mar-23 12:34:21.646 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: HUMAN_TRANSFORMER (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8f/b72148545bcdcb9cab86e46a063bf2]
Mar-23 12:34:21.662 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:21.663 [Task submitter] INFO nextflow.Session - [5f/c1a0dc] Submitted process > GET_FINAL_METABOLITES_STATIC (17)
Mar-23 12:34:23.293 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: GET_FINAL_METABOLITES_STATIC (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/33/3c10fd8d2d91c9e47891327246402e]
Mar-23 12:34:23.307 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:23.308 [Task submitter] INFO nextflow.Session - [27/4e94a8] Submitted process > CONPLEX_ALL (14)
Mar-23 12:34:26.594 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: GET_FINAL_METABOLITES_STATIC (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/57/5023ee10166882143a1e04f4172bd7]
Mar-23 12:34:26.638 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:26.640 [Task submitter] INFO nextflow.Session - [4f/914e0e] Submitted process > CONPLEX_ALL (15)
Mar-23 12:34:34.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: GET_FINAL_METABOLITES_STATIC (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0e/b1ba678c16290a330b694983921f5c]
Mar-23 12:34:34.235 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:34.236 [Task submitter] INFO nextflow.Session - [45/a19ccf] Submitted process > CONPLEX_ALL (16)
Mar-23 12:34:37.582 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: GET_FINAL_METABOLITES_STATIC (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5f/c1a0dc784da101e044346af396812d]
Mar-23 12:34:37.597 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:37.598 [Task submitter] INFO nextflow.Session - [38/9d4acc] Submitted process > CONPLEX_ALL (17)
Mar-23 12:34:49.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: HUMAN_TRANSFORMER (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9c/1072348f82658bff6118dd98dff95e]
Mar-23 12:34:49.051 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:34:49.052 [Task submitter] INFO nextflow.Session - [d1/c7c098] Submitted process > GET_FINAL_METABOLITES_STATIC (18)
Mar-23 12:35:01.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: GET_FINAL_METABOLITES_STATIC (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d1/c7c098985598b18afe2fe2f36fd599]
Mar-23 12:35:01.967 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:35:01.968 [Task submitter] INFO nextflow.Session - [ec/eb9042] Submitted process > CONPLEX_ALL (18)
Mar-23 12:35:16.248 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: HUMAN_TRANSFORMER (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/7f/fffcfc20b885868645588ea0184dec]
Mar-23 12:35:16.265 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:35:16.267 [Task submitter] INFO nextflow.Session - [74/02c4c2] Submitted process > GET_FINAL_METABOLITES_STATIC (19)
Mar-23 12:35:24.543 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: GET_FINAL_METABOLITES_STATIC (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/74/02c4c29cbca0ab154f2bf45979058b]
Mar-23 12:35:24.572 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:35:24.573 [Task submitter] INFO nextflow.Session - [d3/59e768] Submitted process > CONPLEX_ALL (19)
Mar-23 12:35:24.682 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: HUMAN_TRANSFORMER (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/02/5069402b2776a3ea94e1260994e70e]
Mar-23 12:35:24.725 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:35:24.726 [Task submitter] INFO nextflow.Session - [08/e2ff02] Submitted process > GET_FINAL_METABOLITES_STATIC (20)
Mar-23 12:35:39.562 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: GET_FINAL_METABOLITES_STATIC (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/08/e2ff02a72b3bc58a7dc651a408e61e]
Mar-23 12:35:39.581 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:35:39.582 [Task submitter] INFO nextflow.Session - [0f/05554b] Submitted process > CONPLEX_ALL (20)
Mar-23 12:36:08.369 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: HUMAN_TRANSFORMER (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/20/1a7d4d52fa8531ca500e62fff149e0]
Mar-23 12:36:08.387 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:08.388 [Task submitter] INFO nextflow.Session - [59/20c57b] Submitted process > GET_FINAL_METABOLITES_STATIC (21)
Mar-23 12:36:08.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: HUMAN_TRANSFORMER (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/30/24835fc80891aeb227cb5f6bee92b6]
Mar-23 12:36:08.555 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:08.556 [Task submitter] INFO nextflow.Session - [a4/5d15d8] Submitted process > GET_FINAL_METABOLITES_STATIC (22)
Mar-23 12:36:28.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: GET_FINAL_METABOLITES_STATIC (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/59/20c57b919b048249caea887376f7cf]
Mar-23 12:36:28.269 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:28.270 [Task submitter] INFO nextflow.Session - [05/1a80de] Submitted process > CONPLEX_ALL (21)
Mar-23 12:36:28.294 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: GET_FINAL_METABOLITES_STATIC (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a4/5d15d8c541c82fc8fd5c20a4ecfa6f]
Mar-23 12:36:28.318 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:28.319 [Task submitter] INFO nextflow.Session - [bb/6e26ea] Submitted process > CONPLEX_ALL (22)
Mar-23 12:36:34.979 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a5/23b628f89e2a7835409a6c7d718387]
Mar-23 12:36:35.019 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:35.020 [Task submitter] INFO nextflow.Session - [13/14251c] Submitted process > TISSUE_DISTRIBUTION (1)
Mar-23 12:36:35.028 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:35.029 [Task submitter] INFO nextflow.Session - [2d/e5bbd5] Submitted process > BIO_METRICS (1)
Mar-23 12:36:35.049 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:36:35.050 [Task submitter] INFO nextflow.Session - [e4/66e3d5] Submitted process > NETWORK_ENRICHMENT (1)
Mar-23 12:36:45.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 34 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f7/f16540761aee41c7248ad1fe8f3eee]
~> TaskHandler[id: 16; name: HUMAN_TRANSFORMER (16); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f1/b1e309add0f1cd88797c7527fdf6f3]
~> TaskHandler[id: 4; name: HUMAN_TRANSFORMER (4); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f3/2167e6d747c6ad3334197c296e88d9]
~> TaskHandler[id: 9; name: HUMAN_TRANSFORMER (9); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/35/b8dc93d08d0110ce4b508b43b52dff]
~> TaskHandler[id: 7; name: HUMAN_TRANSFORMER (7); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ce/eac613e5ebba4a75ecd7d8352f7c99]
~> TaskHandler[id: 10; name: HUMAN_TRANSFORMER (10); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/de/d2b3dae152dc4064dd3caf84986f07]
~> TaskHandler[id: 29; name: HUMAN_TRANSFORMER (29); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/d7/93d38d4103afc3e0a87aa8fb1ae84d]
~> TaskHandler[id: 12; name: HUMAN_TRANSFORMER (12); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/d6/937a35d19297dce8b144bc2aa88b04]
~> TaskHandler[id: 30; name: HUMAN_TRANSFORMER (30); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ba/11e874c2fb4e51162424748812e93d]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f8/10a61c18a03652d1b03d448e2b9f99]
.. remaining tasks omitted.
Mar-23 12:37:00.095 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/13/14251cf5407e48cccef51699b56e1d]
Mar-23 12:37:01.585 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e4/66e3d504c2bd118ecb08f6aefd542d]
Mar-23 12:37:13.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2d/e5bbd5fc1420d3b5e51dcff10ee00e]
Mar-23 12:37:20.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: HUMAN_TRANSFORMER (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/de/d2b3dae152dc4064dd3caf84986f07]
Mar-23 12:37:20.152 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:20.154 [Task submitter] INFO nextflow.Session - [eb/c954be] Submitted process > GET_FINAL_METABOLITES_STATIC (23)
Mar-23 12:37:25.363 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: GET_FINAL_METABOLITES_STATIC (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/eb/c954bec177186d1d22d0f840ba29c3]
Mar-23 12:37:25.390 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:25.391 [Task submitter] INFO nextflow.Session - [33/07094f] Submitted process > CONPLEX_ALL (23)
Mar-23 12:37:29.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: HUMAN_TRANSFORMER (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/35/b8dc93d08d0110ce4b508b43b52dff]
Mar-23 12:37:29.684 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:29.685 [Task submitter] INFO nextflow.Session - [01/bec09d] Submitted process > GET_FINAL_METABOLITES_STATIC (24)
Mar-23 12:37:35.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: GET_FINAL_METABOLITES_STATIC (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/01/bec09d3e94eb30f39b777429901529]
Mar-23 12:37:35.176 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:35.176 [Task submitter] INFO nextflow.Session - [9e/eb3ea1] Submitted process > CONPLEX_ALL (24)
Mar-23 12:37:37.560 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: CONPLEX_ALL (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/69/3bf75df83d44f572f4b434c2c06735]
Mar-23 12:37:37.579 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:37.579 [Task submitter] INFO nextflow.Session - [4f/f22d29] Submitted process > NETWORK_ENRICHMENT (2)
Mar-23 12:37:37.584 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:37.584 [Task submitter] INFO nextflow.Session - [29/a97dbb] Submitted process > TISSUE_DISTRIBUTION (2)
Mar-23 12:37:37.590 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:37.590 [Task submitter] INFO nextflow.Session - [d6/3961cf] Submitted process > BIO_METRICS (2)
Mar-23 12:37:48.785 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: CONPLEX_ALL (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/11/41fa416225698c2a4a337496069fbe]
Mar-23 12:37:48.807 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:48.807 [Task submitter] INFO nextflow.Session - [f3/d557be] Submitted process > TISSUE_DISTRIBUTION (3)
Mar-23 12:37:48.815 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:48.816 [Task submitter] INFO nextflow.Session - [50/5fcb68] Submitted process > NETWORK_ENRICHMENT (3)
Mar-23 12:37:48.825 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:48.826 [Task submitter] INFO nextflow.Session - [95/4f5cd2] Submitted process > BIO_METRICS (3)
Mar-23 12:37:48.842 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: CONPLEX_ALL (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/dd/50d7305b7f7abb66d81414f76920cb]
Mar-23 12:37:49.286 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:49.287 [Task submitter] INFO nextflow.Session - [3a/c26113] Submitted process > NETWORK_ENRICHMENT (4)
Mar-23 12:37:49.296 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:49.297 [Task submitter] INFO nextflow.Session - [f0/c644ac] Submitted process > BIO_METRICS (4)
Mar-23 12:37:49.316 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:49.317 [Task submitter] INFO nextflow.Session - [b3/5cf0e3] Submitted process > TISSUE_DISTRIBUTION (4)
Mar-23 12:37:51.027 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: CONPLEX_ALL (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f1/5e18e2e5c18fe745b07b36bec151d6]
Mar-23 12:37:51.044 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:51.045 [Task submitter] INFO nextflow.Session - [d6/b41e0c] Submitted process > TISSUE_DISTRIBUTION (5)
Mar-23 12:37:51.050 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:51.050 [Task submitter] INFO nextflow.Session - [24/ff2c47] Submitted process > NETWORK_ENRICHMENT (5)
Mar-23 12:37:51.056 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:51.056 [Task submitter] INFO nextflow.Session - [93/3e3be9] Submitted process > BIO_METRICS (5)
Mar-23 12:37:53.706 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: CONPLEX_ALL (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/47/e3689cad62beb34489586494b2cbaf]
Mar-23 12:37:53.736 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:53.737 [Task submitter] INFO nextflow.Session - [c0/371e2e] Submitted process > NETWORK_ENRICHMENT (6)
Mar-23 12:37:53.749 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:53.750 [Task submitter] INFO nextflow.Session - [06/c8de2a] Submitted process > TISSUE_DISTRIBUTION (6)
Mar-23 12:37:53.765 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:37:53.766 [Task submitter] INFO nextflow.Session - [ad/3874d7] Submitted process > BIO_METRICS (6)
Mar-23 12:38:01.136 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: CONPLEX_ALL (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2b/1f832e20c7d01f6d40033975ca1a15]
Mar-23 12:38:01.153 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:01.154 [Task submitter] INFO nextflow.Session - [07/6783cd] Submitted process > TISSUE_DISTRIBUTION (7)
Mar-23 12:38:01.160 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:01.161 [Task submitter] INFO nextflow.Session - [b2/3de5d2] Submitted process > NETWORK_ENRICHMENT (7)
Mar-23 12:38:01.169 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:01.170 [Task submitter] INFO nextflow.Session - [49/9986ab] Submitted process > BIO_METRICS (7)
Mar-23 12:38:03.159 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: CONPLEX_ALL (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8a/d9678534e279927c670d8e3cbc76dd]
Mar-23 12:38:03.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: CONPLEX_ALL (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/31/8a1dcdbe63608cb636165b802ba3ee]
Mar-23 12:38:03.178 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.179 [Task submitter] INFO nextflow.Session - [22/af8d38] Submitted process > TISSUE_DISTRIBUTION (9)
Mar-23 12:38:03.192 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.193 [Task submitter] INFO nextflow.Session - [0c/31da68] Submitted process > TISSUE_DISTRIBUTION (8)
Mar-23 12:38:03.202 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.203 [Task submitter] INFO nextflow.Session - [7b/9bfa0d] Submitted process > NETWORK_ENRICHMENT (8)
Mar-23 12:38:03.212 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.212 [Task submitter] INFO nextflow.Session - [e8/8b5576] Submitted process > NETWORK_ENRICHMENT (9)
Mar-23 12:38:03.222 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.222 [Task submitter] INFO nextflow.Session - [44/6aa7bc] Submitted process > BIO_METRICS (9)
Mar-23 12:38:03.230 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:03.231 [Task submitter] INFO nextflow.Session - [11/bd53f9] Submitted process > BIO_METRICS (8)
Mar-23 12:38:06.801 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: CONPLEX_ALL (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/de/729b4378fdd22d1e8923d20d20b68f]
Mar-23 12:38:06.816 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:06.817 [Task submitter] INFO nextflow.Session - [90/dbf361] Submitted process > NETWORK_ENRICHMENT (10)
Mar-23 12:38:06.821 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:06.821 [Task submitter] INFO nextflow.Session - [54/ebab16] Submitted process > TISSUE_DISTRIBUTION (10)
Mar-23 12:38:06.827 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:06.827 [Task submitter] INFO nextflow.Session - [9d/f715d0] Submitted process > BIO_METRICS (10)
Mar-23 12:38:13.153 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: CONPLEX_ALL (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9a/2fecc9ed2b4eba73680416b03cb2a6]
Mar-23 12:38:13.172 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:13.173 [Task submitter] INFO nextflow.Session - [e5/8cf296] Submitted process > TISSUE_DISTRIBUTION (11)
Mar-23 12:38:13.177 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:13.178 [Task submitter] INFO nextflow.Session - [80/eb1340] Submitted process > NETWORK_ENRICHMENT (11)
Mar-23 12:38:13.183 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:13.183 [Task submitter] INFO nextflow.Session - [3b/8d8bae] Submitted process > BIO_METRICS (11)
Mar-23 12:38:21.439 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: NETWORK_ENRICHMENT (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4f/f22d295989de10b2dfc29f2c1e6f66]
Mar-23 12:38:31.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: CONPLEX_ALL (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/89/e57fd5f026ab500a7afd27b1efbc59]
Mar-23 12:38:31.148 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:31.149 [Task submitter] INFO nextflow.Session - [23/e0edb4] Submitted process > TISSUE_DISTRIBUTION (12)
Mar-23 12:38:31.157 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:31.157 [Task submitter] INFO nextflow.Session - [01/ccfeaf] Submitted process > NETWORK_ENRICHMENT (12)
Mar-23 12:38:31.165 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:31.165 [Task submitter] INFO nextflow.Session - [be/1a62f0] Submitted process > BIO_METRICS (12)
Mar-23 12:38:35.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: CONPLEX_ALL (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/27/4e94a8b156b5b5b67d4cb0e08f0410]
Mar-23 12:38:35.655 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:35.655 [Task submitter] INFO nextflow.Session - [df/37378b] Submitted process > TISSUE_DISTRIBUTION (13)
Mar-23 12:38:35.659 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:35.660 [Task submitter] INFO nextflow.Session - [ae/161ea0] Submitted process > NETWORK_ENRICHMENT (13)
Mar-23 12:38:35.664 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:35.665 [Task submitter] INFO nextflow.Session - [9a/2588bd] Submitted process > BIO_METRICS (13)
Mar-23 12:38:38.539 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: CONPLEX_ALL (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4f/914e0ed20b550030977102ec634240]
Mar-23 12:38:38.558 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:38.558 [Task submitter] INFO nextflow.Session - [bb/e5559b] Submitted process > TISSUE_DISTRIBUTION (14)
Mar-23 12:38:38.567 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:38.568 [Task submitter] INFO nextflow.Session - [da/58f57a] Submitted process > NETWORK_ENRICHMENT (14)
Mar-23 12:38:38.576 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:38.577 [Task submitter] INFO nextflow.Session - [41/44f65d] Submitted process > BIO_METRICS (14)
Mar-23 12:38:44.202 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: CONPLEX_ALL (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/6b/d6191a21da8e951e3b5e3fe4777c19]
Mar-23 12:38:44.217 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:44.217 [Task submitter] INFO nextflow.Session - [2a/b7677d] Submitted process > BIO_METRICS (15)
Mar-23 12:38:44.222 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:44.222 [Task submitter] INFO nextflow.Session - [74/ab9e37] Submitted process > TISSUE_DISTRIBUTION (15)
Mar-23 12:38:44.233 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:44.233 [Task submitter] INFO nextflow.Session - [15/d4d10b] Submitted process > NETWORK_ENRICHMENT (15)
Mar-23 12:38:49.342 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: CONPLEX_ALL (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/38/9d4acc90f36d106b7cac368917e550]
Mar-23 12:38:49.361 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:49.361 [Task submitter] INFO nextflow.Session - [4c/876912] Submitted process > BIO_METRICS (16)
Mar-23 12:38:49.368 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:49.369 [Task submitter] INFO nextflow.Session - [77/9891c5] Submitted process > TISSUE_DISTRIBUTION (16)
Mar-23 12:38:49.477 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:49.478 [Task submitter] INFO nextflow.Session - [6b/fdd0b6] Submitted process > NETWORK_ENRICHMENT (16)
Mar-23 12:38:51.241 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: CONPLEX_ALL (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/45/a19ccfb8ec236e0945dbed55042d80]
Mar-23 12:38:51.260 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:51.261 [Task submitter] INFO nextflow.Session - [33/88746a] Submitted process > BIO_METRICS (17)
Mar-23 12:38:51.272 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:51.272 [Task submitter] INFO nextflow.Session - [a7/3ea963] Submitted process > TISSUE_DISTRIBUTION (17)
Mar-23 12:38:51.277 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:51.277 [Task submitter] INFO nextflow.Session - [16/232012] Submitted process > NETWORK_ENRICHMENT (17)
Mar-23 12:38:54.493 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: NETWORK_ENRICHMENT (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3a/c26113bb0d9cbc2cd6ffa649e984bb]
Mar-23 12:38:55.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: HUMAN_TRANSFORMER (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f3/2167e6d747c6ad3334197c296e88d9]
Mar-23 12:38:55.990 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:38:55.990 [Task submitter] INFO nextflow.Session - [95/f2bdb4] Submitted process > GET_FINAL_METABOLITES_STATIC (25)
Mar-23 12:39:03.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: NETWORK_ENRICHMENT (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c0/371e2e1eb6c520d6cbd8551d527bbf]
Mar-23 12:39:04.694 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: NETWORK_ENRICHMENT (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/24/ff2c475fceb977db4d2b5997a021aa]
Mar-23 12:39:05.817 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: HUMAN_TRANSFORMER (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ce/eac613e5ebba4a75ecd7d8352f7c99]
Mar-23 12:39:05.835 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:05.836 [Task submitter] INFO nextflow.Session - [51/532018] Submitted process > GET_FINAL_METABOLITES_STATIC (26)
Mar-23 12:39:10.024 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: NETWORK_ENRICHMENT (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b2/3de5d2d296ef7d0cb0e0efd1b8bfa9]
Mar-23 12:39:10.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: NETWORK_ENRICHMENT (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e8/8b5576e0a0da896d8c4563708a6349]
Mar-23 12:39:10.449 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: NETWORK_ENRICHMENT (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/50/5fcb68e7c6d0ba17c6ac0d933c1bb0]
Mar-23 12:39:13.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: CONPLEX_ALL (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ec/eb90424872ea2ef085458b17b9d492]
Mar-23 12:39:13.334 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:13.339 [Task submitter] INFO nextflow.Session - [07/eb3846] Submitted process > TISSUE_DISTRIBUTION (18)
Mar-23 12:39:13.348 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:13.348 [Task submitter] INFO nextflow.Session - [71/d6e25b] Submitted process > BIO_METRICS (18)
Mar-23 12:39:13.360 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:13.361 [Task submitter] INFO nextflow.Session - [3e/2c8de8] Submitted process > NETWORK_ENRICHMENT (18)
Mar-23 12:39:31.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: NETWORK_ENRICHMENT (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/90/dbf3618498e513aac253cd058fd607]
Mar-23 12:39:34.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f8/10a61c18a03652d1b03d448e2b9f99]
Mar-23 12:39:34.665 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:34.665 [Task submitter] INFO nextflow.Session - [33/a93fae] Submitted process > GET_FINAL_METABOLITES_STATIC (27)
Mar-23 12:39:35.548 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: NETWORK_ENRICHMENT (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/7b/9bfa0d7db2e92177e7ac89f660ddcf]
Mar-23 12:39:35.931 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 111; name: NETWORK_ENRICHMENT (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/80/eb1340f1819de2da6c04fc667c0862]
Mar-23 12:39:36.507 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 114; name: NETWORK_ENRICHMENT (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/01/ccfeaf7ba27e6a72be85662f791d0c]
Mar-23 12:39:39.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 132; name: GET_FINAL_METABOLITES_STATIC (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/95/f2bdb4530d0ac3c1f3ff00f2e5d9d1]
Mar-23 12:39:39.190 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:39.190 [Task submitter] INFO nextflow.Session - [08/033ef2] Submitted process > CONPLEX_ALL (25)
Mar-23 12:39:41.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 133; name: GET_FINAL_METABOLITES_STATIC (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/51/53201879a33a087d8def46956e30ef]
Mar-23 12:39:41.767 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:41.767 [Task submitter] INFO nextflow.Session - [2e/5eca88] Submitted process > CONPLEX_ALL (26)
Mar-23 12:39:43.198 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f7/f16540761aee41c7248ad1fe8f3eee]
Mar-23 12:39:43.215 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:43.215 [Task submitter] INFO nextflow.Session - [5e/fd8e5e] Submitted process > GET_FINAL_METABOLITES_STATIC (28)
Mar-23 12:39:46.363 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 123; name: NETWORK_ENRICHMENT (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/15/d4d10b05f38730d049401c5fe85786]
Mar-23 12:39:47.959 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 118; name: NETWORK_ENRICHMENT (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ae/161ea0024d53dc3bfd63e24b85f039]
Mar-23 12:39:49.774 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 128; name: NETWORK_ENRICHMENT (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/6b/fdd0b657c77c21dc5e2c9c569a1a75]
Mar-23 12:39:51.400 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 135; name: NETWORK_ENRICHMENT (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3e/2c8de8d100be5dcb969e5862c56c36]
Mar-23 12:39:51.501 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 120; name: NETWORK_ENRICHMENT (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/da/58f57a81f0b6279a3662cef7c8b069]
Mar-23 12:39:51.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 130; name: NETWORK_ENRICHMENT (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/16/232012a2858c1b774c7ff8dd8ff8a6]
Mar-23 12:39:53.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: TISSUE_DISTRIBUTION (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/29/a97dbb292f4ded621fbc410922dd16]
Mar-23 12:39:57.351 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: CONPLEX_ALL (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d3/59e76867961a8af5b324f9dd41e8ca]
Mar-23 12:39:57.368 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:57.368 [Task submitter] INFO nextflow.Session - [43/7b1489] Submitted process > NETWORK_ENRICHMENT (19)
Mar-23 12:39:57.373 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:57.373 [Task submitter] INFO nextflow.Session - [20/365d8d] Submitted process > TISSUE_DISTRIBUTION (19)
Mar-23 12:39:57.379 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:57.379 [Task submitter] INFO nextflow.Session - [3a/83663f] Submitted process > BIO_METRICS (19)
Mar-23 12:39:59.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: HUMAN_TRANSFORMER (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ba/11e874c2fb4e51162424748812e93d]
Mar-23 12:39:59.217 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:39:59.218 [Task submitter] INFO nextflow.Session - [da/1d1b41] Submitted process > GET_FINAL_METABOLITES_STATIC (29)
Mar-23 12:40:01.754 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: HUMAN_TRANSFORMER (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d7/93d38d4103afc3e0a87aa8fb1ae84d]
Mar-23 12:40:01.768 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:01.769 [Task submitter] INFO nextflow.Session - [3a/04d53e] Submitted process > GET_FINAL_METABOLITES_STATIC (30)
Mar-23 12:40:03.823 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: CONPLEX_ALL (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0f/05554b5b13f98da9dbd653ecd2b483]
Mar-23 12:40:03.840 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:03.840 [Task submitter] INFO nextflow.Session - [60/32b570] Submitted process > NETWORK_ENRICHMENT (20)
Mar-23 12:40:03.846 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:03.847 [Task submitter] INFO nextflow.Session - [11/082da7] Submitted process > TISSUE_DISTRIBUTION (20)
Mar-23 12:40:03.854 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:03.855 [Task submitter] INFO nextflow.Session - [dc/26dfd8] Submitted process > BIO_METRICS (20)
Mar-23 12:40:14.513 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 137; name: GET_FINAL_METABOLITES_STATIC (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/33/a93fae31481f246b097b2aa33dfd28]
Mar-23 12:40:14.533 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:14.534 [Task submitter] INFO nextflow.Session - [17/80ca83] Submitted process > CONPLEX_ALL (27)
Mar-23 12:40:14.542 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 140; name: GET_FINAL_METABOLITES_STATIC (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5e/fd8e5e54cb4f183b2ce8d52af21e94]
Mar-23 12:40:14.562 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:14.563 [Task submitter] INFO nextflow.Session - [b1/057b65] Submitted process > CONPLEX_ALL (28)
Mar-23 12:40:16.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: BIO_METRICS (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d6/3961cfb71a9ca8371fe4115528c8b5]
Mar-23 12:40:30.984 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 143; name: NETWORK_ENRICHMENT (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/43/7b1489d70ac412e0cab45c8f67df8c]
Mar-23 12:40:32.161 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 148; name: NETWORK_ENRICHMENT (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/60/32b570e65114e89cc469b5c9bb57ba]
Mar-23 12:40:35.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 145; name: GET_FINAL_METABOLITES_STATIC (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3a/04d53e8b7d32e0e1abcd6974cd75ad]
Mar-23 12:40:35.099 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:35.099 [Task submitter] INFO nextflow.Session - [0f/26ca05] Submitted process > CONPLEX_ALL (29)
Mar-23 12:40:35.166 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 144; name: GET_FINAL_METABOLITES_STATIC (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/da/1d1b412830b1587ece28bac11c9469]
Mar-23 12:40:35.184 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:40:35.185 [Task submitter] INFO nextflow.Session - [e6/bffd78] Submitted process > CONPLEX_ALL (30)
Mar-23 12:40:48.469 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: TISSUE_DISTRIBUTION (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f3/d557beb05b9a2f2f94c9bbf0699f74]
Mar-23 12:41:11.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: TISSUE_DISTRIBUTION (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d6/b41e0c0e6da6d488e749655f7e3c07]
Mar-23 12:41:21.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: BIO_METRICS (5); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/93/3e3be92e196d43903b3ab0ab53e533]
Mar-23 12:41:23.435 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: CONPLEX_ALL (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/bb/6e26ea2dad5145467b34925806585b]
Mar-23 12:41:23.455 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:23.456 [Task submitter] INFO nextflow.Session - [7b/fb352b] Submitted process > TISSUE_DISTRIBUTION (21)
Mar-23 12:41:23.460 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:23.461 [Task submitter] INFO nextflow.Session - [fb/887e51] Submitted process > NETWORK_ENRICHMENT (21)
Mar-23 12:41:23.466 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:23.466 [Task submitter] INFO nextflow.Session - [4f/7fe0cb] Submitted process > BIO_METRICS (21)
Mar-23 12:41:26.018 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: TISSUE_DISTRIBUTION (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b3/5cf0e3f2e08e8e9e60a13940ff9a4a]
Mar-23 12:41:27.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: CONPLEX_ALL (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/05/1a80de9a1ebeace669f6f6012c9d72]
Mar-23 12:41:27.227 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:27.227 [Task submitter] INFO nextflow.Session - [57/539445] Submitted process > TISSUE_DISTRIBUTION (22)
Mar-23 12:41:27.232 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:27.232 [Task submitter] INFO nextflow.Session - [99/22ebf4] Submitted process > NETWORK_ENRICHMENT (22)
Mar-23 12:41:27.239 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:41:27.239 [Task submitter] INFO nextflow.Session - [73/7f0338] Submitted process > BIO_METRICS (22)
Mar-23 12:41:33.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: BIO_METRICS (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/95/4f5cd24f3efc2e219247618f44651f]
Mar-23 12:41:40.921 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: TISSUE_DISTRIBUTION (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/07/6783cdc83d5ffb569734dddb53b723]
Mar-23 12:41:44.186 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: BIO_METRICS (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f0/c644acab981f0e2a200a49d011d24a]
Mar-23 12:41:45.591 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 45 -- submitted tasks are shown below
~> TaskHandler[id: 16; name: HUMAN_TRANSFORMER (16); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f1/b1e309add0f1cd88797c7527fdf6f3]
~> TaskHandler[id: 12; name: HUMAN_TRANSFORMER (12); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/d6/937a35d19297dce8b144bc2aa88b04]
~> TaskHandler[id: 81; name: CONPLEX_ALL (23); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/33/07094f1b16e171068beb4d45f0d323]
~> TaskHandler[id: 83; name: CONPLEX_ALL (24); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/9e/eb3ea15b69c05a2e60cd0a088cf8c1]
~> TaskHandler[id: 97; name: TISSUE_DISTRIBUTION (6); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/06/c8de2ac82664b8e4ea4fa2d0ace04c]
~> TaskHandler[id: 98; name: BIO_METRICS (6); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ad/3874d7773511b299a0cd2ac9667439]
~> TaskHandler[id: 101; name: BIO_METRICS (7); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/49/9986abc0e786727dd60bc1e7bc9e1b]
~> TaskHandler[id: 106; name: TISSUE_DISTRIBUTION (9); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/22/af8d38620c99efde756aac21397250]
~> TaskHandler[id: 103; name: TISSUE_DISTRIBUTION (8); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0c/31da68f73ca6075ec6eb53e51150df]
~> TaskHandler[id: 107; name: BIO_METRICS (9); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/44/6aa7bc6c7377f12a92c16187d56a9b]
.. remaining tasks omitted.
Mar-23 12:41:48.802 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: TISSUE_DISTRIBUTION (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0c/31da68f73ca6075ec6eb53e51150df]
Mar-23 12:41:57.796 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 157; name: NETWORK_ENRICHMENT (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/99/22ebf44395545226bf7ec246f27fc1]
Mar-23 12:41:57.812 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 154; name: NETWORK_ENRICHMENT (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/fb/887e5104f41ba7c6ada83e6273068a]
Mar-23 12:42:02.049 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: BIO_METRICS (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ad/3874d7773511b299a0cd2ac9667439]
Mar-23 12:42:03.645 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: BIO_METRICS (8); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/11/bd53f98856474786ea24da75e2ee1b]
Mar-23 12:42:06.492 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: TISSUE_DISTRIBUTION (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/22/af8d38620c99efde756aac21397250]
Mar-23 12:42:15.864 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: CONPLEX_ALL (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/33/07094f1b16e171068beb4d45f0d323]
Mar-23 12:42:15.880 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:15.881 [Task submitter] INFO nextflow.Session - [81/57b8bf] Submitted process > BIO_METRICS (23)
Mar-23 12:42:15.885 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:15.885 [Task submitter] INFO nextflow.Session - [e0/27ecec] Submitted process > TISSUE_DISTRIBUTION (23)
Mar-23 12:42:15.889 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:15.889 [Task submitter] INFO nextflow.Session - [30/367e53] Submitted process > NETWORK_ENRICHMENT (23)
Mar-23 12:42:17.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: BIO_METRICS (7); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/49/9986abc0e786727dd60bc1e7bc9e1b]
Mar-23 12:42:20.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: TISSUE_DISTRIBUTION (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/54/ebab16dd4258d0ee83b4afa0f14f0e]
Mar-23 12:42:22.679 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: BIO_METRICS (9); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/44/6aa7bc6c7377f12a92c16187d56a9b]
Mar-23 12:42:27.342 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 139; name: CONPLEX_ALL (26); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/2e/5eca88b0106f9b71dfbcdc4bd48329]
Mar-23 12:42:27.352 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (26); work-dir=/data/bugra/digital_trials/work/2e/5eca88b0106f9b71dfbcdc4bd48329
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (26)` terminated with an error exit status (137)
Mar-23 12:42:27.369 [TaskFinalizer-4] INFO nextflow.processor.TaskProcessor - [2e/5eca88] NOTE: Process `CONPLEX_ALL (26)` terminated with an error exit status (137) -- Execution is retried (1)
Mar-23 12:42:27.381 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:27.381 [Task submitter] INFO nextflow.Session - [b0/f4117d] Re-submitted process > CONPLEX_ALL (26)
Mar-23 12:42:33.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 152; name: CONPLEX_ALL (30); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/e6/bffd78b931d61bc7d3d448de37dd5d]
Mar-23 12:42:33.876 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (30); work-dir=/data/bugra/digital_trials/work/e6/bffd78b931d61bc7d3d448de37dd5d
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (30)` terminated with an error exit status (137)
Mar-23 12:42:33.877 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [e6/bffd78] NOTE: Process `CONPLEX_ALL (30)` terminated with an error exit status (137) -- Execution is retried (1)
Mar-23 12:42:33.888 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:33.888 [Task submitter] INFO nextflow.Session - [7d/fdb02c] Re-submitted process > CONPLEX_ALL (30)
Mar-23 12:42:36.888 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 150; name: CONPLEX_ALL (28); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/b1/057b65a97a41bbe473ee2f46eb9b40]
Mar-23 12:42:36.893 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (28); work-dir=/data/bugra/digital_trials/work/b1/057b65a97a41bbe473ee2f46eb9b40
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (28)` terminated with an error exit status (137)
Mar-23 12:42:36.894 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [b1/057b65] NOTE: Process `CONPLEX_ALL (28)` terminated with an error exit status (137) -- Execution is retried (1)
Mar-23 12:42:36.902 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:36.903 [Task submitter] INFO nextflow.Session - [8a/d50b0a] Re-submitted process > CONPLEX_ALL (28)
Mar-23 12:42:38.762 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 149; name: CONPLEX_ALL (27); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/17/80ca834858cd7e184c1bda62c00603]
Mar-23 12:42:38.764 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (27); work-dir=/data/bugra/digital_trials/work/17/80ca834858cd7e184c1bda62c00603
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (27)` terminated with an error exit status (137)
Mar-23 12:42:38.765 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [17/80ca83] NOTE: Process `CONPLEX_ALL (27)` terminated with an error exit status (137) -- Execution is retried (1)
Mar-23 12:42:38.770 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:38.770 [Task submitter] INFO nextflow.Session - [34/389a02] Re-submitted process > CONPLEX_ALL (27)
Mar-23 12:42:38.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 117; name: TISSUE_DISTRIBUTION (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/df/37378b71bdf76c2878dd171863bb83]
Mar-23 12:42:45.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 134; name: TISSUE_DISTRIBUTION (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/07/eb38462f5d9bdba6ad8eb32015e50d]
Mar-23 12:42:45.650 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: BIO_METRICS (10); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9d/f715d039ac5b83b554f8480c11c08b]
Mar-23 12:42:47.104 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 159; name: NETWORK_ENRICHMENT (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/30/367e53a63fb710ffd441deac10d977]
Mar-23 12:42:48.514 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 115; name: TISSUE_DISTRIBUTION (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/23/e0edb40b343cab6e97f10f55f5ed5a]
Mar-23 12:42:49.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: CONPLEX_ALL (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9e/eb3ea15b69c05a2e60cd0a088cf8c1]
Mar-23 12:42:49.142 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:49.142 [Task submitter] INFO nextflow.Session - [ca/82ccc0] Submitted process > TISSUE_DISTRIBUTION (24)
Mar-23 12:42:49.148 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:49.148 [Task submitter] INFO nextflow.Session - [2c/a4ea8f] Submitted process > BIO_METRICS (24)
Mar-23 12:42:49.154 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:49.155 [Task submitter] INFO nextflow.Session - [ba/75b2a6] Submitted process > NETWORK_ENRICHMENT (24)
Mar-23 12:42:51.112 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 124; name: TISSUE_DISTRIBUTION (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/74/ab9e376731231ee4d73b8f8e018b03]
Mar-23 12:42:53.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 151; name: CONPLEX_ALL (29); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/0f/26ca056cde3d0a0faccc5d4300ad77]
Mar-23 12:42:53.009 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (29); work-dir=/data/bugra/digital_trials/work/0f/26ca056cde3d0a0faccc5d4300ad77
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (29)` terminated with an error exit status (137)
Mar-23 12:42:53.009 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [0f/26ca05] NOTE: Process `CONPLEX_ALL (29)` terminated with an error exit status (137) -- Execution is retried (1)
Mar-23 12:42:53.019 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:42:53.019 [Task submitter] INFO nextflow.Session - [36/87bdb0] Re-submitted process > CONPLEX_ALL (29)
Mar-23 12:42:53.120 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 113; name: TISSUE_DISTRIBUTION (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e5/8cf2969c5ca16cfee21167ab260e6a]
Mar-23 12:42:59.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 119; name: BIO_METRICS (13); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9a/2588bd738c68f1f0b9c3430ff00ba6]
Mar-23 12:43:00.711 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 121; name: TISSUE_DISTRIBUTION (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/bb/e5559b9c17fe9fe9f8bfe2e025c183]
Mar-23 12:43:04.334 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 112; name: BIO_METRICS (11); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3b/8d8bae39a0214c412b57c1436e3d18]
Mar-23 12:43:06.770 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 129; name: TISSUE_DISTRIBUTION (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a7/3ea963b0cb5accd9c0cf7dcef07ca0]
Mar-23 12:43:07.775 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 127; name: TISSUE_DISTRIBUTION (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/77/9891c577fca50a494253f4a5120458]
Mar-23 12:43:09.983 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 116; name: BIO_METRICS (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/be/1a62f09fbfc5a13f64656527d26476]
Mar-23 12:43:11.024 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 125; name: BIO_METRICS (15); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2a/b7677df131761a1fc65c1ae07cc506]
Mar-23 12:43:18.627 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 167; name: NETWORK_ENRICHMENT (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ba/75b2a67efede49e2757e606a1c8caf]
Mar-23 12:43:23.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 122; name: BIO_METRICS (14); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/41/44f65ddd2463c35daf1512af64ad53]
Mar-23 12:43:25.318 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 126; name: BIO_METRICS (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4c/8769120a19babc0bd6325e0a971ddf]
Mar-23 12:43:31.525 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 136; name: BIO_METRICS (18); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/71/d6e25b32e8710641786734a3527926]
Mar-23 12:43:38.096 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: TISSUE_DISTRIBUTION (6); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/06/c8de2ac82664b8e4ea4fa2d0ace04c]
Mar-23 12:43:41.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 147; name: TISSUE_DISTRIBUTION (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/11/082da7bfa22391d70b7ccec1f21cbe]
Mar-23 12:43:57.244 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 131; name: BIO_METRICS (17); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/33/88746ad8a88226e3f9c903ab251a72]
Mar-23 12:44:03.502 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 142; name: TISSUE_DISTRIBUTION (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/20/365d8d2bad0b7a7928b3b5ccb16ef5]
Mar-23 12:44:30.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: HUMAN_TRANSFORMER (12); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d6/937a35d19297dce8b144bc2aa88b04]
Mar-23 12:44:30.579 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:44:30.580 [Task submitter] INFO nextflow.Session - [45/f1829b] Submitted process > GET_FINAL_METABOLITES_STATIC (31)
Mar-23 12:44:37.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 170; name: GET_FINAL_METABOLITES_STATIC (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/45/f1829b25b4f3df485be705cc48b802]
Mar-23 12:44:38.097 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:44:38.098 [Task submitter] INFO nextflow.Session - [ab/ae2b82] Submitted process > CONPLEX_ALL (31)
Mar-23 12:44:46.347 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 141; name: BIO_METRICS (19); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3a/83663f248b80abd0bd711b5851e130]
Mar-23 12:44:52.756 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 138; name: CONPLEX_ALL (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/08/033ef25b49e18111d147d94fa5e9cc]
Mar-23 12:44:52.773 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:44:52.774 [Task submitter] INFO nextflow.Session - [1d/835cc1] Submitted process > TISSUE_DISTRIBUTION (25)
Mar-23 12:44:52.780 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:44:52.780 [Task submitter] INFO nextflow.Session - [6b/e16abe] Submitted process > NETWORK_ENRICHMENT (25)
Mar-23 12:44:52.787 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:44:52.787 [Task submitter] INFO nextflow.Session - [aa/55bfe8] Submitted process > BIO_METRICS (25)
Mar-23 12:44:56.670 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 146; name: BIO_METRICS (20); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/dc/26dfd877e58d766955e8a73e475a07]
Mar-23 12:44:58.289 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 153; name: TISSUE_DISTRIBUTION (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/7b/fb352b6e09abc1540368c2236e8256]
Mar-23 12:45:00.346 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 158; name: TISSUE_DISTRIBUTION (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/57/539445dedec26946d36643db2589db]
Mar-23 12:45:01.619 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 172; name: NETWORK_ENRICHMENT (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/6b/e16abeb9a9c0520d86e7f1541b5743]
Mar-23 12:45:36.525 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 160; name: TISSUE_DISTRIBUTION (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e0/27ecec03371e5c50a226da16062585]
Mar-23 12:46:01.360 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: HUMAN_TRANSFORMER (16); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f1/b1e309add0f1cd88797c7527fdf6f3]
Mar-23 12:46:01.384 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:46:01.385 [Task submitter] INFO nextflow.Session - [0a/d4196d] Submitted process > GET_FINAL_METABOLITES_STATIC (32)
Mar-23 12:46:07.899 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 175; name: GET_FINAL_METABOLITES_STATIC (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0a/d4196d87e1a8ef468783e1e1c79ce0]
Mar-23 12:46:07.922 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:46:07.922 [Task submitter] INFO nextflow.Session - [a5/442c00] Submitted process > CONPLEX_ALL (32)
Mar-23 12:46:10.425 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 168; name: TISSUE_DISTRIBUTION (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ca/82ccc0e2a0af7a1bf260340e34c41e]
Mar-23 12:46:14.425 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 155; name: BIO_METRICS (21); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4f/7fe0cb8a6e108636ff6e7ed72823dc]
Mar-23 12:46:16.494 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 156; name: BIO_METRICS (22); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/73/7f03385bcff8b67e3e71660f0b2be3]
Mar-23 12:46:45.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 11 -- submitted tasks are shown below
~> TaskHandler[id: 161; name: BIO_METRICS (23); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/81/57b8bf8804037a9684d53e7fcbe5b3]
~> TaskHandler[id: 162; name: CONPLEX_ALL (26); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/b0/f4117da8bcb4e3fc730d2c03ba15dd]
~> TaskHandler[id: 163; name: CONPLEX_ALL (30); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/7d/fdb02caa4facf542099ed7099fc3be]
~> TaskHandler[id: 164; name: CONPLEX_ALL (28); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/8a/d50b0a94c90015f90f3e362b3d7d66]
~> TaskHandler[id: 165; name: CONPLEX_ALL (27); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/34/389a021aae6a91d9c31b4617ed5f9b]
~> TaskHandler[id: 166; name: BIO_METRICS (24); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/2c/a4ea8fafbe9245f2e726a094c64255]
~> TaskHandler[id: 169; name: CONPLEX_ALL (29); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/36/87bdb06ca1815d4a2c374961f0b77b]
~> TaskHandler[id: 171; name: CONPLEX_ALL (31); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ab/ae2b82ac588f8923a06cb0eed5c49b]
~> TaskHandler[id: 174; name: TISSUE_DISTRIBUTION (25); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/1d/835cc1e8516441e62d198308716622]
~> TaskHandler[id: 173; name: BIO_METRICS (25); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/aa/55bfe82411e2b1e6eed1e4f477aa67]
Mar-23 12:46:58.038 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 162; name: CONPLEX_ALL (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b0/f4117da8bcb4e3fc730d2c03ba15dd]
Mar-23 12:46:58.056 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:46:58.056 [Task submitter] INFO nextflow.Session - [be/3ae495] Submitted process > TISSUE_DISTRIBUTION (26)
Mar-23 12:46:58.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:46:58.063 [Task submitter] INFO nextflow.Session - [46/111673] Submitted process > NETWORK_ENRICHMENT (26)
Mar-23 12:46:58.071 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:46:58.071 [Task submitter] INFO nextflow.Session - [ea/71f9ff] Submitted process > BIO_METRICS (26)
Mar-23 12:47:15.106 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 161; name: BIO_METRICS (23); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/81/57b8bf8804037a9684d53e7fcbe5b3]
Mar-23 12:47:21.919 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 178; name: NETWORK_ENRICHMENT (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/46/111673a303dccfac38753031b1bec3]
Mar-23 12:47:23.281 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 163; name: CONPLEX_ALL (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/7d/fdb02caa4facf542099ed7099fc3be]
Mar-23 12:47:23.303 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:23.304 [Task submitter] INFO nextflow.Session - [88/263dd7] Submitted process > TISSUE_DISTRIBUTION (27)
Mar-23 12:47:23.311 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:23.311 [Task submitter] INFO nextflow.Session - [22/774136] Submitted process > NETWORK_ENRICHMENT (27)
Mar-23 12:47:23.319 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:23.319 [Task submitter] INFO nextflow.Session - [ee/901f77] Submitted process > BIO_METRICS (27)
Mar-23 12:47:29.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 165; name: CONPLEX_ALL (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/34/389a021aae6a91d9c31b4617ed5f9b]
Mar-23 12:47:29.185 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:29.185 [Task submitter] INFO nextflow.Session - [31/4d6017] Submitted process > TISSUE_DISTRIBUTION (28)
Mar-23 12:47:29.197 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:29.198 [Task submitter] INFO nextflow.Session - [71/4770d2] Submitted process > BIO_METRICS (28)
Mar-23 12:47:29.206 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:29.207 [Task submitter] INFO nextflow.Session - [e6/75c16c] Submitted process > NETWORK_ENRICHMENT (28)
Mar-23 12:47:35.455 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 164; name: CONPLEX_ALL (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8a/d50b0a94c90015f90f3e362b3d7d66]
Mar-23 12:47:35.475 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:35.476 [Task submitter] INFO nextflow.Session - [cd/02c261] Submitted process > NETWORK_ENRICHMENT (29)
Mar-23 12:47:35.481 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:35.482 [Task submitter] INFO nextflow.Session - [66/756e3b] Submitted process > TISSUE_DISTRIBUTION (29)
Mar-23 12:47:35.490 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:35.490 [Task submitter] INFO nextflow.Session - [73/6a98d9] Submitted process > BIO_METRICS (29)
Mar-23 12:47:38.389 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 169; name: CONPLEX_ALL (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/36/87bdb06ca1815d4a2c374961f0b77b]
Mar-23 12:47:38.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:38.405 [Task submitter] INFO nextflow.Session - [56/a7eff7] Submitted process > NETWORK_ENRICHMENT (30)
Mar-23 12:47:38.410 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:38.411 [Task submitter] INFO nextflow.Session - [e6/6470b7] Submitted process > BIO_METRICS (30)
Mar-23 12:47:38.416 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:47:38.416 [Task submitter] INFO nextflow.Session - [84/87263a] Submitted process > TISSUE_DISTRIBUTION (30)
Mar-23 12:47:46.501 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 166; name: BIO_METRICS (24); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2c/a4ea8fafbe9245f2e726a094c64255]
Mar-23 12:47:57.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 181; name: NETWORK_ENRICHMENT (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/22/7741360aff319d2cc7a86045382efc]
Mar-23 12:48:08.279 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 185; name: NETWORK_ENRICHMENT (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e6/75c16cbf79da0b24beceff8e168ca0]
Mar-23 12:48:09.527 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 186; name: NETWORK_ENRICHMENT (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/cd/02c261e8fb5efe121619696a80eaa9]
Mar-23 12:48:19.727 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 189; name: NETWORK_ENRICHMENT (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/56/a7eff72cc801847e15229fc8c18689]
Mar-23 12:48:27.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 174; name: TISSUE_DISTRIBUTION (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/1d/835cc1e8516441e62d198308716622]
Mar-23 12:49:53.547 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 173; name: BIO_METRICS (25); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/aa/55bfe82411e2b1e6eed1e4f477aa67]
Mar-23 12:50:15.102 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 179; name: TISSUE_DISTRIBUTION (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/be/3ae4956f6f27c011788bb1ac918559]
Mar-23 12:50:21.853 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 171; name: CONPLEX_ALL (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ab/ae2b82ac588f8923a06cb0eed5c49b]
Mar-23 12:50:21.876 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:21.877 [Task submitter] INFO nextflow.Session - [a7/cd7d1e] Submitted process > NETWORK_ENRICHMENT (31)
Mar-23 12:50:21.884 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:21.885 [Task submitter] INFO nextflow.Session - [c1/90656b] Submitted process > TISSUE_DISTRIBUTION (31)
Mar-23 12:50:21.892 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:21.893 [Task submitter] INFO nextflow.Session - [00/9f994b] Submitted process > BIO_METRICS (31)
Mar-23 12:50:41.432 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 180; name: TISSUE_DISTRIBUTION (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/88/263dd77fb345314be930f39cd14482]
Mar-23 12:50:45.129 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 193; name: NETWORK_ENRICHMENT (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a7/cd7d1e33e61aec81febf58824af86a]
Mar-23 12:50:50.660 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 176; name: CONPLEX_ALL (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a5/442c0005dd3b8de416fbc41833aad1]
Mar-23 12:50:50.685 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:50.685 [Task submitter] INFO nextflow.Session - [ab/e04a6b] Submitted process > TISSUE_DISTRIBUTION (32)
Mar-23 12:50:50.692 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:50.692 [Task submitter] INFO nextflow.Session - [f4/c186c7] Submitted process > NETWORK_ENRICHMENT (32)
Mar-23 12:50:50.699 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-23 12:50:50.700 [Task submitter] INFO nextflow.Session - [4f/1c0edc] Submitted process > BIO_METRICS (32)
Mar-23 12:50:57.650 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 190; name: TISSUE_DISTRIBUTION (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/84/87263a9f4c58567a49ffca61693a9d]
Mar-23 12:50:59.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 183; name: TISSUE_DISTRIBUTION (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/31/4d60170d7411af2597d44531f936d6]
Mar-23 12:51:01.431 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 187; name: TISSUE_DISTRIBUTION (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/66/756e3b7cedd5360359f276390f6a76]
Mar-23 12:51:14.271 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 195; name: NETWORK_ENRICHMENT (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f4/c186c727624024d8307b91a07ccd87]
Mar-23 12:51:45.712 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 9 -- submitted tasks are shown below
~> TaskHandler[id: 177; name: BIO_METRICS (26); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ea/71f9ff3cd694cabbbd2cc9e6fb0f10]
~> TaskHandler[id: 182; name: BIO_METRICS (27); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ee/901f7799c39e4f135cef17a6fb192f]
~> TaskHandler[id: 184; name: BIO_METRICS (28); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/71/4770d26c1683d21b8608dfa37b2007]
~> TaskHandler[id: 188; name: BIO_METRICS (29); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/73/6a98d9dfb6cac2596cfad30611988e]
~> TaskHandler[id: 191; name: BIO_METRICS (30); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/e6/6470b7d646985f5c5c2beb931703b1]
~> TaskHandler[id: 192; name: TISSUE_DISTRIBUTION (31); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/c1/90656b98274556b91bbec9df9b84a4]
~> TaskHandler[id: 194; name: BIO_METRICS (31); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/00/9f994bbf43db001db949e4b5d4aee5]
~> TaskHandler[id: 196; name: TISSUE_DISTRIBUTION (32); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ab/e04a6b36921f8a90c0ea146cf5304f]
~> TaskHandler[id: 197; name: BIO_METRICS (32); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/4f/1c0edc01e00b16365405f69ec56ac7]
Mar-23 12:52:18.652 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 177; name: BIO_METRICS (26); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ea/71f9ff3cd694cabbbd2cc9e6fb0f10]
Mar-23 12:52:43.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 184; name: BIO_METRICS (28); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/71/4770d26c1683d21b8608dfa37b2007]
Mar-23 12:52:54.873 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 188; name: BIO_METRICS (29); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/73/6a98d9dfb6cac2596cfad30611988e]
Mar-23 12:52:59.195 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 182; name: BIO_METRICS (27); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ee/901f7799c39e4f135cef17a6fb192f]
Mar-23 12:53:14.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 191; name: BIO_METRICS (30); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e6/6470b7d646985f5c5c2beb931703b1]
Mar-23 12:55:10.091 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 196; name: TISSUE_DISTRIBUTION (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ab/e04a6b36921f8a90c0ea146cf5304f]
Mar-23 12:56:14.510 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 197; name: BIO_METRICS (32); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4f/1c0edc01e00b16365405f69ec56ac7]
Mar-23 12:56:24.917 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 192; name: TISSUE_DISTRIBUTION (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c1/90656b98274556b91bbec9df9b84a4]
Mar-23 12:56:45.747 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 194; name: BIO_METRICS (31); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/00/9f994bbf43db001db949e4b5d4aee5]
Mar-23 12:58:48.217 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 194; name: BIO_METRICS (31); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/00/9f994bbf43db001db949e4b5d4aee5]
Mar-23 12:58:48.222 [main] DEBUG nextflow.Session - Session await > all processes finished
Mar-23 12:58:48.318 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Mar-23 12:58:48.318 [main] DEBUG nextflow.Session - Session await > all barriers passed
Mar-23 12:58:48.321 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Mar-23 12:58:48.322 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Mar-23 12:58:48.339 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=192; failedCount=5; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=5; abortedCount=0; succeedDuration=9h 44m 45s; failedDuration=11m 48s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=62; peakCpus=62; peakMemory=250 GB; ]
Mar-23 12:58:48.481 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Mar-23 12:58:48.552 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Mar-23 12:58:48.552 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Mar-23 12:58:48.553 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Mar-23 12:58:48.554 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

971
.nextflow.log.2 Normal file
View File

@@ -0,0 +1,971 @@
Mar-18 21:20:15.931 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/digital-trials-data/gabe-run3/gabe-run3.json
Mar-18 21:20:16.316 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Mar-18 21:20:16.347 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Mar-18 21:20:16.384 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-18 21:20:16.386 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-18 21:20:16.389 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Mar-18 21:20:16.403 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-18 21:20:16.429 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Mar-18 21:20:16.432 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Mar-18 21:20:16.471 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Mar-18 21:20:16.476 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Mar-18 21:20:16.506 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-18 21:20:17.272 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Mar-18 21:20:17.293 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [zen_sax] DSL2 - revision: 0e14afbd94
Mar-18 21:20:17.295 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-18 21:20:17.296 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Mar-18 21:20:17.299 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Mar-18 21:20:17.312 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Mar-18 21:20:17.312 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Mar-18 21:20:17.328 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Mar-18 21:20:17.398 [main] DEBUG nextflow.Session - Session UUID: e75e46d9-ad7d-4b56-bdf1-9a1c0923dd64
Mar-18 21:20:17.398 [main] DEBUG nextflow.Session - Run name: zen_sax
Mar-18 21:20:17.399 [main] DEBUG nextflow.Session - Executor pool size: 80
Mar-18 21:20:17.410 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Mar-18 21:20:17.418 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-18 21:20:17.450 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 761650@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (27.7 GB) - Swap: 0 (0)
Mar-18 21:20:17.481 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Mar-18 21:20:17.482 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Mar-18 21:20:17.499 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-18 21:20:17.519 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-18 21:20:17.525 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Mar-18 21:20:17.528 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Mar-18 21:20:17.561 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-18 21:20:17.574 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Mar-18 21:20:17.799 [main] DEBUG nextflow.Session - Session start
Mar-18 21:20:18.332 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-18 21:20:19.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.274 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-18 21:20:19.284 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Mar-18 21:20:19.287 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Mar-18 21:20:19.324 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Mar-18 21:20:19.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.431 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.433 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Mar-18 21:20:19.447 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Mar-18 21:20:19.453 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.453 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.455 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Mar-18 21:20:19.524 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.525 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.526 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Mar-18 21:20:19.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.559 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.560 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Mar-18 21:20:19.569 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.569 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.570 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Mar-18 21:20:19.595 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-18 21:20:19.596 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-18 21:20:19.597 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Mar-18 21:20:19.600 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Mar-18 21:20:19.604 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Mar-18 21:20:19.612 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Mar-18 21:20:19.613 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Mar-18 21:20:19.614 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/digital-trials-data/gabe-run3/input/ligands/; pattern: *.csv; options: [:]
Mar-18 21:20:19.614 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Mar-18 21:20:19.614 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Mar-18 21:20:19.615 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Mar-18 21:20:19.616 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Mar-18 21:20:19.616 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Mar-18 21:20:19.617 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Mar-18 21:20:19.618 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec2c89c0dbf76553: /data/bugra/digital_trials/test.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Mar-18 21:20:19.618 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Mar-18 21:20:19.618 [main] DEBUG nextflow.Session - Session await
Mar-18 21:20:20.162 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.171 [Task submitter] INFO nextflow.Session - [72/b877a7] Submitted process > HUMAN_TRANSFORMER (22)
Mar-18 21:20:20.185 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.185 [Task submitter] INFO nextflow.Session - [b8/36834c] Submitted process > HUMAN_TRANSFORMER (17)
Mar-18 21:20:20.193 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.193 [Task submitter] INFO nextflow.Session - [7a/0eb83a] Submitted process > HUMAN_TRANSFORMER (45)
Mar-18 21:20:20.201 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.202 [Task submitter] INFO nextflow.Session - [0f/9a0cd5] Submitted process > HUMAN_TRANSFORMER (74)
Mar-18 21:20:20.209 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.210 [Task submitter] INFO nextflow.Session - [c4/e32501] Submitted process > HUMAN_TRANSFORMER (29)
Mar-18 21:20:20.217 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.217 [Task submitter] INFO nextflow.Session - [32/fb9e93] Submitted process > HUMAN_TRANSFORMER (54)
Mar-18 21:20:20.224 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.224 [Task submitter] INFO nextflow.Session - [fb/faa4aa] Submitted process > HUMAN_TRANSFORMER (55)
Mar-18 21:20:20.232 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.233 [Task submitter] INFO nextflow.Session - [5a/faa523] Submitted process > HUMAN_TRANSFORMER (40)
Mar-18 21:20:20.240 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.241 [Task submitter] INFO nextflow.Session - [7d/2fa815] Submitted process > HUMAN_TRANSFORMER (67)
Mar-18 21:20:20.250 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.251 [Task submitter] INFO nextflow.Session - [2a/96b957] Submitted process > HUMAN_TRANSFORMER (35)
Mar-18 21:20:20.265 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.265 [Task submitter] INFO nextflow.Session - [b9/e57dda] Submitted process > HUMAN_TRANSFORMER (9)
Mar-18 21:20:20.272 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.273 [Task submitter] INFO nextflow.Session - [fd/0b14fd] Submitted process > HUMAN_TRANSFORMER (86)
Mar-18 21:20:20.281 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.282 [Task submitter] INFO nextflow.Session - [a6/cc7c28] Submitted process > HUMAN_TRANSFORMER (51)
Mar-18 21:20:20.290 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.291 [Task submitter] INFO nextflow.Session - [b9/7e54d8] Submitted process > HUMAN_TRANSFORMER (48)
Mar-18 21:20:20.297 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.298 [Task submitter] INFO nextflow.Session - [a4/4bea8f] Submitted process > HUMAN_TRANSFORMER (1)
Mar-18 21:20:20.305 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.305 [Task submitter] INFO nextflow.Session - [a4/46870e] Submitted process > HUMAN_TRANSFORMER (25)
Mar-18 21:20:20.312 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.313 [Task submitter] INFO nextflow.Session - [99/0bf7d9] Submitted process > HUMAN_TRANSFORMER (13)
Mar-18 21:20:20.322 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.323 [Task submitter] INFO nextflow.Session - [7f/996282] Submitted process > HUMAN_TRANSFORMER (73)
Mar-18 21:20:20.333 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.333 [Task submitter] INFO nextflow.Session - [95/e721b6] Submitted process > HUMAN_TRANSFORMER (58)
Mar-18 21:20:20.342 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.343 [Task submitter] INFO nextflow.Session - [4c/6bcf63] Submitted process > HUMAN_TRANSFORMER (95)
Mar-18 21:20:20.352 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.353 [Task submitter] INFO nextflow.Session - [75/1131f1] Submitted process > HUMAN_TRANSFORMER (80)
Mar-18 21:20:20.364 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.365 [Task submitter] INFO nextflow.Session - [21/9c8453] Submitted process > HUMAN_TRANSFORMER (70)
Mar-18 21:20:20.375 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.376 [Task submitter] INFO nextflow.Session - [45/5aca40] Submitted process > HUMAN_TRANSFORMER (50)
Mar-18 21:20:20.385 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.386 [Task submitter] INFO nextflow.Session - [9f/6ebe51] Submitted process > HUMAN_TRANSFORMER (100)
Mar-18 21:20:20.394 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.395 [Task submitter] INFO nextflow.Session - [ab/216ae0] Submitted process > HUMAN_TRANSFORMER (5)
Mar-18 21:20:20.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.405 [Task submitter] INFO nextflow.Session - [da/540299] Submitted process > HUMAN_TRANSFORMER (46)
Mar-18 21:20:20.411 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.412 [Task submitter] INFO nextflow.Session - [b5/f38923] Submitted process > HUMAN_TRANSFORMER (39)
Mar-18 21:20:20.418 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.418 [Task submitter] INFO nextflow.Session - [68/1826f5] Submitted process > HUMAN_TRANSFORMER (78)
Mar-18 21:20:20.424 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.424 [Task submitter] INFO nextflow.Session - [ed/3b042b] Submitted process > HUMAN_TRANSFORMER (33)
Mar-18 21:20:20.431 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.431 [Task submitter] INFO nextflow.Session - [3f/075456] Submitted process > HUMAN_TRANSFORMER (6)
Mar-18 21:20:20.436 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.437 [Task submitter] INFO nextflow.Session - [7a/791a5f] Submitted process > HUMAN_TRANSFORMER (31)
Mar-18 21:20:20.442 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.443 [Task submitter] INFO nextflow.Session - [74/3c1d46] Submitted process > HUMAN_TRANSFORMER (60)
Mar-18 21:20:20.449 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.449 [Task submitter] INFO nextflow.Session - [03/bc533b] Submitted process > HUMAN_TRANSFORMER (42)
Mar-18 21:20:20.456 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.456 [Task submitter] INFO nextflow.Session - [22/fd1af0] Submitted process > HUMAN_TRANSFORMER (49)
Mar-18 21:20:20.465 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.466 [Task submitter] INFO nextflow.Session - [43/60db45] Submitted process > HUMAN_TRANSFORMER (61)
Mar-18 21:20:20.475 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.476 [Task submitter] INFO nextflow.Session - [c3/96d9ca] Submitted process > HUMAN_TRANSFORMER (47)
Mar-18 21:20:20.485 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.486 [Task submitter] INFO nextflow.Session - [1e/136b16] Submitted process > HUMAN_TRANSFORMER (28)
Mar-18 21:20:20.494 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.495 [Task submitter] INFO nextflow.Session - [b3/18f2d8] Submitted process > HUMAN_TRANSFORMER (21)
Mar-18 21:20:20.503 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.504 [Task submitter] INFO nextflow.Session - [eb/bd1719] Submitted process > HUMAN_TRANSFORMER (26)
Mar-18 21:20:20.511 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.512 [Task submitter] INFO nextflow.Session - [2d/813f73] Submitted process > HUMAN_TRANSFORMER (69)
Mar-18 21:20:20.518 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.518 [Task submitter] INFO nextflow.Session - [d6/469d3a] Submitted process > HUMAN_TRANSFORMER (62)
Mar-18 21:20:20.524 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.524 [Task submitter] INFO nextflow.Session - [7d/6149e5] Submitted process > HUMAN_TRANSFORMER (15)
Mar-18 21:20:20.533 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.533 [Task submitter] INFO nextflow.Session - [b0/358e08] Submitted process > HUMAN_TRANSFORMER (4)
Mar-18 21:20:20.539 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.540 [Task submitter] INFO nextflow.Session - [97/d91d94] Submitted process > HUMAN_TRANSFORMER (79)
Mar-18 21:20:20.545 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.546 [Task submitter] INFO nextflow.Session - [58/36391d] Submitted process > HUMAN_TRANSFORMER (52)
Mar-18 21:20:20.551 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.552 [Task submitter] INFO nextflow.Session - [16/6dd6cf] Submitted process > HUMAN_TRANSFORMER (66)
Mar-18 21:20:20.558 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.558 [Task submitter] INFO nextflow.Session - [44/42e04d] Submitted process > HUMAN_TRANSFORMER (43)
Mar-18 21:20:20.570 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.571 [Task submitter] INFO nextflow.Session - [34/bc34df] Submitted process > HUMAN_TRANSFORMER (123)
Mar-18 21:20:20.578 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.579 [Task submitter] INFO nextflow.Session - [23/9ecd04] Submitted process > HUMAN_TRANSFORMER (44)
Mar-18 21:20:20.585 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-18 21:20:20.586 [Task submitter] INFO nextflow.Session - [72/752728] Submitted process > HUMAN_TRANSFORMER (30)
Mar-18 21:20:28.975 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Mar-18 21:20:28.996 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active:
[process] GET_FINAL_METABOLITES_STATIC
status=ACTIVE
port 0: (queue) OPEN ; channel: smiles_csv
port 1: (value) bound ; channel: chembl_db
port 2: (cntrl) - ; channel: $
[process] CONPLEX_ALL
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: input_zarr
port 2: (cntrl) - ; channel: $
[process] NETWORK_ENRICHMENT
status=ACTIVE
port 0: (queue) OPEN ; channel: interactions
port 1: (cntrl) - ; channel: $
[process] TISSUE_DISTRIBUTION
status=ACTIVE
port 0: (queue) OPEN ; channel: interaction
port 1: (cntrl) - ; channel: $
[process] BIO_METRICS
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
Mar-18 21:20:29.001 [main] DEBUG nextflow.Session - Session await > all processes finished
Mar-18 21:20:29.002 [main] DEBUG nextflow.Session - Session await > all barriers passed
Mar-18 21:20:29.008 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (50)
Mar-18 21:20:29.204 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: HUMAN_TRANSFORMER (74); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/0f/9a0cd5d97aee26e6b419677d571f1d]
Mar-18 21:20:29.206 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-18 21:20:29.211 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: HUMAN_TRANSFORMER (29); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/c4/e32501010caae58fa439c623a2fecd]
Mar-18 21:20:29.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: HUMAN_TRANSFORMER (54); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/32/fb9e93711155e96b0eca9ca1a8454e]
Mar-18 21:20:29.214 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: HUMAN_TRANSFORMER (55); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/fb/faa4aaa5a507b07f6ad9fb9cdf2127]
Mar-18 21:20:29.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: HUMAN_TRANSFORMER (40); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/5a/faa523c3ce4d70240791b474747fde]
Mar-18 21:20:29.217 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: HUMAN_TRANSFORMER (67); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/7d/2fa8150c57d90a74cd338cd5ce8bfe]
Mar-18 21:20:29.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: HUMAN_TRANSFORMER (35); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/2a/96b957dfb012e27d77c31f4b94d051]
Mar-18 21:20:29.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: HUMAN_TRANSFORMER (86); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/fd/0b14fd788e43705a0d86419395e93c]
Mar-18 21:20:29.221 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (45) -- command: kill -TERM 762008; exit: 1
bash: line 1: kill: (762008) - No such process
Mar-18 21:20:29.222 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: HUMAN_TRANSFORMER (51); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/a6/cc7c28680437f5e2c42a1709323bb7]
Mar-18 21:20:29.223 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: HUMAN_TRANSFORMER (48); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/b9/7e54d83d949dca0466afe4c816d12d]
Mar-18 21:20:29.225 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/a4/4bea8fb78d84cb4e6a1b3b78de1a1d]
Mar-18 21:20:29.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: HUMAN_TRANSFORMER (25); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/a4/46870eb8ce5691c0f2149045550ad7]
Mar-18 21:20:29.227 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (29); work-dir=/data/bugra/digital_trials/work/c4/e32501010caae58fa439c623a2fecd
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (29)` terminated with an error exit status (130)
Mar-18 21:20:29.227 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: HUMAN_TRANSFORMER (13); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/99/0bf7d908b80de58cfef30a9ae30875]
Mar-18 21:20:29.228 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: HUMAN_TRANSFORMER (73); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/7f/99628294d9fb367576004fc4cff3eb]
Mar-18 21:20:29.229 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (25) -- command: kill -TERM 762373; exit: 1
bash: line 1: kill: (762373) - No such process
Mar-18 21:20:29.229 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: HUMAN_TRANSFORMER (58); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/95/e721b6a649d83eb7e942021377d531]
Mar-18 21:20:29.231 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: HUMAN_TRANSFORMER (95); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/4c/6bcf63f1afb66a1ed51a58c8ef54a3]
Mar-18 21:20:29.232 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: HUMAN_TRANSFORMER (80); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/75/1131f1d70cc028dd7b726be37d1e31]
Mar-18 21:20:29.233 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: HUMAN_TRANSFORMER (70); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/21/9c8453efe5eeb789846c2451f0a13f]
Mar-18 21:20:29.234 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: HUMAN_TRANSFORMER (50); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/45/5aca403dc4da2c3d24fe10177924c8]
Mar-18 21:20:29.234 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (80) -- command: kill -TERM 762532; exit: 1
bash: line 1: kill: (762532) - No such process
Mar-18 21:20:29.235 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: HUMAN_TRANSFORMER (100); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/9f/6ebe51bfe8573e36f728abd651796c]
Mar-18 21:20:29.237 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: HUMAN_TRANSFORMER (5); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/ab/216ae0fc95fd279206b22f34dc000a]
Mar-18 21:20:29.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: HUMAN_TRANSFORMER (46); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/da/540299373969ef3de95545b6de644f]
Mar-18 21:20:29.239 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: HUMAN_TRANSFORMER (39); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/b5/f389239211a370dc32541c3a4fa3e7]
Mar-18 21:20:29.239 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (5) -- command: kill -TERM 762695; exit: 1
bash: line 1: kill: (762695) - No such process
Mar-18 21:20:29.240 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: HUMAN_TRANSFORMER (78); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/68/1826f56db8ca6748424d2048035406]
Mar-18 21:20:29.240 [TaskFinalizer-2] INFO nextflow.processor.TaskProcessor - [c4/e32501] NOTE: Process `HUMAN_TRANSFORMER (29)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.241 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (48); work-dir=/data/bugra/digital_trials/work/b9/7e54d83d949dca0466afe4c816d12d
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (48)` terminated with an error exit status (130)
Mar-18 21:20:29.241 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: HUMAN_TRANSFORMER (33); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/ed/3b042b5b484c9ff44f2901ae29af3b]
Mar-18 21:20:29.242 [TaskFinalizer-10] INFO nextflow.processor.TaskProcessor - [b9/7e54d8] NOTE: Process `HUMAN_TRANSFORMER (48)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.242 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: HUMAN_TRANSFORMER (6); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/3f/075456044e2114e2f07d282a4652f8]
Mar-18 21:20:29.242 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (67); work-dir=/data/bugra/digital_trials/work/7d/2fa8150c57d90a74cd338cd5ce8bfe
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (67)` terminated with an error exit status (130)
Mar-18 21:20:29.243 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [7d/2fa815] NOTE: Process `HUMAN_TRANSFORMER (67)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.243 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: HUMAN_TRANSFORMER (31); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/7a/791a5fc3d48e3532dd905a9d6ffe60]
Mar-18 21:20:29.244 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (54); work-dir=/data/bugra/digital_trials/work/32/fb9e93711155e96b0eca9ca1a8454e
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (54)` terminated with an error exit status (130)
Mar-18 21:20:29.245 [TaskFinalizer-3] INFO nextflow.processor.TaskProcessor - [32/fb9e93] NOTE: Process `HUMAN_TRANSFORMER (54)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.245 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (40); work-dir=/data/bugra/digital_trials/work/5a/faa523c3ce4d70240791b474747fde
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (40)` terminated with an error exit status (130)
Mar-18 21:20:29.245 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (33) -- command: kill -TERM 762806; exit: 1
bash: line 1: kill: (762806) - No such process
Mar-18 21:20:29.246 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [5a/faa523] NOTE: Process `HUMAN_TRANSFORMER (40)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.247 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (35); work-dir=/data/bugra/digital_trials/work/2a/96b957dfb012e27d77c31f4b94d051
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (35)` terminated with an error exit status (130)
Mar-18 21:20:29.247 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: HUMAN_TRANSFORMER (60); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/74/3c1d464c97545d0573e617639c1996]
Mar-18 21:20:29.248 [TaskFinalizer-7] INFO nextflow.processor.TaskProcessor - [2a/96b957] NOTE: Process `HUMAN_TRANSFORMER (35)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.248 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (74); work-dir=/data/bugra/digital_trials/work/0f/9a0cd5d97aee26e6b419677d571f1d
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (74)` terminated with an error exit status (130)
Mar-18 21:20:29.248 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: HUMAN_TRANSFORMER (42); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/03/bc533b3f0412ff4170434e49742e08]
Mar-18 21:20:29.249 [TaskFinalizer-1] INFO nextflow.processor.TaskProcessor - [0f/9a0cd5] NOTE: Process `HUMAN_TRANSFORMER (74)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.249 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (60) -- command: kill -TERM 762866; exit: 1
bash: line 1: kill: (762866) - No such process
Mar-18 21:20:29.249 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (86); work-dir=/data/bugra/digital_trials/work/fd/0b14fd788e43705a0d86419395e93c
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (86)` terminated with an error exit status (130)
Mar-18 21:20:29.250 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [fd/0b14fd] NOTE: Process `HUMAN_TRANSFORMER (86)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.251 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (51); work-dir=/data/bugra/digital_trials/work/a6/cc7c28680437f5e2c42a1709323bb7
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (51)` terminated with an error exit status (130)
Mar-18 21:20:29.251 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: HUMAN_TRANSFORMER (49); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/22/fd1af06b9e3d47711a38d32e512b6a]
Mar-18 21:20:29.252 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: HUMAN_TRANSFORMER (61); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/43/60db45ede0bd4446d23695ada0d61e]
Mar-18 21:20:29.252 [TaskFinalizer-9] INFO nextflow.processor.TaskProcessor - [a6/cc7c28] NOTE: Process `HUMAN_TRANSFORMER (51)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.252 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (55); work-dir=/data/bugra/digital_trials/work/fb/faa4aaa5a507b07f6ad9fb9cdf2127
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (55)` terminated with an error exit status (130)
Mar-18 21:20:29.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: HUMAN_TRANSFORMER (47); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/c3/96d9ca9db58d7b185d3a1593398cf5]
Mar-18 21:20:29.253 [TaskFinalizer-4] INFO nextflow.processor.TaskProcessor - [fb/faa4aa] NOTE: Process `HUMAN_TRANSFORMER (55)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.253 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (70); work-dir=/data/bugra/digital_trials/work/21/9c8453efe5eeb789846c2451f0a13f
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (70)` terminated with an error exit status (130)
Mar-18 21:20:29.254 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (49) -- command: kill -TERM 762944; exit: 1
bash: line 1: kill: (762944) - No such process
Mar-18 21:20:29.254 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: HUMAN_TRANSFORMER (28); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/1e/136b163a14f2e329c0a63def34303a]
Mar-18 21:20:29.254 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [21/9c8453] NOTE: Process `HUMAN_TRANSFORMER (70)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.255 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (80); work-dir=/data/bugra/digital_trials/work/75/1131f1d70cc028dd7b726be37d1e31
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (80)` terminated with an error exit status (130)
Mar-18 21:20:29.255 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: HUMAN_TRANSFORMER (21); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/b3/18f2d8de1dee7ebd1e29c36766bb38]
Mar-18 21:20:29.256 [TaskFinalizer-1] INFO nextflow.processor.TaskProcessor - [75/1131f1] NOTE: Process `HUMAN_TRANSFORMER (80)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.256 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (95); work-dir=/data/bugra/digital_trials/work/4c/6bcf63f1afb66a1ed51a58c8ef54a3
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (95)` terminated with an error exit status (130)
Mar-18 21:20:29.256 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: HUMAN_TRANSFORMER (26); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/eb/bd17199be64672ed1cd2a9c2de98fc]
Mar-18 21:20:29.257 [TaskFinalizer-7] INFO nextflow.processor.TaskProcessor - [4c/6bcf63] NOTE: Process `HUMAN_TRANSFORMER (95)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.257 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: HUMAN_TRANSFORMER (69); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/2d/813f736812d2fe55b217ee6f3a6080]
Mar-18 21:20:29.257 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (58); work-dir=/data/bugra/digital_trials/work/95/e721b6a649d83eb7e942021377d531
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (58)` terminated with an error exit status (130)
Mar-18 21:20:29.258 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: HUMAN_TRANSFORMER (62); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/d6/469d3a52fd3e47c31e3f9629531225]
Mar-18 21:20:29.258 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [95/e721b6] NOTE: Process `HUMAN_TRANSFORMER (58)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.258 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (73); work-dir=/data/bugra/digital_trials/work/7f/99628294d9fb367576004fc4cff3eb
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (73)` terminated with an error exit status (130)
Mar-18 21:20:29.259 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (21) -- command: kill -TERM 763075; exit: 1
bash: line 1: kill: (763075) - No such process
Mar-18 21:20:29.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: HUMAN_TRANSFORMER (15); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/7d/6149e5bb637d5906e412e869847053]
Mar-18 21:20:29.259 [TaskFinalizer-3] INFO nextflow.processor.TaskProcessor - [7f/996282] NOTE: Process `HUMAN_TRANSFORMER (73)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.260 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (13); work-dir=/data/bugra/digital_trials/work/99/0bf7d908b80de58cfef30a9ae30875
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (13)` terminated with an error exit status (130)
Mar-18 21:20:29.260 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [99/0bf7d9] NOTE: Process `HUMAN_TRANSFORMER (13)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: HUMAN_TRANSFORMER (4); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/b0/358e0857d3fc84723c4c6f68449def]
Mar-18 21:20:29.261 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (25); work-dir=/data/bugra/digital_trials/work/a4/46870eb8ce5691c0f2149045550ad7
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (25)` terminated with an error exit status (130)
Mar-18 21:20:29.261 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: HUMAN_TRANSFORMER (79); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/97/d91d948e50cf63f8b4ff02716cae35]
Mar-18 21:20:29.262 [TaskFinalizer-10] INFO nextflow.processor.TaskProcessor - [a4/46870e] NOTE: Process `HUMAN_TRANSFORMER (25)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.262 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (1); work-dir=/data/bugra/digital_trials/work/a4/4bea8fb78d84cb4e6a1b3b78de1a1d
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (1)` terminated with an error exit status (130)
Mar-18 21:20:29.263 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: HUMAN_TRANSFORMER (52); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/58/36391d12e7f01e89c4c4b007a48fdf]
Mar-18 21:20:29.263 [TaskFinalizer-2] INFO nextflow.processor.TaskProcessor - [a4/4bea8f] NOTE: Process `HUMAN_TRANSFORMER (1)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.263 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (6); work-dir=/data/bugra/digital_trials/work/3f/075456044e2114e2f07d282a4652f8
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (6)` terminated with an error exit status (130)
Mar-18 21:20:29.264 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (4) -- command: kill -TERM 763174; exit: 1
bash: line 1: kill: (763174) - No such process
Mar-18 21:20:29.264 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [3f/075456] NOTE: Process `HUMAN_TRANSFORMER (6)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.264 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (33); work-dir=/data/bugra/digital_trials/work/ed/3b042b5b484c9ff44f2901ae29af3b
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (33)` terminated with an error exit status (130)
Mar-18 21:20:29.264 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: HUMAN_TRANSFORMER (66); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/16/6dd6cfac099d7134782d3b80712847]
Mar-18 21:20:29.265 [TaskFinalizer-3] INFO nextflow.processor.TaskProcessor - [ed/3b042b] NOTE: Process `HUMAN_TRANSFORMER (33)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.265 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: HUMAN_TRANSFORMER (43); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/44/42e04d6d950d65bdc5c53a29f24aff]
Mar-18 21:20:29.266 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (78); work-dir=/data/bugra/digital_trials/work/68/1826f56db8ca6748424d2048035406
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (78)` terminated with an error exit status (130)
Mar-18 21:20:29.266 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 123; name: HUMAN_TRANSFORMER (123); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/34/bc34dfc5b77bd45bf850bbefd1ade3]
Mar-18 21:20:29.266 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [68/1826f5] NOTE: Process `HUMAN_TRANSFORMER (78)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.267 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (39); work-dir=/data/bugra/digital_trials/work/b5/f389239211a370dc32541c3a4fa3e7
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (39)` terminated with an error exit status (130)
Mar-18 21:20:29.268 [TaskFinalizer-7] INFO nextflow.processor.TaskProcessor - [b5/f38923] NOTE: Process `HUMAN_TRANSFORMER (39)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.268 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: HUMAN_TRANSFORMER (44); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/23/9ecd04cb0afa1a6189c69d0c0fe507]
Mar-18 21:20:29.268 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (46); work-dir=/data/bugra/digital_trials/work/da/540299373969ef3de95545b6de644f
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (46)` terminated with an error exit status (130)
Mar-18 21:20:29.268 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill HUMAN_TRANSFORMER (43) -- command: kill -TERM 763252; exit: 1
bash: line 1: kill: (763252) - No such process
Mar-18 21:20:29.269 [TaskFinalizer-1] INFO nextflow.processor.TaskProcessor - [da/540299] NOTE: Process `HUMAN_TRANSFORMER (46)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.269 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: HUMAN_TRANSFORMER (30); status: COMPLETED; exit: 130; error: -; workDir: /data/bugra/digital_trials/work/72/7527282097aa9de800c0e570242280]
Mar-18 21:20:29.269 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (5); work-dir=/data/bugra/digital_trials/work/ab/216ae0fc95fd279206b22f34dc000a
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (5)` terminated with an error exit status (130)
Mar-18 21:20:29.270 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [ab/216ae0] NOTE: Process `HUMAN_TRANSFORMER (5)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.270 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (100); work-dir=/data/bugra/digital_trials/work/9f/6ebe51bfe8573e36f728abd651796c
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (100)` terminated with an error exit status (130)
Mar-18 21:20:29.271 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Mar-18 21:20:29.271 [TaskFinalizer-4] INFO nextflow.processor.TaskProcessor - [9f/6ebe51] NOTE: Process `HUMAN_TRANSFORMER (100)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.272 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (50); work-dir=/data/bugra/digital_trials/work/45/5aca403dc4da2c3d24fe10177924c8
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (50)` terminated with an error exit status (130)
Mar-18 21:20:29.272 [TaskFinalizer-9] INFO nextflow.processor.TaskProcessor - [45/5aca40] NOTE: Process `HUMAN_TRANSFORMER (50)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.273 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (21); work-dir=/data/bugra/digital_trials/work/b3/18f2d8de1dee7ebd1e29c36766bb38
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (21)` terminated with an error exit status (130)
Mar-18 21:20:29.273 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=24; ignoredCount=0; cachedCount=0; pendingCount=524; submittedCount=0; runningCount=13; retriesCount=24; abortedCount=13; succeedDuration=0ms; failedDuration=3m 33s; cachedDuration=0ms;loadCpus=13; loadMemory=65 GB; peakRunning=50; peakCpus=50; peakMemory=250 GB; ]
Mar-18 21:20:29.274 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [b3/18f2d8] NOTE: Process `HUMAN_TRANSFORMER (21)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.274 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (28); work-dir=/data/bugra/digital_trials/work/1e/136b163a14f2e329c0a63def34303a
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (28)` terminated with an error exit status (130)
Mar-18 21:20:29.275 [TaskFinalizer-1] INFO nextflow.processor.TaskProcessor - [1e/136b16] NOTE: Process `HUMAN_TRANSFORMER (28)` terminated with an error exit status (130) -- Execution is retried (1)
Mar-18 21:20:29.275 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (47); work-dir=/data/bugra/digital_trials/work/c3/96d9ca9db58d7b185d3a1593398cf5
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (47)` terminated with an error exit status (130)
Mar-18 21:20:29.277 [TaskFinalizer-7] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.293 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (61); work-dir=/data/bugra/digital_trials/work/43/60db45ede0bd4446d23695ada0d61e
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (61)` terminated with an error exit status (130)
Mar-18 21:20:29.294 [TaskFinalizer-5] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.295 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (49); work-dir=/data/bugra/digital_trials/work/22/fd1af06b9e3d47711a38d32e512b6a
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (49)` terminated with an error exit status (130)
Mar-18 21:20:29.295 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.296 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (42); work-dir=/data/bugra/digital_trials/work/03/bc533b3f0412ff4170434e49742e08
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (42)` terminated with an error exit status (130)
Mar-18 21:20:29.296 [TaskFinalizer-6] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.297 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (60); work-dir=/data/bugra/digital_trials/work/74/3c1d464c97545d0573e617639c1996
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (60)` terminated with an error exit status (130)
Mar-18 21:20:29.297 [TaskFinalizer-2] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.298 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (31); work-dir=/data/bugra/digital_trials/work/7a/791a5fc3d48e3532dd905a9d6ffe60
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (31)` terminated with an error exit status (130)
Mar-18 21:20:29.298 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.299 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (52); work-dir=/data/bugra/digital_trials/work/58/36391d12e7f01e89c4c4b007a48fdf
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (52)` terminated with an error exit status (130)
Mar-18 21:20:29.299 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.300 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (79); work-dir=/data/bugra/digital_trials/work/97/d91d948e50cf63f8b4ff02716cae35
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (79)` terminated with an error exit status (130)
Mar-18 21:20:29.301 [TaskFinalizer-5] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.301 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (4); work-dir=/data/bugra/digital_trials/work/b0/358e0857d3fc84723c4c6f68449def
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (4)` terminated with an error exit status (130)
Mar-18 21:20:29.301 [TaskFinalizer-7] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.302 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (15); work-dir=/data/bugra/digital_trials/work/7d/6149e5bb637d5906e412e869847053
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (15)` terminated with an error exit status (130)
Mar-18 21:20:29.302 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.303 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (62); work-dir=/data/bugra/digital_trials/work/d6/469d3a52fd3e47c31e3f9629531225
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (62)` terminated with an error exit status (130)
Mar-18 21:20:29.304 [TaskFinalizer-8] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.304 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (69); work-dir=/data/bugra/digital_trials/work/2d/813f736812d2fe55b217ee6f3a6080
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (69)` terminated with an error exit status (130)
Mar-18 21:20:29.305 [TaskFinalizer-9] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.305 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (26); work-dir=/data/bugra/digital_trials/work/eb/bd17199be64672ed1cd2a9c2de98fc
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (26)` terminated with an error exit status (130)
Mar-18 21:20:29.306 [TaskFinalizer-4] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.306 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (30); work-dir=/data/bugra/digital_trials/work/72/7527282097aa9de800c0e570242280
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (30)` terminated with an error exit status (130)
Mar-18 21:20:29.307 [TaskFinalizer-7] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.307 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (44); work-dir=/data/bugra/digital_trials/work/23/9ecd04cb0afa1a6189c69d0c0fe507
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (44)` terminated with an error exit status (130)
Mar-18 21:20:29.308 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.308 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (123); work-dir=/data/bugra/digital_trials/work/34/bc34dfc5b77bd45bf850bbefd1ade3
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (123)` terminated with an error exit status (130)
Mar-18 21:20:29.309 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.309 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (43); work-dir=/data/bugra/digital_trials/work/44/42e04d6d950d65bdc5c53a29f24aff
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (43)` terminated with an error exit status (130)
Mar-18 21:20:29.310 [TaskFinalizer-2] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.310 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=HUMAN_TRANSFORMER (66); work-dir=/data/bugra/digital_trials/work/16/6dd6cfac099d7134782d3b80712847
error [nextflow.exception.ProcessFailedException]: Process `HUMAN_TRANSFORMER (66)` terminated with an error exit status (130)
Mar-18 21:20:29.311 [TaskFinalizer-6] ERROR nextflow.processor.TaskProcessor - Execution aborted due to an unexpected error
java.lang.NullPointerException: Cannot invoke method submit() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:113)
at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.checkErrorStrategy(TaskProcessor.groovy:1163)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.resumeOrDie(TaskProcessor.groovy:1077)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2402)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:696)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:686)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:676)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Mar-18 21:20:29.452 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Mar-18 21:20:29.612 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Mar-18 21:20:29.612 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Mar-18 21:20:29.614 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

117
.nextflow.log.3 Normal file
View File

@@ -0,0 +1,117 @@
Mar-09 15:03:54.815 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/caline-run6/digtrial/caline-run6.json
Mar-09 15:03:55.224 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Mar-09 15:03:55.255 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Mar-09 15:03:55.294 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-09 15:03:55.295 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-09 15:03:55.299 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Mar-09 15:03:55.314 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-09 15:03:55.342 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Mar-09 15:03:55.346 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Mar-09 15:03:55.386 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Mar-09 15:03:55.391 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Mar-09 15:03:55.422 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-09 15:03:56.211 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Mar-09 15:03:56.234 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [dreamy_panini] DSL2 - revision: 0e14afbd94
Mar-09 15:03:56.236 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-09 15:03:56.238 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Mar-09 15:03:56.240 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Mar-09 15:03:56.252 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Mar-09 15:03:56.252 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Mar-09 15:03:56.269 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Mar-09 15:03:56.340 [main] DEBUG nextflow.Session - Session UUID: c52cdca5-7bcc-4d96-8a19-824595cbfc30
Mar-09 15:03:56.341 [main] DEBUG nextflow.Session - Run name: dreamy_panini
Mar-09 15:03:56.341 [main] DEBUG nextflow.Session - Executor pool size: 80
Mar-09 15:03:56.354 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Mar-09 15:03:56.362 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-09 15:03:56.395 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 2939340@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (33.6 GB) - Swap: 0 (0)
Mar-09 15:03:56.430 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Mar-09 15:03:56.430 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Mar-09 15:03:56.457 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-09 15:03:56.477 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-09 15:03:56.483 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Mar-09 15:03:56.486 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Mar-09 15:03:56.520 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-09 15:03:56.533 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Mar-09 15:03:56.691 [main] DEBUG nextflow.Session - Session start
Mar-09 15:03:57.165 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-09 15:03:58.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.083 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.093 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-09 15:03:58.108 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Mar-09 15:03:58.111 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Mar-09 15:03:58.146 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Mar-09 15:03:58.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.247 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.249 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Mar-09 15:03:58.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Mar-09 15:03:58.269 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.270 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.271 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Mar-09 15:03:58.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.337 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.338 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Mar-09 15:03:58.371 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.371 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.372 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Mar-09 15:03:58.380 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.380 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.381 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Mar-09 15:03:58.393 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 15:03:58.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 15:03:58.395 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Mar-09 15:03:58.398 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Mar-09 15:03:58.401 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Mar-09 15:03:58.408 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Mar-09 15:03:58.410 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Mar-09 15:03:58.411 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Mar-09 15:03:58.412 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Mar-09 15:03:58.412 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Mar-09 15:03:58.412 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Mar-09 15:03:58.412 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/caline-run6/digtrial/input/; pattern: *.csv; options: [:]
Mar-09 15:03:58.413 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Mar-09 15:03:58.414 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Mar-09 15:03:58.415 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec2c89c0dbf76553: /data/bugra/digital_trials/test.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Mar-09 15:03:58.415 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Mar-09 15:03:58.415 [main] DEBUG nextflow.Session - Session await
Mar-09 15:03:58.625 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:03:58.629 [Task submitter] INFO nextflow.Session - [9f/8b91ca] Submitted process > HUMAN_TRANSFORMER (1)
Mar-09 15:04:06.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9f/8b91caff0c52ded09b143e6e91cbc0]
Mar-09 15:04:06.591 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-09 15:04:06.623 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-09 15:04:06.635 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:04:06.636 [Task submitter] INFO nextflow.Session - [08/710d4c] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Mar-09 15:04:11.034 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/08/710d4cc4e2be03a44b2df2383e7d9b]
Mar-09 15:04:11.122 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:04:11.125 [Task submitter] INFO nextflow.Session - [53/ea8e99] Submitted process > CONPLEX_ALL (1)
Mar-09 15:06:33.396 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/53/ea8e99cffaf7ca1272d091bfac2929]
Mar-09 15:06:33.433 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:06:33.434 [Task submitter] INFO nextflow.Session - [fb/95c05c] Submitted process > TISSUE_DISTRIBUTION (1)
Mar-09 15:06:33.442 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:06:33.442 [Task submitter] INFO nextflow.Session - [9a/9129e3] Submitted process > BIO_METRICS (1)
Mar-09 15:06:33.448 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 15:06:33.449 [Task submitter] INFO nextflow.Session - [16/77a5f6] Submitted process > NETWORK_ENRICHMENT (1)
Mar-09 15:06:43.140 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/16/77a5f693ac1bd2bc124ddc7ec802e3]
Mar-09 15:06:44.636 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/fb/95c05c31fa620d6901fbfc0de32259]
Mar-09 15:06:56.374 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9a/9129e302133c74df23101091230822]
Mar-09 15:06:56.382 [main] DEBUG nextflow.Session - Session await > all processes finished
Mar-09 15:06:56.476 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Mar-09 15:06:56.477 [main] DEBUG nextflow.Session - Session await > all barriers passed
Mar-09 15:06:56.486 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Mar-09 15:06:56.487 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Mar-09 15:06:56.501 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3m 18s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=3; peakMemory=11 GB; ]
Mar-09 15:06:56.581 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Mar-09 15:06:56.671 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Mar-09 15:06:56.671 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Mar-09 15:06:56.673 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Mar-09 15:06:56.674 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

117
.nextflow.log.4 Normal file
View File

@@ -0,0 +1,117 @@
Feb-27 17:43:13.583 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/caline-run6/digtrial/caline-run6.json
Feb-27 17:43:13.956 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-27 17:43:13.997 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-27 17:43:14.037 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-27 17:43:14.038 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-27 17:43:14.042 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-27 17:43:14.057 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-27 17:43:14.085 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-27 17:43:14.088 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-27 17:43:14.130 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-27 17:43:14.136 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-27 17:43:14.166 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-27 17:43:14.913 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-27 17:43:14.935 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [wise_snyder] DSL2 - revision: 5cb3581ad6
Feb-27 17:43:14.938 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-27 17:43:14.939 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-27 17:43:14.942 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-27 17:43:14.955 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-27 17:43:14.955 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-27 17:43:14.972 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-27 17:43:15.045 [main] DEBUG nextflow.Session - Session UUID: ab7a7317-9f8e-49f9-8ba6-8349b24a36ef
Feb-27 17:43:15.046 [main] DEBUG nextflow.Session - Run name: wise_snyder
Feb-27 17:43:15.047 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-27 17:43:15.059 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-27 17:43:15.067 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:43:15.104 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3937567@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (5.3 GB) - Swap: 0 (0)
Feb-27 17:43:15.139 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-27 17:43:15.140 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-27 17:43:15.158 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-27 17:43:15.176 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-27 17:43:15.182 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-27 17:43:15.185 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-27 17:43:15.217 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-27 17:43:15.229 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-27 17:43:15.409 [main] DEBUG nextflow.Session - Session start
Feb-27 17:43:15.879 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-27 17:43:16.759 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:16.760 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:16.767 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-27 17:43:16.777 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-27 17:43:16.780 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-27 17:43:16.815 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-27 17:43:16.900 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:16.900 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:16.902 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-27 17:43:16.915 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-27 17:43:16.920 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:16.920 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:16.922 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-27 17:43:16.984 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:16.984 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:16.985 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-27 17:43:17.016 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:17.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:17.017 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-27 17:43:17.025 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:17.025 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:17.026 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-27 17:43:17.039 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:43:17.039 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:43:17.040 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-27 17:43:17.043 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Feb-27 17:43:17.046 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-27 17:43:17.053 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-27 17:43:17.069 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-27 17:43:17.071 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-27 17:43:17.071 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/caline-run6/digtrial/input/; pattern: *.csv; options: [:]
Feb-27 17:43:17.071 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-27 17:43:17.071 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-27 17:43:17.072 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-27 17:43:17.073 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-27 17:43:17.073 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-27 17:43:17.074 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-27 17:43:17.075 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-27 17:43:17.075 [main] DEBUG nextflow.Session - Session await
Feb-27 17:43:17.299 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:43:17.303 [Task submitter] INFO nextflow.Session - [b8/48fb21] Submitted process > HUMAN_TRANSFORMER (1)
Feb-27 17:43:24.518 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b8/48fb213f9b113a32b1649ada113509]
Feb-27 17:43:24.519 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:43:24.547 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:43:24.559 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:43:24.560 [Task submitter] INFO nextflow.Session - [f5/a871d4] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Feb-27 17:43:28.371 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f5/a871d46063710b8620594ede8bc8f2]
Feb-27 17:43:28.423 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:43:28.424 [Task submitter] INFO nextflow.Session - [54/3e3c99] Submitted process > CONPLEX_ALL (1)
Feb-27 17:45:36.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/54/3e3c99cd7077434aa2732f31dd7b5c]
Feb-27 17:45:36.075 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:45:36.075 [Task submitter] INFO nextflow.Session - [24/f1f52e] Submitted process > TISSUE_DISTRIBUTION (1)
Feb-27 17:45:36.081 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:45:36.082 [Task submitter] INFO nextflow.Session - [aa/de8363] Submitted process > BIO_METRICS (1)
Feb-27 17:45:36.087 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:45:36.088 [Task submitter] INFO nextflow.Session - [f3/73824b] Submitted process > NETWORK_ENRICHMENT (1)
Feb-27 17:45:44.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f3/73824bf939c5be1858680c6af0e5e6]
Feb-27 17:45:47.754 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/24/f1f52e39bf1496db70950a7c5a04c8]
Feb-27 17:45:58.442 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/aa/de8363f3884d595a7a7df0291508ef]
Feb-27 17:45:58.448 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-27 17:45:58.542 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-27 17:45:58.542 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-27 17:45:58.548 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Feb-27 17:45:58.549 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Feb-27 17:45:58.557 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3m 1s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=3; peakMemory=11 GB; ]
Feb-27 17:45:58.693 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-27 17:45:58.772 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-27 17:45:58.772 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-27 17:45:58.774 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-27 17:45:58.775 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

122
.nextflow.log.5 Normal file
View File

@@ -0,0 +1,122 @@
Feb-27 17:41:44.642 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/caline-run6/digtrial/caline-run6.json
Feb-27 17:41:45.022 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-27 17:41:45.053 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-27 17:41:45.091 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-27 17:41:45.092 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-27 17:41:45.096 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-27 17:41:45.109 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-27 17:41:45.142 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-27 17:41:45.146 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-27 17:41:45.190 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-27 17:41:45.196 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-27 17:41:45.226 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-27 17:41:45.999 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-27 17:41:46.021 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [chaotic_leakey] DSL2 - revision: 5cb3581ad6
Feb-27 17:41:46.024 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-27 17:41:46.025 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-27 17:41:46.028 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-27 17:41:46.042 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-27 17:41:46.043 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-27 17:41:46.062 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-27 17:41:46.139 [main] DEBUG nextflow.Session - Session UUID: 6d6a967c-f1c2-433b-8c30-4f047e71a910
Feb-27 17:41:46.140 [main] DEBUG nextflow.Session - Run name: chaotic_leakey
Feb-27 17:41:46.140 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-27 17:41:46.153 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-27 17:41:46.161 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:41:46.198 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3934402@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (5 GB) - Swap: 0 (0)
Feb-27 17:41:46.237 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-27 17:41:46.238 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-27 17:41:46.254 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-27 17:41:46.273 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-27 17:41:46.279 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-27 17:41:46.281 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-27 17:41:46.315 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-27 17:41:46.328 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-27 17:41:46.574 [main] DEBUG nextflow.Session - Session start
Feb-27 17:41:47.067 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-27 17:41:47.963 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:47.964 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:47.971 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-27 17:41:47.981 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-27 17:41:47.984 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-27 17:41:48.018 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-27 17:41:48.112 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.112 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.114 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-27 17:41:48.127 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-27 17:41:48.132 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.132 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.134 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-27 17:41:48.193 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.193 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.194 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-27 17:41:48.226 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.226 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.227 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-27 17:41:48.235 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.235 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.236 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-27 17:41:48.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-27 17:41:48.248 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-27 17:41:48.248 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-27 17:41:48.251 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Feb-27 17:41:48.254 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-27 17:41:48.261 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-27 17:41:48.277 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-27 17:41:48.278 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-27 17:41:48.279 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-27 17:41:48.279 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-27 17:41:48.279 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/caline-run6/digtrial/input/; pattern: *.csv; options: [:]
Feb-27 17:41:48.280 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-27 17:41:48.280 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-27 17:41:48.281 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-27 17:41:48.282 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-27 17:41:48.282 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-27 17:41:48.282 [main] DEBUG nextflow.Session - Session await
Feb-27 17:41:48.510 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:41:48.514 [Task submitter] INFO nextflow.Session - [9c/1a79a1] Submitted process > HUMAN_TRANSFORMER (1)
Feb-27 17:41:56.073 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9c/1a79a1afef130a28212413d1c010fd]
Feb-27 17:41:56.075 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:41:56.102 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-27 17:41:56.117 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:41:56.118 [Task submitter] INFO nextflow.Session - [3b/c06172] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Feb-27 17:42:01.333 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/3b/c061720cd41597e8b90414cc4a66b0]
Feb-27 17:42:01.387 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-27 17:42:01.388 [Task submitter] INFO nextflow.Session - [18/8af203] Submitted process > CONPLEX_ALL (1)
Feb-27 17:42:14.026 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Feb-27 17:42:14.046 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active:
[process] NETWORK_ENRICHMENT
status=ACTIVE
port 0: (queue) OPEN ; channel: interactions
port 1: (cntrl) - ; channel: $
[process] TISSUE_DISTRIBUTION
status=ACTIVE
port 0: (queue) OPEN ; channel: interaction
port 1: (cntrl) - ; channel: $
[process] BIO_METRICS
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
Feb-27 17:42:14.050 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-27 17:42:14.051 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-27 17:42:14.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-27 17:42:14.062 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1)
Feb-27 17:42:14.084 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=1; succeedDuration=12.6s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=5 GB; ]
Feb-27 17:42:14.099 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-27 17:42:14.172 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-27 17:42:14.173 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-27 17:42:14.175 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

203
.nextflow.log.6 Normal file
View File

@@ -0,0 +1,203 @@
Feb-21 08:26:11.901 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/gpr55-caline/digtrial/gpr55-2.json
Feb-21 08:26:12.274 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-21 08:26:12.306 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-21 08:26:12.344 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-21 08:26:12.345 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-21 08:26:12.349 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-21 08:26:12.363 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-21 08:26:12.391 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-21 08:26:12.394 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-21 08:26:12.433 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-21 08:26:12.439 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-21 08:26:12.470 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-21 08:26:13.224 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-21 08:26:13.248 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [happy_einstein] DSL2 - revision: 5cb3581ad6
Feb-21 08:26:13.250 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-21 08:26:13.252 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-21 08:26:13.254 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-21 08:26:13.266 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-21 08:26:13.266 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-21 08:26:13.282 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-21 08:26:13.348 [main] DEBUG nextflow.Session - Session UUID: aaa33539-42d2-4a58-bb4f-dbf3ef8277f7
Feb-21 08:26:13.349 [main] DEBUG nextflow.Session - Run name: happy_einstein
Feb-21 08:26:13.350 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-21 08:26:13.360 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-21 08:26:13.368 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-21 08:26:13.399 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 2226167@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (54.1 GB) - Swap: 0 (0)
Feb-21 08:26:13.429 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-21 08:26:13.430 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-21 08:26:13.445 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-21 08:26:13.462 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-21 08:26:13.467 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-21 08:26:13.470 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-21 08:26:13.502 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-21 08:26:13.514 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-21 08:26:13.743 [main] DEBUG nextflow.Session - Session start
Feb-21 08:26:14.238 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-21 08:26:15.158 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.158 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.167 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-21 08:26:15.179 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-21 08:26:15.182 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-21 08:26:15.220 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-21 08:26:15.319 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.319 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.321 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-21 08:26:15.338 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-21 08:26:15.344 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.344 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.346 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-21 08:26:15.417 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.417 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.419 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-21 08:26:15.452 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.453 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.454 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-21 08:26:15.462 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.464 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-21 08:26:15.478 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 08:26:15.478 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 08:26:15.479 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-21 08:26:15.483 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, ORDERED_SEQUENCE, PREPROCESS_PROTEIN
Feb-21 08:26:15.486 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-21 08:26:15.493 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-21 08:26:15.494 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-21 08:26:15.496 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-21 08:26:15.496 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/gpr55-caline/digtrial/input/ligands-2/; pattern: *.csv; options: [:]
Feb-21 08:26:15.496 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-21 08:26:15.497 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-21 08:26:15.498 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-21 08:26:15.499 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-21 08:26:15.499 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-21 08:26:15.500 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-21 08:26:15.501 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-21 08:26:15.501 [main] DEBUG nextflow.Session - Session await
Feb-21 08:26:15.782 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:26:15.786 [Task submitter] INFO nextflow.Session - [ca/885a1e] Submitted process > HUMAN_TRANSFORMER (2)
Feb-21 08:26:15.805 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:26:15.806 [Task submitter] INFO nextflow.Session - [2d/bb32e3] Submitted process > HUMAN_TRANSFORMER (1)
Feb-21 08:26:15.817 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:26:15.817 [Task submitter] INFO nextflow.Session - [0f/b91ea0] Submitted process > HUMAN_TRANSFORMER (3)
Feb-21 08:31:15.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/2d/bb32e3b5f28c9eec85c5bb37846523]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 08:36:15.480 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/2d/bb32e3b5f28c9eec85c5bb37846523]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 08:41:15.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/2d/bb32e3b5f28c9eec85c5bb37846523]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 08:43:29.942 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2d/bb32e3b5f28c9eec85c5bb37846523]
Feb-21 08:43:29.945 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-21 08:43:29.985 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-21 08:43:30.002 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:43:30.003 [Task submitter] INFO nextflow.Session - [6a/f2fe26] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Feb-21 08:44:16.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/6a/f2fe266d28b090525b076c6971a9ac]
Feb-21 08:44:16.071 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:44:16.072 [Task submitter] INFO nextflow.Session - [b4/24dd60] Submitted process > CONPLEX_ALL (1)
Feb-21 08:45:20.806 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b4/24dd60196c0971a4af54b5ad1565b0]
Feb-21 08:45:20.838 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:45:20.838 [Task submitter] INFO nextflow.Session - [41/675f1d] Submitted process > TISSUE_DISTRIBUTION (1)
Feb-21 08:45:20.846 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:45:20.847 [Task submitter] INFO nextflow.Session - [f4/4b8797] Submitted process > BIO_METRICS (1)
Feb-21 08:45:20.854 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 08:45:20.854 [Task submitter] INFO nextflow.Session - [20/a798aa] Submitted process > NETWORK_ENRICHMENT (1)
Feb-21 08:45:30.689 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/20/a798aac4125b2c858745f2db23b064]
Feb-21 08:46:15.561 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
~> TaskHandler[id: 7; name: TISSUE_DISTRIBUTION (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/41/675f1daadc6833d1ba6e5b5b97f981]
~> TaskHandler[id: 6; name: BIO_METRICS (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/f4/4b8797cf0b654d2d69742b17114257]
Feb-21 08:46:26.149 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f4/4b8797cf0b654d2d69742b17114257]
Feb-21 08:46:43.111 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/41/675f1daadc6833d1ba6e5b5b97f981]
Feb-21 08:51:15.624 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 08:56:15.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:01:15.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:04:21.812 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ca/885a1e737e907d9d68c641155b12a7]
Feb-21 09:04:21.842 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:04:21.844 [Task submitter] INFO nextflow.Session - [bc/640502] Submitted process > GET_FINAL_METABOLITES_STATIC (2)
Feb-21 09:06:15.670 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
~> TaskHandler[id: 9; name: GET_FINAL_METABOLITES_STATIC (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/bc/640502221e58476eee68f371fe82bb]
Feb-21 09:06:26.151 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: GET_FINAL_METABOLITES_STATIC (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/bc/640502221e58476eee68f371fe82bb]
Feb-21 09:06:26.183 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:06:26.184 [Task submitter] INFO nextflow.Session - [fc/c19a15] Submitted process > CONPLEX_ALL (2)
Feb-21 09:07:46.502 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: CONPLEX_ALL (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/fc/c19a15943208e08e3abb897eb631c0]
Feb-21 09:07:46.745 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:07:46.746 [Task submitter] INFO nextflow.Session - [1a/a9da00] Submitted process > BIO_METRICS (2)
Feb-21 09:07:46.758 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:07:46.759 [Task submitter] INFO nextflow.Session - [88/9bf0d8] Submitted process > NETWORK_ENRICHMENT (2)
Feb-21 09:07:46.771 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:07:46.772 [Task submitter] INFO nextflow.Session - [8f/a0549f] Submitted process > TISSUE_DISTRIBUTION (2)
Feb-21 09:07:54.952 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NETWORK_ENRICHMENT (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/88/9bf0d88d7aeba1db6fb5b607608d47]
Feb-21 09:08:30.010 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: BIO_METRICS (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/1a/a9da0011763bb8b8bedaa177c7ad4d]
Feb-21 09:09:17.348 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: TISSUE_DISTRIBUTION (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/8f/a0549f011b0670ee0efe79c24eed12]
Feb-21 09:11:15.719 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:16:15.741 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:21:15.743 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:26:15.759 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:31:15.772 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:33:12.492 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0f/b91ea06be4270d20b24cf9066994d1]
Feb-21 09:33:12.519 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:33:12.521 [Task submitter] INFO nextflow.Session - [5a/66192c] Submitted process > GET_FINAL_METABOLITES_STATIC (3)
Feb-21 09:36:15.836 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 14; name: GET_FINAL_METABOLITES_STATIC (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/5a/66192c1bce02251dae996035f42b6c]
Feb-21 09:36:49.412 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: GET_FINAL_METABOLITES_STATIC (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5a/66192c1bce02251dae996035f42b6c]
Feb-21 09:36:49.436 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:36:49.437 [Task submitter] INFO nextflow.Session - [1b/e37700] Submitted process > CONPLEX_ALL (3)
Feb-21 09:37:18.524 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: CONPLEX_ALL (3); status: COMPLETED; exit: 137; error: -; workDir: /data/bugra/digital_trials/work/1b/e377009d05a6c1b5bb554d679c7b6d]
Feb-21 09:37:18.539 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=CONPLEX_ALL (3); work-dir=/data/bugra/digital_trials/work/1b/e377009d05a6c1b5bb554d679c7b6d
error [nextflow.exception.ProcessFailedException]: Process `CONPLEX_ALL (3)` terminated with an error exit status (137)
Feb-21 09:37:18.555 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [1b/e37700] NOTE: Process `CONPLEX_ALL (3)` terminated with an error exit status (137) -- Execution is retried (1)
Feb-21 09:37:18.569 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:37:18.570 [Task submitter] INFO nextflow.Session - [f9/d09bf9] Re-submitted process > CONPLEX_ALL (3)
Feb-21 09:39:45.775 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: CONPLEX_ALL (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/f9/d09bf98e06da2eff5d1cc7e692395e]
Feb-21 09:39:45.801 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:39:45.803 [Task submitter] INFO nextflow.Session - [c5/08ec8c] Submitted process > TISSUE_DISTRIBUTION (3)
Feb-21 09:39:45.812 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:39:45.813 [Task submitter] INFO nextflow.Session - [0a/3a0af0] Submitted process > NETWORK_ENRICHMENT (3)
Feb-21 09:39:45.833 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 09:39:45.834 [Task submitter] INFO nextflow.Session - [49/7a1605] Submitted process > BIO_METRICS (3)
Feb-21 09:39:58.587 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NETWORK_ENRICHMENT (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0a/3a0af0240fb975245cb9cab1214683]
Feb-21 09:41:15.781 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: BIO_METRICS (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/49/7a16055c1c8edcda53d29edbffefb3]
Feb-21 09:41:15.882 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/c5/08ec8c52e99f1e5f8284b75bd0523d]
Feb-21 09:42:16.950 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c5/08ec8c52e99f1e5f8284b75bd0523d]
Feb-21 09:42:16.957 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-21 09:42:17.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-21 09:42:17.051 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-21 09:42:17.054 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Feb-21 09:42:17.104 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Feb-21 09:42:17.122 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=18; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=1; abortedCount=0; succeedDuration=2h 22m 49s; failedDuration=29s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=5; peakCpus=5; peakMemory=21 GB; ]
Feb-21 09:42:17.188 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-21 09:42:17.292 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-21 09:42:17.292 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-21 09:42:17.294 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-21 09:42:17.295 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

189
.nextflow.log.7 Normal file
View File

@@ -0,0 +1,189 @@
Feb-20 12:47:41.705 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/gpr55-caline/digtrial/gpr55-2.json
Feb-20 12:47:42.085 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-20 12:47:42.117 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-20 12:47:42.156 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-20 12:47:42.157 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-20 12:47:42.161 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-20 12:47:42.176 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-20 12:47:42.204 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-20 12:47:42.207 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-20 12:47:42.249 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-20 12:47:42.254 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-20 12:47:42.284 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-20 12:47:43.029 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-20 12:47:43.053 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [voluminous_meucci] DSL2 - revision: 5cb3581ad6
Feb-20 12:47:43.055 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-20 12:47:43.057 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-20 12:47:43.059 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-20 12:47:43.073 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-20 12:47:43.073 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-20 12:47:43.090 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-20 12:47:43.163 [main] DEBUG nextflow.Session - Session UUID: a63634f0-49a8-483c-8fd6-7fb017f33c21
Feb-20 12:47:43.163 [main] DEBUG nextflow.Session - Run name: voluminous_meucci
Feb-20 12:47:43.164 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-20 12:47:43.176 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-20 12:47:43.183 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-20 12:47:43.216 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 854173@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (57.9 GB) - Swap: 0 (0)
Feb-20 12:47:43.251 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-20 12:47:43.252 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-20 12:47:43.270 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-20 12:47:43.287 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-20 12:47:43.294 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-20 12:47:43.296 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-20 12:47:43.328 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-20 12:47:43.340 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-20 12:47:43.528 [main] DEBUG nextflow.Session - Session start
Feb-20 12:47:44.002 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-20 12:47:44.878 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:44.879 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:44.887 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-20 12:47:44.897 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-20 12:47:44.900 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-20 12:47:44.935 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-20 12:47:45.021 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.022 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.024 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-20 12:47:45.036 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-20 12:47:45.041 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.041 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.043 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-20 12:47:45.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.102 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-20 12:47:45.132 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.132 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.133 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-20 12:47:45.141 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.141 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.142 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-20 12:47:45.174 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:47:45.174 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:47:45.175 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-20 12:47:45.179 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Feb-20 12:47:45.182 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-20 12:47:45.190 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-20 12:47:45.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-20 12:47:45.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-20 12:47:45.192 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/gpr55-caline/digtrial/input/ligands-2/; pattern: *.csv; options: [:]
Feb-20 12:47:45.192 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-20 12:47:45.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-20 12:47:45.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-20 12:47:45.194 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-20 12:47:45.194 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-20 12:47:45.195 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-20 12:47:45.195 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-20 12:47:45.195 [main] DEBUG nextflow.Session - Session await
Feb-20 12:47:45.473 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:47:45.477 [Task submitter] INFO nextflow.Session - [97/35ef6b] Submitted process > HUMAN_TRANSFORMER (1)
Feb-20 12:47:45.496 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:47:45.497 [Task submitter] INFO nextflow.Session - [2d/780298] Submitted process > HUMAN_TRANSFORMER (3)
Feb-20 12:47:45.505 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:47:45.506 [Task submitter] INFO nextflow.Session - [61/1051d3] Submitted process > HUMAN_TRANSFORMER (2)
Feb-20 12:47:45.516 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:47:45.517 [Task submitter] INFO nextflow.Session - [70/a09372] Submitted process > HUMAN_TRANSFORMER (4)
Feb-20 12:50:49.469 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/2d/780298364720d78ead18d8c29fdde5]
Feb-20 12:50:49.471 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-20 12:50:49.509 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-20 12:50:49.533 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:50:49.534 [Task submitter] INFO nextflow.Session - [00/400028] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Feb-20 12:51:03.390 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/00/400028dec573753492b97923ca40a4]
Feb-20 12:51:03.450 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:51:03.452 [Task submitter] INFO nextflow.Session - [ab/173fd5] Submitted process > CONPLEX_ALL (1)
Feb-20 12:51:40.012 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: HUMAN_TRANSFORMER (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/70/a09372fc0300634e7a2d63c19eca9e]
Feb-20 12:51:40.036 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:51:40.037 [Task submitter] INFO nextflow.Session - [93/602233] Submitted process > GET_FINAL_METABOLITES_STATIC (2)
Feb-20 12:51:57.731 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: GET_FINAL_METABOLITES_STATIC (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/93/602233592598ae353bc191fe5eb511]
Feb-20 12:51:57.751 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:51:57.751 [Task submitter] INFO nextflow.Session - [27/09061e] Submitted process > CONPLEX_ALL (2)
Feb-20 12:52:04.582 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ab/173fd53ee5af1f9a99547c251a3860]
Feb-20 12:52:04.619 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:04.620 [Task submitter] INFO nextflow.Session - [97/9f27dd] Submitted process > TISSUE_DISTRIBUTION (1)
Feb-20 12:52:04.631 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:04.632 [Task submitter] INFO nextflow.Session - [15/a3f493] Submitted process > BIO_METRICS (1)
Feb-20 12:52:04.641 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:04.642 [Task submitter] INFO nextflow.Session - [9b/22fd33] Submitted process > NETWORK_ENRICHMENT (1)
Feb-20 12:52:19.322 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/9b/22fd33156ac8f5e161b52c59cefc81]
Feb-20 12:52:45.073 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 5 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/97/35ef6b0fb9a5705089e16cf692f080]
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
~> TaskHandler[id: 8; name: CONPLEX_ALL (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/27/09061ebd4aed37c8d9f75c62e056c9]
~> TaskHandler[id: 11; name: TISSUE_DISTRIBUTION (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/97/9f27dd23c432d4c981bc33a9fdea9d]
~> TaskHandler[id: 10; name: BIO_METRICS (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/15/a3f493c3f2ce41178d29e8ab6347a5]
Feb-20 12:52:47.429 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: CONPLEX_ALL (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/27/09061ebd4aed37c8d9f75c62e056c9]
Feb-20 12:52:47.452 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:47.453 [Task submitter] INFO nextflow.Session - [0a/f14dfa] Submitted process > NETWORK_ENRICHMENT (2)
Feb-20 12:52:47.463 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:47.464 [Task submitter] INFO nextflow.Session - [e7/226b4c] Submitted process > TISSUE_DISTRIBUTION (2)
Feb-20 12:52:47.471 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:52:47.472 [Task submitter] INFO nextflow.Session - [d6/fb313d] Submitted process > BIO_METRICS (2)
Feb-20 12:52:57.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NETWORK_ENRICHMENT (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/0a/f14dfa87e070755e2a9c79353c721d]
Feb-20 12:53:05.991 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/15/a3f493c3f2ce41178d29e8ab6347a5]
Feb-20 12:53:21.010 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: BIO_METRICS (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/d6/fb313d80c7d4a29ba04f1238d20f9f]
Feb-20 12:53:40.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/97/9f27dd23c432d4c981bc33a9fdea9d]
Feb-20 12:54:14.723 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: TISSUE_DISTRIBUTION (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/e7/226b4ced31f47b82c4a3f8aa57125e]
Feb-20 12:55:18.592 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/97/35ef6b0fb9a5705089e16cf692f080]
Feb-20 12:55:18.619 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:55:18.620 [Task submitter] INFO nextflow.Session - [69/5d280f] Submitted process > GET_FINAL_METABOLITES_STATIC (3)
Feb-20 12:55:51.877 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: GET_FINAL_METABOLITES_STATIC (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/69/5d280fbd362e9d8b61059bbd73baf8]
Feb-20 12:55:51.907 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:55:51.908 [Task submitter] INFO nextflow.Session - [74/48a2a7] Submitted process > CONPLEX_ALL (3)
Feb-20 12:57:06.254 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: CONPLEX_ALL (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/74/48a2a7780c3f777bbb2ae0f25f0a8c]
Feb-20 12:57:06.278 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:57:06.279 [Task submitter] INFO nextflow.Session - [4a/6f0805] Submitted process > TISSUE_DISTRIBUTION (3)
Feb-20 12:57:06.289 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:57:06.290 [Task submitter] INFO nextflow.Session - [b8/073303] Submitted process > NETWORK_ENRICHMENT (3)
Feb-20 12:57:06.300 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 12:57:06.301 [Task submitter] INFO nextflow.Session - [06/d7b03a] Submitted process > BIO_METRICS (3)
Feb-20 12:57:14.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NETWORK_ENRICHMENT (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b8/073303b55a5a4562ac607a9627b4ce]
Feb-20 12:57:45.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
~> TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/4a/6f0805028d05f5942ff8c0dd6e0fb6]
~> TaskHandler[id: 17; name: BIO_METRICS (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/06/d7b03ab59a78de182f97d57a4af883]
Feb-20 12:58:34.071 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: BIO_METRICS (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/06/d7b03ab59a78de182f97d57a4af883]
Feb-20 12:59:57.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4a/6f0805028d05f5942ff8c0dd6e0fb6]
Feb-20 13:02:45.233 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
Feb-20 13:07:45.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
Feb-20 13:12:45.271 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
Feb-20 13:14:43.334 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/61/1051d32de7028657b1414e31f05229]
Feb-20 13:14:43.363 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 13:14:43.364 [Task submitter] INFO nextflow.Session - [5f/44be98] Submitted process > GET_FINAL_METABOLITES_STATIC (4)
Feb-20 13:16:13.312 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: GET_FINAL_METABOLITES_STATIC (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5f/44be985eebec27883ed97d8dc19c80]
Feb-20 13:16:13.349 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 13:16:13.350 [Task submitter] INFO nextflow.Session - [b4/630a29] Submitted process > CONPLEX_ALL (4)
Feb-20 13:17:45.345 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 21; name: CONPLEX_ALL (4); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/b4/630a2983878cda3d03d42c45cca98f]
Feb-20 13:17:48.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: CONPLEX_ALL (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b4/630a2983878cda3d03d42c45cca98f]
Feb-20 13:17:48.045 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 13:17:48.046 [Task submitter] INFO nextflow.Session - [5c/ee7ebf] Submitted process > TISSUE_DISTRIBUTION (4)
Feb-20 13:17:48.057 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 13:17:48.057 [Task submitter] INFO nextflow.Session - [09/a6adcd] Submitted process > BIO_METRICS (4)
Feb-20 13:17:48.066 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-20 13:17:48.067 [Task submitter] INFO nextflow.Session - [5d/16d116] Submitted process > NETWORK_ENRICHMENT (4)
Feb-20 13:17:56.561 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: NETWORK_ENRICHMENT (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5d/16d1169328307314e2ca18b0d54c1f]
Feb-20 13:18:46.519 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: BIO_METRICS (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/09/a6adcd0a29467e13550a9805afd96b]
Feb-20 13:20:03.461 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: TISSUE_DISTRIBUTION (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/5c/ee7ebf9a1241900d75d373a0f55c6a]
Feb-20 13:20:03.466 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-20 13:20:03.563 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-20 13:20:03.563 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-20 13:20:03.572 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Feb-20 13:20:03.576 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Feb-20 13:20:03.592 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=24; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1h 1m 34s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=7; peakCpus=7; peakMemory=31 GB; ]
Feb-20 13:20:03.653 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-20 13:20:03.735 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-20 13:20:03.735 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-20 13:20:03.737 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-20 13:20:03.738 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

96
.nextflow.log.8 Normal file
View File

@@ -0,0 +1,96 @@
Feb-20 12:45:31.438 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/dreamdock-data/gpr55-caline/digtrial/gpr55-2.json
Feb-20 12:45:31.816 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-20 12:45:31.845 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-20 12:45:31.879 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-20 12:45:31.880 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-20 12:45:31.884 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-20 12:45:31.897 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-20 12:45:31.922 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-20 12:45:31.925 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-20 12:45:31.961 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-20 12:45:31.966 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-20 12:45:31.995 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-20 12:45:32.749 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-20 12:45:32.771 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [mad_jepsen] DSL2 - revision: 5cb3581ad6
Feb-20 12:45:32.773 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-20 12:45:32.775 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-20 12:45:32.777 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-20 12:45:32.790 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-20 12:45:32.790 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-20 12:45:32.808 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-20 12:45:32.881 [main] DEBUG nextflow.Session - Session UUID: 9b7d6ce5-46a6-43c0-accf-fd12d7d33e5d
Feb-20 12:45:32.882 [main] DEBUG nextflow.Session - Run name: mad_jepsen
Feb-20 12:45:32.883 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-20 12:45:32.896 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-20 12:45:32.905 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-20 12:45:32.940 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 851238@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (56.5 GB) - Swap: 0 (0)
Feb-20 12:45:32.977 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-20 12:45:32.978 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-20 12:45:32.997 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-20 12:45:33.016 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-20 12:45:33.022 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-20 12:45:33.025 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-20 12:45:33.059 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-20 12:45:33.073 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-20 12:45:33.221 [main] DEBUG nextflow.Session - Session start
Feb-20 12:45:33.684 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-20 12:45:34.592 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.592 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.600 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-20 12:45:34.611 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-20 12:45:34.614 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-20 12:45:34.649 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-20 12:45:34.755 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.755 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.757 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-20 12:45:34.772 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-20 12:45:34.778 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.779 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.781 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-20 12:45:34.850 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.850 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.851 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-20 12:45:34.887 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.887 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.888 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-20 12:45:34.897 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.897 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.899 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-20 12:45:34.927 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-20 12:45:34.927 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-20 12:45:34.928 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-20 12:45:34.933 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Feb-20 12:45:34.935 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-20 12:45:34.942 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-20 12:45:34.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-20 12:45:34.945 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-20 12:45:34.946 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-20 12:45:34.946 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-20 12:45:34.946 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/dreamdock-data/gpr55-caline/digtrial/input/ligands2/; pattern: *.csv; options: [:]
Feb-20 12:45:34.947 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-20 12:45:34.947 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-20 12:45:34.948 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-20 12:45:34.949 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-20 12:45:34.949 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-20 12:45:34.949 [main] DEBUG nextflow.Session - Session await
Feb-20 12:45:34.951 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - No such file or directory: /data/dreamdock-data/gpr55-caline/digtrial/input/ligands2/ -- Skipping visit
Feb-20 12:45:34.966 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-20 12:45:35.028 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-20 12:45:35.028 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-20 12:45:35.037 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Feb-20 12:45:35.083 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-20 12:45:35.175 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-20 12:45:35.175 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-20 12:45:35.179 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-20 12:45:35.180 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

189
.nextflow.log.9 Normal file
View File

@@ -0,0 +1,189 @@
Feb-18 08:16:32.779 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf -params-file /data/digital-trials-data/caline-run5/caline-run5.json
Feb-18 08:16:33.190 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Feb-18 08:16:33.221 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Feb-18 08:16:33.261 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Feb-18 08:16:33.262 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Feb-18 08:16:33.266 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Feb-18 08:16:33.284 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Feb-18 08:16:33.314 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/digital_trials/nextflow.config
Feb-18 08:16:33.318 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/digital_trials/nextflow.config
Feb-18 08:16:33.362 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Feb-18 08:16:33.368 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6ef81f31] - activable => nextflow.secret.LocalSecretsProvider@6ef81f31
Feb-18 08:16:33.406 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Feb-18 08:16:34.180 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Feb-18 08:16:34.202 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [fabulous_marconi] DSL2 - revision: 5cb3581ad6
Feb-18 08:16:34.204 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Feb-18 08:16:34.206 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.11.3]
Feb-18 08:16:34.208 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.11.3
Feb-18 08:16:34.221 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.11.3' resolved
Feb-18 08:16:34.222 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.11.3'
Feb-18 08:16:34.239 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.11.3
Feb-18 08:16:34.310 [main] DEBUG nextflow.Session - Session UUID: ece3d722-9ceb-41e2-826d-635604e82e89
Feb-18 08:16:34.311 [main] DEBUG nextflow.Session - Run name: fabulous_marconi
Feb-18 08:16:34.311 [main] DEBUG nextflow.Session - Executor pool size: 80
Feb-18 08:16:34.324 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Feb-18 08:16:34.332 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-18 08:16:34.414 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 1283371@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (50.5 GB) - Swap: 0 (0)
Feb-18 08:16:34.449 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/digital_trials/work [btrfs]
Feb-18 08:16:34.450 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/digital_trials/bin
Feb-18 08:16:34.467 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Feb-18 08:16:34.486 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-18 08:16:34.492 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-18 08:16:34.495 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Feb-18 08:16:34.544 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Feb-18 08:16:34.560 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Feb-18 08:16:34.812 [main] DEBUG nextflow.Session - Session start
Feb-18 08:16:35.337 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-18 08:16:36.243 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.252 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-18 08:16:36.262 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Feb-18 08:16:36.265 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Feb-18 08:16:36.300 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'HUMAN_TRANSFORMER': maxForks=0; fair=false; array=0
Feb-18 08:16:36.400 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.400 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.402 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'GET_FINAL_METABOLITES_STATIC': maxForks=0; fair=false; array=0
Feb-18 08:16:36.417 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:gpu_process` matches labels `gpu_process` for process with name PREPROCESS_PROTEIN
Feb-18 08:16:36.422 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.422 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.424 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PREPROCESS_PROTEIN': maxForks=0; fair=false; array=0
Feb-18 08:16:36.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.486 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.487 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'CONPLEX_ALL': maxForks=0; fair=false; array=0
Feb-18 08:16:36.516 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.516 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.518 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NETWORK_ENRICHMENT': maxForks=0; fair=false; array=0
Feb-18 08:16:36.525 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.525 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.526 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'TISSUE_DISTRIBUTION': maxForks=0; fair=false; array=0
Feb-18 08:16:36.537 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-18 08:16:36.537 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-18 08:16:36.538 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'BIO_METRICS': maxForks=0; fair=false; array=0
Feb-18 08:16:36.541 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: HUMAN_TRANSFORMER, METABOLITES_BY_MASS, GET_FINAL_METABOLITES_STATIC, CONPLEX_ALL, NETWORK_ENRICHMENT, GET_FINAL_METABOLITES, CONPLEX, BIO_METRICS, SUPER_TRANSFORMER, TISSUE_DISTRIBUTION, MERGE_DRUG, MERGE_INTERACTIONS, PREPROCESS_PROTEIN, ORDERED_SEQUENCE
Feb-18 08:16:36.544 [main] DEBUG nextflow.Session - Igniting dataflow network (11)
Feb-18 08:16:36.551 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HUMAN_TRANSFORMER
Feb-18 08:16:36.552 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GET_FINAL_METABOLITES_STATIC
Feb-18 08:16:36.553 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PREPROCESS_PROTEIN
Feb-18 08:16:36.554 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > CONPLEX_ALL
Feb-18 08:16:36.554 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/dreamdock-data/digital_trials/input/blank/; pattern: *.fasta; options: [:]
Feb-18 08:16:36.554 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /data/digital-trials-data/caline-run5/input/ligands/; pattern: *.csv; options: [:]
Feb-18 08:16:36.555 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NETWORK_ENRICHMENT
Feb-18 08:16:36.555 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TISSUE_DISTRIBUTION
Feb-18 08:16:36.556 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BIO_METRICS
Feb-18 08:16:36.557 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c432c676a3e7c0cb: /data/bugra/digital_trials/test.nf
Script_e39e54e7aa543fd0: /data/bugra/digital_trials/main_biotransformer.nf
Script_d345b7a65a8f3255: /data/bugra/digital_trials/main_conplex.nf
Script_ec01f2a38db15aa5: /data/bugra/digital_trials/main_tissue.nf
Feb-18 08:16:36.557 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Feb-18 08:16:36.557 [main] DEBUG nextflow.Session - Session await
Feb-18 08:16:36.797 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:16:36.800 [Task submitter] INFO nextflow.Session - [b1/69b46f] Submitted process > HUMAN_TRANSFORMER (4)
Feb-18 08:16:36.815 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:16:36.816 [Task submitter] INFO nextflow.Session - [10/2fb928] Submitted process > HUMAN_TRANSFORMER (3)
Feb-18 08:16:36.823 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:16:36.824 [Task submitter] INFO nextflow.Session - [10/6b721f] Submitted process > HUMAN_TRANSFORMER (2)
Feb-18 08:16:36.831 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:16:36.831 [Task submitter] INFO nextflow.Session - [ac/d9d808] Submitted process > HUMAN_TRANSFORMER (1)
Feb-18 08:19:47.743 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: HUMAN_TRANSFORMER (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/10/2fb9287851aa5e184a108c2622d322]
Feb-18 08:19:47.747 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-18 08:19:47.788 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Feb-18 08:19:47.801 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:19:47.802 [Task submitter] INFO nextflow.Session - [4a/22722f] Submitted process > GET_FINAL_METABOLITES_STATIC (1)
Feb-18 08:19:56.711 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: GET_FINAL_METABOLITES_STATIC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4a/22722f5d74d0ebe540d7d39ea06b1b]
Feb-18 08:19:56.775 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:19:56.776 [Task submitter] INFO nextflow.Session - [7e/903d0b] Submitted process > CONPLEX_ALL (1)
Feb-18 08:20:40.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: HUMAN_TRANSFORMER (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b1/69b46f4ee44257fa109faa38046f22]
Feb-18 08:20:40.586 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:20:40.587 [Task submitter] INFO nextflow.Session - [c6/ebbabc] Submitted process > GET_FINAL_METABOLITES_STATIC (2)
Feb-18 08:20:48.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: GET_FINAL_METABOLITES_STATIC (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c6/ebbabc26d328ed82ed29fa3420b345]
Feb-18 08:20:48.196 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:20:48.197 [Task submitter] INFO nextflow.Session - [a8/9dfebd] Submitted process > CONPLEX_ALL (2)
Feb-18 08:21:02.719 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: CONPLEX_ALL (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/7e/903d0be26b0f46094fa4124ea7429e]
Feb-18 08:21:02.753 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:02.754 [Task submitter] INFO nextflow.Session - [80/5291a1] Submitted process > TISSUE_DISTRIBUTION (1)
Feb-18 08:21:02.761 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:02.761 [Task submitter] INFO nextflow.Session - [b1/0c641f] Submitted process > BIO_METRICS (1)
Feb-18 08:21:02.768 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:02.769 [Task submitter] INFO nextflow.Session - [41/ada4cf] Submitted process > NETWORK_ENRICHMENT (1)
Feb-18 08:21:13.500 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NETWORK_ENRICHMENT (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/41/ada4cffa7038bb6a904ad7adffab70]
Feb-18 08:21:36.459 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 5 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
~> TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/ac/d9d808f5e7ff0bc9ce47fce956e109]
~> TaskHandler[id: 8; name: CONPLEX_ALL (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/a8/9dfebda5ca5c8d25917ad9721d5ed6]
~> TaskHandler[id: 10; name: TISSUE_DISTRIBUTION (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/80/5291a1b8a9df4f84137206aab3afef]
~> TaskHandler[id: 9; name: BIO_METRICS (1); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/b1/0c641f36428a66f82eaaca889dfcc4]
Feb-18 08:21:36.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: BIO_METRICS (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/b1/0c641f36428a66f82eaaca889dfcc4]
Feb-18 08:21:45.303 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: CONPLEX_ALL (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/a8/9dfebda5ca5c8d25917ad9721d5ed6]
Feb-18 08:21:45.329 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:45.330 [Task submitter] INFO nextflow.Session - [c7/e9aec0] Submitted process > TISSUE_DISTRIBUTION (2)
Feb-18 08:21:45.337 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:45.337 [Task submitter] INFO nextflow.Session - [59/c2fca6] Submitted process > BIO_METRICS (2)
Feb-18 08:21:45.342 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:21:45.343 [Task submitter] INFO nextflow.Session - [85/b01dc2] Submitted process > NETWORK_ENRICHMENT (2)
Feb-18 08:21:53.257 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NETWORK_ENRICHMENT (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/85/b01dc209496674d3dc3d3272884c01]
Feb-18 08:22:17.459 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: BIO_METRICS (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/59/c2fca62fef3a938fdbc8b0223f741d]
Feb-18 08:22:50.627 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: TISSUE_DISTRIBUTION (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/80/5291a1b8a9df4f84137206aab3afef]
Feb-18 08:23:28.694 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: TISSUE_DISTRIBUTION (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c7/e9aec0a45e4143e662078f6751029f]
Feb-18 08:24:20.543 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HUMAN_TRANSFORMER (1); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ac/d9d808f5e7ff0bc9ce47fce956e109]
Feb-18 08:24:20.570 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:24:20.571 [Task submitter] INFO nextflow.Session - [81/2dab34] Submitted process > GET_FINAL_METABOLITES_STATIC (3)
Feb-18 08:24:28.312 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: GET_FINAL_METABOLITES_STATIC (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/81/2dab347a00f1c46abab44c67984a92]
Feb-18 08:24:28.339 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:24:28.340 [Task submitter] INFO nextflow.Session - [c7/3c6e3d] Submitted process > CONPLEX_ALL (3)
Feb-18 08:25:56.687 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: CONPLEX_ALL (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/c7/3c6e3d019680ae4510c31fc27d9df0]
Feb-18 08:25:56.912 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:25:56.913 [Task submitter] INFO nextflow.Session - [81/f77500] Submitted process > TISSUE_DISTRIBUTION (3)
Feb-18 08:25:56.920 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:25:56.921 [Task submitter] INFO nextflow.Session - [6d/83c7a3] Submitted process > NETWORK_ENRICHMENT (3)
Feb-18 08:25:56.930 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:25:56.931 [Task submitter] INFO nextflow.Session - [60/56dbb4] Submitted process > BIO_METRICS (3)
Feb-18 08:26:05.728 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NETWORK_ENRICHMENT (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/6d/83c7a3352024b70f27bbb97877137d]
Feb-18 08:26:36.497 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
~> TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/81/f775001059255636bc93e7534e6f1b]
~> TaskHandler[id: 17; name: BIO_METRICS (3); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/60/56dbb481dcd9014f733e6adcd305ac]
Feb-18 08:28:21.708 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: BIO_METRICS (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/60/56dbb481dcd9014f733e6adcd305ac]
Feb-18 08:29:23.190 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: TISSUE_DISTRIBUTION (3); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/81/f775001059255636bc93e7534e6f1b]
Feb-18 08:31:36.595 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
Feb-18 08:36:36.600 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
Feb-18 08:41:36.633 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
Feb-18 08:45:15.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: HUMAN_TRANSFORMER (2); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/10/6b721ff03cf9bb6fdc069b2318e358]
Feb-18 08:45:15.999 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:45:16.001 [Task submitter] INFO nextflow.Session - [ca/ecd442] Submitted process > GET_FINAL_METABOLITES_STATIC (4)
Feb-18 08:45:36.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: GET_FINAL_METABOLITES_STATIC (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/ca/ecd44260f39786b4230f8c7740d148]
Feb-18 08:45:36.037 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:45:36.038 [Task submitter] INFO nextflow.Session - [46/a43ec7] Submitted process > CONPLEX_ALL (4)
Feb-18 08:46:36.691 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 21; name: CONPLEX_ALL (4); status: RUNNING; exit: -; error: -; workDir: /data/bugra/digital_trials/work/46/a43ec7ee9aa22e1e774cee2c12ad30]
Feb-18 08:47:29.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: CONPLEX_ALL (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/46/a43ec7ee9aa22e1e774cee2c12ad30]
Feb-18 08:47:29.251 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:47:29.252 [Task submitter] INFO nextflow.Session - [cc/bb7703] Submitted process > TISSUE_DISTRIBUTION (4)
Feb-18 08:47:29.261 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:47:29.262 [Task submitter] INFO nextflow.Session - [31/fe7897] Submitted process > NETWORK_ENRICHMENT (4)
Feb-18 08:47:29.273 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-18 08:47:29.274 [Task submitter] INFO nextflow.Session - [4b/086a46] Submitted process > BIO_METRICS (4)
Feb-18 08:47:39.063 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: NETWORK_ENRICHMENT (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/31/fe78970d1a3fa2033c4c4ace31eeea]
Feb-18 08:50:24.140 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: TISSUE_DISTRIBUTION (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/cc/bb7703233cc2a65dbcc3a2cba4229f]
Feb-18 08:50:34.666 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: BIO_METRICS (4); status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/digital_trials/work/4b/086a4619532ee364d68e77bd33000f]
Feb-18 08:50:34.672 [main] DEBUG nextflow.Session - Session await > all processes finished
Feb-18 08:50:34.768 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Feb-18 08:50:34.768 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-18 08:50:34.775 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Feb-18 08:50:34.776 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Feb-18 08:50:34.789 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=24; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1h 6m 51s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=6; peakMemory=26 GB; ]
Feb-18 08:50:34.967 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Feb-18 08:50:35.030 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.11.3'
Feb-18 08:50:35.030 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Feb-18 08:50:35.032 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Feb-18 08:50:35.033 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

1
.nextflow.pid Executable file
View File

@@ -0,0 +1 @@
1195666

121
CLAUDE.md Normal file
View File

@@ -0,0 +1,121 @@
# CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
## What This Is
Digital Trials is a Nextflow pipeline that simulates drug-protein interactions for digital clinical trials. Given a drug (as SMILES), it predicts metabolites, screens the drug and its metabolites against a proteome, performs pathway enrichment, and maps tissue distribution of interacting proteins.
## Running the Pipeline
```bash
# Local test run (uses params defined in main.nf)
nextflow run main.nf
# With parameter file for cluster runs
nextflow run main.nf -params-file params/input_to_run.json
# Kubernetes via Tower
export TOWER_ACCESS_TOKEN=68358d90995ae27fe78b4c1818f9f0097d834b00
nextflow run main.nf -profile k8s -with-tower https://tower.stg.cluster.omic.ai/api -params-file params/input_to_run.json
```
## Building Containers
```bash
# Build and tag individual containers via docker-compose
docker-compose build tissue
docker-compose build chembl
docker-compose build network
# Images push to harbor.cluster.omic.ai/omic/digitaltrials/
```
Each pipeline step has its own Dockerfile: `Dockerfile_biotransformer`, `Dockerfile_conplex`, `Dockerfile_tissue`, `Dockerfile_chembl`, `Dockerfile_network`.
## Pipeline Architecture
The pipeline is orchestrated in `main.nf` (entry point and parameter definitions) and composed from three module files:
### Stage 1: Metabolite Prediction (`main_biotransformer.nf`)
- **HUMAN_TRANSFORMER** — Runs BioTransformer (Java) to predict human metabolites from input SMILES. Only `HUMAN` mode is fully implemented.
- **GET_FINAL_METABOLITES_STATIC** — Filters to terminal metabolites (not precursors), checks against local ChEMBL SQLite DB and PubChem, outputs canonical SMILES list.
### Stage 2: Proteome Screening (`main_conplex.nf`)
- **PREPROCESS_PROTEIN** — Merges patient FASTA files and projects them into a Zarr vector store (GPU, uses `/app/project.py` inside container).
- **CONPLEX** — Screens drug + metabolite SMILES against protein Zarr DBs using ConPLex model. Runs `/app/convert.py`, `/app/screen.py`, `/app/get_round_2.py` inside the `metabolite-screen` container. Outputs drug scores and significant interactions TSVs.
- **NETWORK_ENRICHMENT** — Queries STRING DB API for pathway enrichment and protein-protein interactions from significant hits.
### Stage 3: Tissue & Biological Properties (`main_tissue.nf`)
- **TISSUE_DISTRIBUTION** — Maps interacting proteins to tissue expression using HPA data (`drug_tissue_distribution.py`).
- **BIO_METRICS** — Aggregates biological properties across metabolites, drug scores, and interactions (`digital_patient_extract_metrics.py`).
### Data Flow
```
Input CSVs (SMILES+TARGET) → HUMAN_TRANSFORMER → GET_FINAL_METABOLITES_STATIC
↓
Patient FASTA → PREPROCESS_PROTEIN → Zarr ──→ CONPLEX (drug + metabolites vs proteome)
Pre-built Zarr ─────────────────────────↗ ↓ ↓
NETWORK_ENRICHMENT TISSUE_DISTRIBUTION
↓
BIO_METRICS
```
Channels are joined by ligand ID (CSV `simpleName`), ensuring each drug's metabolites are matched to the correct ConPLex screening run.
## Key Parameters (in `main.nf`)
| Parameter | Purpose | Default |
|-----------|---------|---------|
| `params.mode` | BioTransformer mode — **use `HUMAN` only** | `HUMAN` |
| `params.threshold` | ConPLex binding score cutoff for significant interactions | `0.65` |
| `params.protein_network_threshold` | STRING DB enrichment cutoff | `0.65` |
| `params.keep_enst` | Keep per-protein Zarr results from ConPLex | `false` |
| `params.ligands` | Input directory of per-compound CSV files | — |
| `params.mutated_protein_fasta` | Directory of patient-specific FASTA files (or `blank`) | — |
| `params.protein_zarr` | Pre-built protein sequence Zarr DB | — |
| `params.chembl_db` | Path to ChEMBL SQLite database file | — |
| `params.outdir` | Output root directory | — |
| `params.bt_initial_memory` | Biotransformer starting memory (GB) | `5` |
| `params.bt_growth_memory` | Biotransformer additional memory per retry (GB) | `15` |
| `params.bt_max_retries` | Biotransformer max retry attempts | `10` |
| `params.bt_fail_action` | Biotransformer failure strategy: `'terminate'` or `'ignore'` | `'terminate'` |
| `params.conplex_initial_memory` | ConPLex starting memory (GB) | `5` |
| `params.conplex_growth_memory` | ConPLex additional memory per retry (GB) | `15` |
| `params.conplex_max_retries` | ConPLex max retry attempts | `1` |
| `params.conplex_fail_action` | ConPLex failure strategy: `'terminate'` or `'ignore'` | `'ignore'` |
## Nextflow Gotchas
- Params loaded from JSON are strings — use `.toInteger()` when used in resource directives (e.g., `memory`, `maxRetries`)
- `main.nf` defines all default param values; params files only need to override what they change
## Sub-pipeline: Metabolite Screen Adaptive
`nf_metabol_screen_adaptive/` is a standalone Nextflow pipeline for ConPLex-based metabolite screening. It has its own `main.nf`, `test.nf`, `Dockerfile`, and `nextflow.config`. Used for development/testing of the screening step independently.
## Container Registry
All images are at `harbor.cluster.omic.ai/omic/digitaltrials/`. Container refs in `main.nf` use sha256 digests for reproducibility (except tissue which uses version tags). When updating containers, pin to a digest or explicit version tag.
## Input Format
Per-compound `.csv` files named by identifier (e.g., InChIKey). 4-line key-value format:
```
SMILES
<SMILES string>
TARGET
<ENST transcript ID or empty>
```
Input directories are under `/data/digital-trials-data/` (e.g., `input_to_run/`, `input_knowen_target/`, `input_new/input/`).
See also `/data/runs/docs/digital-trials-input-format.md` for format details.
## Output Structure
Results are organized under `{outdir}/{project_name}/`:
- `1_biotransformer/` — Raw metabolite predictions
- `1b_final_metabolites/` — Filtered terminal metabolites
- `2_conplex/` — Drug scores and significant interaction TSVs
- `3_string/` — Network enrichment and interaction TSVs
- `4_tissue_distribution/` — Tissue distribution and biological properties TSVs

71
Dockerfile_biotransformer Executable file
View File

@@ -0,0 +1,71 @@
FROM debian:bullseye-slim
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
default-jre \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
# main conda env (biotransformer)
RUN conda create -n biotransformer
ENV PATH="$PATH:/opt/conda/envs/biotransformer/bin"
RUN echo "source activate biotransformer" >> ~/.bashrc
RUN conda clean --all -f -y
# Install RDKit
RUN conda install -y -n biotransformer -c conda-forge rdkit
WORKDIR /home/omic
# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/get/6432cf887ed7.zip && \
# unzip 6432cf887ed7.zip && \
# rm 6432cf887ed7.zip && \
# mv wishartlab-biotransformer3.0jar-6432cf887ed7 biotransformer
# RUN git clone https://github.com/Wishartlab-openscience/Biotransformer.git && \
# mv Biotransformer biotransformer
RUN git clone https://bitbucket.org/wishartlab/biotransformer3.0jar biotransformer && mv biotransformer/BioTransformer3.0_20230525.jar biotransformer/biotransformer
WORKDIR /home/omic/biotransformer
# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/raw/6432cf887ed70c7c943c2dfeb60298ccdc788d7d/BioTransformer3.0_20230525.jar && \
# mv BioTransformer3.0_20230525.jar biotransformer && \
# chmod +x biotransformer
ENV PATH="$PATH:/home/omic/biotransformer"
# Create a symlink from /home/omic/biotransformer/database to /home/omic/biotransformer/btkb
RUN ln -s /home/omic/biotransformer/database /home/omic/biotransformer/btkb
## Test
# RUN java -jar biotransformer -multiThread "2 example.csv 36000 3 1 true"
#Download The Human Metabolome Database smiles
RUN wget https://hmdb.ca/system/downloads/current/structures.zip
RUN unzip structures.zip
#install pandas and requests
RUN conda install -y -n biotransformer -c conda-forge pandas requests

15
Dockerfile_chembl Normal file
View File

@@ -0,0 +1,15 @@
FROM mambaorg/micromamba:2.1.1
USER root
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN micromamba install -n base -y -c conda-forge --channel-priority flexible \
python=3.12 \
numpy \
pandas \
rdkit \
procps-ng
# Note: No need for requests or chembl-downloader in the container
# since we're passing the pre-downloaded database as input

127
Dockerfile_conplex Executable file
View File

@@ -0,0 +1,127 @@
ARG CUDA=11.7
FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Add the NVIDIA GPG key directly
RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
RUN apt-get -y update && \
apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (conplex)
RUN conda create -n conplex-dti python=3.9
ENV PATH "$PATH:/opt/conda/envs/conplex-dti/bin"
RUN echo "source activate conplex-dti" >> ~/.bashrc
RUN conda clean --all -f -y
# main conda env (secse)
#RUN conda create --name secse -c conda-forge parallel tqdm biopandas openbabel chemprop xlrd=2 pandarallel python=3.9 perl=5.32
#RUN conda install -y -n secse -c conda-forge pandas=1.3.5
#RUN conda install -y -n secse -c conda-forge rdkit=2022.03.5
#RUN echo "conda activate secse" >> ~/.bashrc
#ENV PATH="$PATH:/opt/conda/envs/secse/bin"
#ARG PATH="$PATH:/opt/conda/envs/secse/bin"
RUN git clone https://github.com/samsledje/ConPLex.git
WORKDIR /home/omic/ConPLex
# Install conplex
RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install conplex-dti
RUN conplex-dti --help
# Package into python script for running in nextflow
COPY conplex.py /home/omic/ConPLex/conplex.py
RUN chmod +x /home/omic/ConPLex/conplex.py
# Install pretrained models
RUN mkdir -p /home/omic/ConPLex/models
RUN wget --no-check-certificate -O /home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt https://cb.csail.mit.edu/cb/conplex/data/models/BindingDB_ExperimentalValidModel.pt
# Test
RUN conplex-dti predict --data-file /home/omic/ConPLex/tests/toy_predict.tsv --model-path /home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt --outfile ./results.tsv
#copy protein reference trascipt fasta file
COPY ensemble_reference.fasta .
COPY MANE_referent_transcipt_reference.fasta .
COPY MANE_all_transcipts.csv .
COPY get_round_2.py .
RUN chmod +x /home/omic/ConPLex/get_round_2.py
#new model weights
COPY Run_best_model_epoch46.pt /home/omic/ConPLex/models/
# Fix predict.py not working on single protein-ligand complex
#COPY predict.py /home/omic/ConPLex/conplex_dti/cli/predict.py
#COPY predict.py /opt/conda/envs/conplex-dti/lib/python3.9/site-packages/conplex_dti/cli/predict.py
#RUN chmod +x /home/omic/ConPLex/conplex_dti/cli/predict.py
#RUN chmod +x /opt/conda/envs/conplex-dti/lib/python3.9/site-packages/conplex_dti/cli/predict.py
# Clone secse
#RUN git clone https://github.com/KeenThera/SECSE.git
#RUN mv /home/omic/ConPLex/SECSE/secse /home/omic/ConPLex/secse && rm -r /home/omic/ConPLex/SECSE && rm -r /home/omic/ConPLex/secse/scoring
#COPY secse/scoring /home/omic/ConPLex/secse/scoring
#COPY secse/grow_processes.py /home/omic/ConPLex/secse/scoring/grow_processes.py
#RUN chmod +x /home/omic/ConPLex/secse/grow_processes.py
#RUN chmod +x /home/omic/ConPLex/secse/scoring/ranking.py
#RUN chmod +x /home/omic/ConPLex/secse/growing/mutation/mutation.py
# Add missing boost
#RUN conda install -n secse -c conda-forge boost
# Install CREM for chemical growth
#RUN git clone https://github.com/DrrDom/crem.git
#RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install crem pandas numpy
#WORKDIR /home/omic/ConPLex
#RUN chmod -R +x /home/omic/ConPLex
#ENV PATH="$PATH:/opt/conda/envs/secse/bin:/home/omic/ConPLex/secse"
#ENV SECSE="/home/omic/ConPLex/secse"
#ENV PYTHONPATH="PYTHONPATH=/home/omic/ConPLex/secse:/home/omic/ConPLex:/home/omic/ConPLex/crem"
#ARG PYTHONPATH="PYTHONPATH=/home/omic/ConPLex/secse:/home/omic/ConPLex:/home/omic/ConPLex/crem"
# Package into python script for running in nextflow
#COPY conplex.py /home/omic/ConPLex/conplex.py
#RUN chmod +x /home/omic/ConPLex/conplex.py
#Mutation file
#RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install crem
#RUN wget https://www.dropbox.com/s/4r48ohopechsd59/replacements02_sa2.db.gz?dl=0
#RUN mv replacements02_sa2.db.gz?dl=0 replacements02_sa2.db.gz
#RUN gzip -d replacements02_sa2.db.gz
#COPY fragment_mutations.py /home/omic/ConPLex/fragment_mutations.py
#RUN chmod +x /home/omic/ConPLex/fragment_mutations.py

21
Dockerfile_network Normal file
View File

@@ -0,0 +1,21 @@
FROM mambaorg/micromamba:2.1.1
USER root
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN micromamba install -n base -y -c conda-forge -c bioconda --channel-priority flexible \
python=3.12 \
numpy \
pandas \
scipy \
r-base=4.3 \
bioconductor-stringdb \
r-tidyverse \
r-argparser \
r-sqldf \
r-rsqlite \
r-argparse \
procps-ng
COPY ./app_network /app

20
Dockerfile_tissue Executable file
View File

@@ -0,0 +1,20 @@
# Use the specified Micromamba base image with CUDA 11.7
FROM mambaorg/micromamba:2.1.1
USER root
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN micromamba install -y python=3.9 procps-ng pandas numpy && \
pip install pandas numpy && \
micromamba clean --all --yes
# Package into python script for running in nextflow
COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
# Copy reference files
COPY HPA_normal_ihc_data.tsv /home/omic/
COPY MANE_all_transcipts.csv /home/omic/
COPY digital_patient_extract_metrics.py /home/omic/

61
Dockerfile_tissue.old Executable file
View File

@@ -0,0 +1,61 @@
ARG CUDA=11.7
FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Add the NVIDIA GPG key directly
RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
RUN apt-get -y update && \
apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (tissue)
RUN conda create -n tissue python=3.9
ENV PATH "$PATH:/opt/conda/envs/tissue/bin"
RUN echo "source activate tissue" >> ~/.bashrc
RUN conda clean --all -f -y
# Install packages
RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
RUN /opt/conda/envs/tissue/bin/python3 -m pip install pandas numpy
# Package into python script for running in nextflow
COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
RUN chmod +x /home/omic/drug_tissue_distribution.py
# copy reference file
COPY HPA_normal_ihc_data.tsv .
COPY MANE_all_transcipts.csv .
COPY digital_patient_extract_metrics.py .

56
Dockerfile_tissue.old2 Executable file
View File

@@ -0,0 +1,56 @@
# Use the specified Micromamba base image with CUDA 11.7
FROM mambaorg/micromamba:2.1.1-cuda11.7.1-ubuntu20.04
USER root
ARG MAMBA_DOCKERFILE_ACTIVATE=1
# WORKDIR /home
# RUN mkdir -p /home/omic
WORKDIR /home/omic
# Install system packages
ARG DEBIAN_FRONTEND=noninteractive
RUN micromamba install -y python=3.9 pandas numpy && \
pip install pandas numpy && \
micromamba clean --all --yes
# Add the NVIDIA GPG key directly
RUN apt-get -y update \
&& apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
&& wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
&& dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb \
&& apt-get install -y --no-install-recommends cuda-command-line-tools-11-7 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Switch to the mamba user for micromamba operations
# USER $MAMBA_USER
# WORKDIR /home/omic
# Install Python and packages into the base environment
# Activate the base environment for subsequent RUN commands
# ARG MAMBA_DOCKERFILE_ACTIVATE=1
# # Install Python packages with pip (now runs in the activated environment)
# RUN python -m pip install pandas numpy
# Package into python script for running in nextflow
COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
RUN chmod +x /home/omic/drug_tissue_distribution.py
# Copy reference files
COPY HPA_normal_ihc_data.tsv .
COPY MANE_all_transcipts.csv .
COPY digital_patient_extract_metrics.py .

5
Note.txt Executable file
View File

@@ -0,0 +1,5 @@
Add options for metabolites not existing and process failed
Remove unnecessary data while process is running, take up too much memory
ncbiproteins_seq_exist.csv is replaced with ncbiproteins_seq_exist_reduce.csv so it will be able to fit to gitlab

248
app_network/network.r Normal file
View File

@@ -0,0 +1,248 @@
#!/usr/bin/env Rscript
#
# Network enrichment and interaction analysis using STRINGdb package.
# R equivalent of the NETWORK_ENRICHMENT Nextflow process.
#
suppressPackageStartupMessages({
library(STRINGdb)
library(data.table)
library(argparse)
})
#' Main function
main <- function() {
# Parse command line arguments
parser <- ArgumentParser(
description = "Network enrichment analysis using STRINGdb package"
)
parser$add_argument(
"interactions_file",
type = "character",
help = "Input TSV file with significant interactions (conplex output)"
)
parser$add_argument(
"--threshold",
type = "double",
default = 0.65,
help = "ConPlex score threshold for protein network"
)
parser$add_argument(
"--max-proteins",
type = "integer",
default = 450L,
help = "Maximum number of proteins to analyze (STRING API limitation)"
)
parser$add_argument(
"--output-dir",
type = "character",
default = ".",
help = "Output directory for results"
)
parser$add_argument(
"--species",
type = "integer",
default = 9606L,
help = "NCBI taxon ID (default: 9606 for Homo sapiens)"
)
parser$add_argument(
"--score-threshold",
type = "integer",
default = 400L,
help = "STRING combined score threshold (0-1000, default: 400)"
)
args <- parser$parse_args()
# Initialize STRINGdb
cat("Initializing STRINGdb...\n")
string_db <- STRINGdb$new(
version = "12.0",
species = args$species,
score_threshold = args$score_threshold,
network_type = "full",
input_directory = "/app"
)
# Load interaction data
cat(sprintf("Loading interaction data from %s...\n", args$interactions_file))
interaction_data <- fread(args$interactions_file, sep = "\t")
interaction_data <- interaction_data[order(-conplex_score)]
# Remove duplicates and limit (replicates Nextflow logic)
interaction_data <- unique(interaction_data, by = "transcipt")
if (nrow(interaction_data) > args$max_proteins) {
cat(sprintf("Limiting to top %d proteins (STRING API limitation)\n", args$max_proteins))
interaction_data <- interaction_data[1:args$max_proteins]
}
# Filter by threshold
filtered_data <- interaction_data[conplex_score > args$threshold]
cat(sprintf("Found %d proteins above threshold %.2f\n",
nrow(filtered_data), args$threshold))
if (nrow(filtered_data) == 0) {
stop("ERROR: No proteins above threshold!")
}
# Prepare data for STRING mapping
gene_list <- data.frame(
gene = filtered_data$transcipt,
stringsAsFactors = FALSE
)
# Map genes to STRING IDs
cat("Mapping genes to STRING database...\n")
mapped <- string_db$map(gene_list, "gene", removeUnmappedRows = TRUE)
if (nrow(mapped) == 0) {
stop("ERROR: No genes could be mapped to STRING database!")
}
cat(sprintf("Successfully mapped %d/%d genes to STRING IDs\n",
nrow(mapped), nrow(gene_list)))
# Get STRING IDs
string_ids <- mapped$STRING_id
# Get enrichment analysis
cat("\nPerforming enrichment analysis...\n")
enrichment_results <- string_db$get_enrichment(string_ids, category = "all", methodMT = "fdr")
if (nrow(enrichment_results) == 0) {
cat("WARNING: No enrichment results found\n")
enrichment_df <- data.table()
} else {
cat(sprintf("Found %d enriched terms\n", nrow(enrichment_results)))
# Convert to data.table and rename columns to match Python output
enrichment_df <- as.data.table(enrichment_results)
# The STRINGdb enrichment output has columns:
# category, term, number_of_genes, number_of_genes_in_background,
# ncbiTaxonId, inputGenes, preferredNames, p_value, fdr, description
# This should already match the Python output format
}
# Get network interactions with detailed scores
cat("\nExtracting network interactions...\n")
interactions <- string_db$get_interactions(string_ids)
if (nrow(interactions) == 0) {
cat("WARNING: No interactions found\n")
interactions_df <- data.table()
} else {
cat(sprintf("Found %d protein-protein interactions\n", nrow(interactions)))
# Convert to data.table
interactions_df <- as.data.table(interactions)
# The get_interactions() function returns:
# from, to, combined_score, and potentially other columns
# We need to get detailed scores separately
# Get the interaction network with all score types
# Use get_png to access the full network data including detailed scores
network_image <- string_db$plot_network(string_ids)
# Alternative: Access the graph directly for detailed scores
# The STRINGdb object stores the full network internally
graph <- string_db$get_graph()
# Extract edge attributes which contain detailed scores
if (!is.null(graph)) {
edge_data <- igraph::as_data_frame(graph, what = "edges")
edge_dt <- as.data.table(edge_data)
# Filter for our query proteins
edge_dt <- edge_dt[from %in% string_ids & to %in% string_ids]
# Rename columns to match Python output format
if ("from" %in% names(edge_dt)) setnames(edge_dt, "from", "stringId_A")
if ("to" %in% names(edge_dt)) setnames(edge_dt, "to", "stringId_B")
# Add preferred names
edge_dt[, preferredName_A := string_db$get_aliases(stringId_A)$alias[1], by = stringId_A]
edge_dt[, preferredName_B := string_db$get_aliases(stringId_B)$alias[1], by = stringId_B]
# Normalize scores to 0-1 range if they're in 0-1000 range
score_cols <- c("combined_score", "neighborhood", "fusion", "cooccurence",
"coexpression", "experimental", "database", "textmining")
target_cols <- c("score", "nscore", "fscore", "pscore",
"ascore", "escore", "dscore", "tscore")
for (i in seq_along(score_cols)) {
src <- score_cols[i]
tgt <- target_cols[i]
if (src %in% names(edge_dt)) {
# Check if scores are in 0-1000 range (need normalization)
max_val <- max(edge_dt[[src]], na.rm = TRUE)
if (max_val > 1) {
edge_dt[, (tgt) := get(src) / 1000.0]
} else {
edge_dt[, (tgt) := get(src)]
}
}
}
# Add ncbiTaxonId
edge_dt[, ncbiTaxonId := args$species]
# Select and order columns to match Python output
output_cols <- c("stringId_A", "stringId_B", "preferredName_A", "preferredName_B",
"ncbiTaxonId", "score", "nscore", "fscore", "pscore",
"ascore", "escore", "dscore", "tscore")
# Keep only columns that exist
existing_cols <- intersect(output_cols, names(edge_dt))
interactions_df <- edge_dt[, ..existing_cols]
} else {
# Fallback: use the interactions data from get_interactions()
# Rename columns to match output format
if ("from" %in% names(interactions_df)) {
setnames(interactions_df, "from", "stringId_A")
}
if ("to" %in% names(interactions_df)) {
setnames(interactions_df, "to", "stringId_B")
}
if ("combined_score" %in% names(interactions_df)) {
interactions_df[, score := combined_score / 1000.0]
}
interactions_df[, ncbiTaxonId := args$species]
}
}
# Generate output filename
output_name <- gsub("_significant_interactions", "",
tools::file_path_sans_ext(basename(args$interactions_file)))
# Create output directory if needed
dir.create(args$output_dir, showWarnings = FALSE, recursive = TRUE)
# Save results
enrichment_file <- file.path(args$output_dir,
sprintf("%s_network_enrichment.tsv", output_name))
interactions_file <- file.path(args$output_dir,
sprintf("%s_network_interactions.tsv", output_name))
fwrite(enrichment_df, enrichment_file, sep = "\t")
fwrite(interactions_df, interactions_file, sep = "\t")
cat("\nResults saved:\n")
cat(sprintf(" Enrichment: %s\n", enrichment_file))
cat(sprintf(" Interactions: %s\n", interactions_file))
}
# Run main function
if (!interactive()) {
main()
}

376
app_network/network2.r Normal file
View File

@@ -0,0 +1,376 @@
#!/usr/bin/env Rscript
#
# Offline network enrichment and interaction analysis using local STRING-DB files.
# Replicates the NETWORK_ENRICHMENT Nextflow process without internet connection.
# R equivalent of the Python script using STRINGdb package.
#
suppressPackageStartupMessages({
library(STRINGdb)
library(data.table)
library(argparse)
})
#' Load STRING-DB data from local files
#'
#' @param string_db_dir Directory containing STRING-DB files
#' @return List containing mappings and data frames
load_string_data <- function(string_db_dir) {
cat("Loading STRING-DB files...\n")
# Load alias mapping (ENST -> ENSP)
aliases <- fread(
file.path(string_db_dir, "9606.protein.aliases.enst.v12.0.tsv"),
sep = "\t",
header = FALSE,
col.names = c("string_protein_id", "alias", "source")
)
enst_to_ensp <- aliases[source == "Ensembl_transcript",
.(string_protein_id, alias)]
setkey(enst_to_ensp, alias)
# Load protein info (for preferred names)
info <- fread(
file.path(string_db_dir, "9606.protein.info.v12.0.txt"),
sep = "\t",
header = FALSE,
col.names = c("string_protein_id", "preferred_name", "protein_size", "annotation")
)
setkey(info, string_protein_id)
# Load protein links - USE DETAILED FILE
links <- fread(
file.path(string_db_dir, "9606.protein.links.detailed.v12.0.txt"),
sep = " "
)
# Load enrichment terms
enrichment <- fread(
file.path(string_db_dir, "9606.protein.enrichment.terms.v12.0.txt"),
sep = "\t",
header = FALSE,
col.names = c("string_protein_id", "category", "term", "description")
)
cat(sprintf("Loaded %d ENST->ENSP mappings\n", nrow(enst_to_ensp)))
cat(sprintf("Loaded %d protein-protein interactions\n", nrow(links)))
cat(sprintf("Loaded %d enrichment annotations\n", nrow(enrichment)))
list(
enst_to_ensp = enst_to_ensp,
ensp_to_name = info,
links = links,
enrichment = enrichment
)
}
#' Perform enrichment analysis using Fisher's exact test
#'
#' @param query_proteins Vector of ENSP protein IDs
#' @param enrichment_df Data table with enrichment annotations
#' @param ensp_to_name Data table mapping ENSP to preferred names
#' @param ensp_to_input_map Named vector mapping ENSP back to ENST
#' @return Data table with enrichment results
perform_enrichment_analysis <- function(query_proteins, enrichment_df,
ensp_to_name, ensp_to_input_map) {
query_set <- unique(query_proteins)
n_query <- length(query_set)
cat(sprintf("Analyzing enrichment for %d proteins...\n", n_query))
results_list <- list()
# Group by category
categories <- unique(enrichment_df$category)
for (cat in categories) {
cat_group <- enrichment_df[category == cat]
# Background: Total unique proteins annotated in this category
category_universe <- unique(cat_group$string_protein_id)
background_size <- length(category_universe)
# Iterate over terms within this category
terms <- unique(cat_group$term)
for (tm in terms) {
term_group <- cat_group[term == tm]
term_proteins <- unique(term_group$string_protein_id)
# Intersection: proteins in both query and term
intersection <- intersect(query_set, term_proteins)
n_intersection <- length(intersection)
if (n_intersection == 0) next
# Background term count
n_term_background <- length(term_proteins)
# Fisher's exact test
# Contingency table:
# In term Not in term
# In query a b
# Not in query c d
a <- n_intersection
b <- n_query - a
c <- n_term_background - a
d <- background_size - n_term_background - b
# Ensure no negative values
if (c < 0 || d < 0) next
# One-sided test for enrichment
contingency_matrix <- matrix(c(a, b, c, d), nrow = 2, byrow = TRUE)
fisher_result <- fisher.test(contingency_matrix, alternative = "greater")
pvalue <- fisher_result$p.value
# Get description
description <- term_group$description[1]
# Get input genes (map ENSP back to ENST input)
intersection_sorted <- sort(intersection)
input_genes_list <- sapply(intersection_sorted, function(ensp) {
if (ensp %in% names(ensp_to_input_map)) {
ensp_to_input_map[ensp]
} else {
ensp
}
})
input_genes <- paste(input_genes_list, collapse = ",")
# Get preferred names
preferred_names_list <- sapply(intersection_sorted, function(p) {
name <- ensp_to_name[string_protein_id == p, preferred_name]
if (length(name) > 0) name[1] else strsplit(p, "\\.")[[1]][length(strsplit(p, "\\.")[[1]])]
})
preferred_names <- paste(preferred_names_list, collapse = ",")
results_list[[length(results_list) + 1]] <- data.table(
category = cat,
term = tm,
number_of_genes = n_intersection,
number_of_genes_in_background = n_term_background,
ncbiTaxonId = 9606,
inputGenes = input_genes,
preferredNames = preferred_names,
p_value = pvalue,
description = description
)
}
}
if (length(results_list) == 0) {
return(data.table())
}
# Combine results
results_df <- rbindlist(results_list)
# Benjamini-Hochberg FDR correction
results_df <- results_df[order(p_value)]
n_tests <- nrow(results_df)
results_df[, fdr := p_value * n_tests / seq_len(n_tests)]
results_df[fdr > 1.0, fdr := 1.0]
# Reorder columns to match API output
setcolorder(results_df, c(
"category", "term", "number_of_genes", "number_of_genes_in_background",
"ncbiTaxonId", "inputGenes", "preferredNames", "p_value", "fdr", "description"
))
return(results_df)
}
#' Extract network interactions for query proteins
#'
#' @param query_proteins Vector of ENSP protein IDs
#' @param links_df Data table with protein-protein interactions
#' @param ensp_to_name Data table mapping ENSP to preferred names
#' @return Data table with network interactions
get_network_interactions <- function(query_proteins, links_df, ensp_to_name) {
query_set <- unique(query_proteins)
# Filter links where both proteins are in query set
interactions <- links_df[protein1 %in% query_set & protein2 %in% query_set]
if (nrow(interactions) == 0) {
return(data.table())
}
# Normalize scores (STRING files are integers 0-1000, API is float 0-1)
score_cols <- c("combined_score", "neighborhood", "fusion", "cooccurence",
"coexpression", "experimental", "database", "textmining")
target_cols <- c("score", "nscore", "fscore", "pscore",
"ascore", "escore", "dscore", "tscore")
for (i in seq_along(score_cols)) {
src <- score_cols[i]
tgt <- target_cols[i]
if (src %in% names(interactions)) {
interactions[, (tgt) := get(src) / 1000.0]
} else {
interactions[, (tgt) := 0.0]
}
}
# Add preferred names
interactions[, preferredName_A := sapply(protein1, function(p) {
name <- ensp_to_name[string_protein_id == p, preferred_name]
if (length(name) > 0) name[1] else strsplit(p, "\\.")[[1]][length(strsplit(p, "\\.")[[1]])]
})]
interactions[, preferredName_B := sapply(protein2, function(p) {
name <- ensp_to_name[string_protein_id == p, preferred_name]
if (length(name) > 0) name[1] else strsplit(p, "\\.")[[1]][length(strsplit(p, "\\.")[[1]])]
})]
# Rename columns to match STRING API output
setnames(interactions, c("protein1", "protein2"), c("stringId_A", "stringId_B"))
interactions[, ncbiTaxonId := 9606]
# Select and order columns to match original output
column_order <- c(
"stringId_A", "stringId_B", "preferredName_A", "preferredName_B",
"ncbiTaxonId", "score", "nscore", "fscore", "pscore",
"ascore", "escore", "dscore", "tscore"
)
interactions <- interactions[, ..column_order]
return(interactions)
}
#' Main function
main <- function() {
# Parse command line arguments
parser <- ArgumentParser(
description = "Offline network enrichment analysis using local STRING-DB files"
)
parser$add_argument(
"interactions_file",
type = "character",
help = "Input TSV file with significant interactions (conplex output)"
)
parser$add_argument(
"--string-db-dir",
type = "character",
default = "/app",
help = "Directory containing STRING-DB files"
)
parser$add_argument(
"--threshold",
type = "double",
default = 0.65,
help = "ConPlex score threshold for protein network"
)
parser$add_argument(
"--max-proteins",
type = "integer",
default = 450L,
help = "Maximum number of proteins to analyze"
)
parser$add_argument(
"--output-dir",
type = "character",
default = ".",
help = "Output directory for results"
)
args <- parser$parse_args()
# Load STRING-DB data
string_data <- load_string_data(args$string_db_dir)
# Load interaction data
cat(sprintf("\nLoading interaction data from %s...\n", args$interactions_file))
interaction_data <- fread(args$interactions_file, sep = "\t")
interaction_data <- interaction_data[order(-conplex_score)]
# Remove duplicates and limit
# Replicates Nextflow logic: drops duplicates on transcript BEFORE limit
interaction_data <- unique(interaction_data, by = "transcipt")
if (nrow(interaction_data) > args$max_proteins) {
cat(sprintf("Limiting to top %d proteins\n", args$max_proteins))
interaction_data <- interaction_data[1:args$max_proteins]
}
# Filter by threshold
filtered_data <- interaction_data[conplex_score > args$threshold]
cat(sprintf("Found %d proteins above threshold %.2f\n",
nrow(filtered_data), args$threshold))
# Map ENST to ENSP and keep track of mapping for output
enst_list <- filtered_data$transcipt
ensp_list <- character()
ensp_to_input_map <- character()
for (enst in enst_list) {
ensp <- string_data$enst_to_ensp[alias == enst, string_protein_id]
if (length(ensp) > 0) {
ensp <- ensp[1]
ensp_list <- c(ensp_list, ensp)
ensp_to_input_map[ensp] <- enst
}
}
cat(sprintf("Mapped %d ENST IDs to ENSP IDs\n", length(ensp_list)))
if (length(ensp_list) == 0) {
stop("ERROR: No valid ENSP mappings found!")
}
# Perform enrichment analysis
cat("\nPerforming enrichment analysis...\n")
enrichment_results <- perform_enrichment_analysis(
ensp_list,
string_data$enrichment,
string_data$ensp_to_name,
ensp_to_input_map
)
cat(sprintf("Found %d enriched terms\n", nrow(enrichment_results)))
# Get network interactions
cat("\nExtracting network interactions...\n")
network_interactions <- get_network_interactions(
ensp_list,
string_data$links,
string_data$ensp_to_name
)
cat(sprintf("Found %d protein-protein interactions\n", nrow(network_interactions)))
# Generate output filename
output_name <- gsub("_significant_interactions", "",
tools::file_path_sans_ext(basename(args$interactions_file)))
# Create output directory if needed
dir.create(args$output_dir, showWarnings = FALSE, recursive = TRUE)
# Save results
enrichment_file <- file.path(args$output_dir,
sprintf("%s_network_enrichment.tsv", output_name))
interactions_file <- file.path(args$output_dir,
sprintf("%s_network_interactions.tsv", output_name))
fwrite(enrichment_results, enrichment_file, sep = "\t")
fwrite(network_interactions, interactions_file, sep = "\t")
cat("\nResults saved:\n")
cat(sprintf(" Enrichment: %s\n", enrichment_file))
cat(sprintf(" Interactions: %s\n", interactions_file))
}
# Run main function
if (!interactive()) {
main()
}

283
app_network/network_enrich.py Normal file
View File

@@ -0,0 +1,283 @@
#!/usr/bin/env python3
"""
Offline network enrichment and interaction analysis using local STRING-DB files.
Replicates the NETWORK_ENRICHMENT Nextflow process without internet connection.
"""
import pandas as pd
import argparse
from pathlib import Path
from scipy import stats
import numpy as np
def load_string_data(string_db_dir):
"""Load all required STRING-DB files."""
string_db_dir = Path(string_db_dir)
print("Loading STRING-DB files...")
# Load alias mapping (ENST -> ENSP)
aliases = pd.read_csv(
string_db_dir / "9606.protein.aliases.enst.v12.0.tsv",
sep='\t',
comment='#',
names=['string_protein_id', 'alias', 'source']
)
enst_to_ensp = aliases[aliases['source'] == 'Ensembl_transcript'].set_index('alias')['string_protein_id'].to_dict()
# Load protein info (for preferred names)
info = pd.read_csv(
string_db_dir / "9606.protein.info.v12.0.txt",
sep='\t',
comment='#',
names=['string_protein_id', 'preferred_name', 'protein_size', 'annotation']
)
ensp_to_name = info.set_index('string_protein_id')['preferred_name'].to_dict()
# Load protein links
# Load protein links - USE DETAILED FILE
links = pd.read_csv(
string_db_dir / "9606.protein.links.detailed.v12.0.txt",
sep=' '
)
# Load enrichment terms
enrichment = pd.read_csv(
string_db_dir / "9606.protein.enrichment.terms.v12.0.txt",
sep='\t',
comment='#',
names=['string_protein_id', 'category', 'term', 'description']
)
print(f"Loaded {len(enst_to_ensp)} ENST->ENSP mappings")
print(f"Loaded {len(links)} protein-protein interactions")
print(f"Loaded {len(enrichment)} enrichment annotations")
return enst_to_ensp, ensp_to_name, links, enrichment
def perform_enrichment_analysis(query_proteins, enrichment_df, ensp_to_name, background_size=20000):
"""
Perform enrichment analysis similar to STRING-DB API.
Uses Fisher's exact test for each term.
"""
results = []
query_set = set(query_proteins)
n_query = len(query_set)
# Group by category and term
for (category, term), group in enrichment_df.groupby(['category', 'term']):
term_proteins = set(group['string_protein_id'])
# Intersection: proteins in both query and term
intersection = query_set & term_proteins
n_intersection = len(intersection)
if n_intersection == 0:
continue
# Background: total proteins with this term
n_term_background = len(term_proteins)
# Fisher's exact test
# Contingency table:
# In term Not in term
# In query a b
# Not in query c d
a = n_intersection
b = n_query - a
c = n_term_background - a
d = background_size - n_term_background - b
# One-sided test for enrichment
oddsratio, pvalue = stats.fisher_exact([[a, b], [c, d]], alternative='greater')
# Get description (take first)
description = group['description'].iloc[0]
# Get gene names
intersection_list = list(intersection)
input_genes = ','.join(intersection_list)
preferred_names = ','.join([ensp_to_name.get(p, p.split('.')[-1]) for p in intersection_list])
results.append({
'category': category,
'term': term,
'number_of_genes': n_intersection,
'number_of_genes_in_background': n_term_background,
'ncbiTaxonId': 9606,
'inputGenes': input_genes,
'preferredNames': preferred_names,
'p_value': pvalue,
'description': description
})
if not results:
return pd.DataFrame()
# Create DataFrame and calculate FDR
results_df = pd.DataFrame(results)
results_df = results_df.sort_values('p_value')
# Benjamini-Hochberg FDR correction
n_tests = len(results_df)
results_df['fdr'] = results_df['p_value'] * n_tests / (np.arange(1, n_tests + 1))
results_df['fdr'] = results_df['fdr'].clip(upper=1.0)
# Sort by p-value
results_df = results_df.sort_values('p_value').reset_index(drop=True)
return results_df
def get_network_interactions(query_proteins, links_df, ensp_to_name):
"""
Extract network interactions for query proteins.
Converts combined_score to normalized scores similar to STRING API.
"""
query_set = set(query_proteins)
# Filter links where both proteins are in query set
interactions = links_df[
links_df['protein1'].isin(query_set) &
links_df['protein2'].isin(query_set)
].copy()
if len(interactions) == 0:
return pd.DataFrame()
interactions['score'] = interactions['combined_score'] / 1000.0
interactions['nscore'] = interactions['neighborhood'] / 1000.0
interactions['fscore'] = interactions['fusion'] / 1000.0
interactions['pscore'] = interactions['cooccurence'] / 1000.0 # Note: typo in STRING file
interactions['ascore'] = interactions['coexpression'] / 1000.0
interactions['escore'] = interactions['experimental'] / 1000.0
interactions['dscore'] = interactions['database'] / 1000.0
interactions['tscore'] = interactions['textmining'] / 1000.0
# Add preferred names
interactions['preferredName_A'] = interactions['protein1'].map(
lambda x: ensp_to_name.get(x, x.split('.')[-1])
)
interactions['preferredName_B'] = interactions['protein2'].map(
lambda x: ensp_to_name.get(x, x.split('.')[-1])
)
# Rename columns to match STRING API output
interactions = interactions.rename(columns={
'protein1': 'stringId_A',
'protein2': 'stringId_B'
})
interactions['ncbiTaxonId'] = 9606
# Select and order columns to match original output
column_order = [
'stringId_A', 'stringId_B', 'preferredName_A', 'preferredName_B',
'ncbiTaxonId', 'score', 'nscore', 'fscore', 'pscore',
'ascore', 'escore', 'dscore', 'tscore'
]
interactions = interactions[column_order].reset_index(drop=True)
return interactions
def main():
parser = argparse.ArgumentParser(
description='Offline network enrichment analysis using local STRING-DB files'
)
parser.add_argument(
'interactions_file',
type=str,
help='Input TSV file with significant interactions (conplex output)'
)
parser.add_argument(
'--string-db-dir',
type=str,
default='/data/bugra/digital_trials/app_network',
help='Directory containing STRING-DB files'
)
parser.add_argument(
'--threshold',
type=float,
default=0.0,
help='ConPlex score threshold for protein network'
)
parser.add_argument(
'--max-proteins',
type=int,
default=450,
help='Maximum number of proteins to analyze'
)
parser.add_argument(
'--output-dir',
type=str,
default='.',
help='Output directory for results'
)
args = parser.parse_args()
# Load STRING-DB data
enst_to_ensp, ensp_to_name, links, enrichment = load_string_data(args.string_db_dir)
# Load interaction data
print(f"\nLoading interaction data from {args.interactions_file}...")
interaction_data = pd.read_csv(args.interactions_file, sep='\t')
interaction_data = interaction_data.sort_values('conplex_score', ascending=False)
# Remove duplicates and limit
interaction_data = interaction_data.drop_duplicates('transcipt')
if interaction_data.shape[0] > args.max_proteins:
print(f"Limiting to top {args.max_proteins} proteins")
interaction_data = interaction_data.iloc[:args.max_proteins]
# Filter by threshold
filtered_data = interaction_data[interaction_data['conplex_score'] > args.threshold]
print(f"Found {len(filtered_data)} proteins above threshold {args.threshold}")
# Convert ENST to ENSP
enst_list = filtered_data['transcipt'].tolist()
ensp_list = [enst_to_ensp.get(enst) for enst in enst_list]
ensp_list = [e for e in ensp_list if e is not None]
print(f"Mapped {len(ensp_list)} ENST IDs to ENSP IDs")
if len(ensp_list) == 0:
print("ERROR: No valid ENSP mappings found!")
return
# Perform enrichment analysis
print("\nPerforming enrichment analysis...")
enrichment_results = perform_enrichment_analysis(ensp_list, enrichment, ensp_to_name)
print(f"Found {len(enrichment_results)} enriched terms")
# Get network interactions
print("\nExtracting network interactions...")
network_interactions = get_network_interactions(ensp_list, links, ensp_to_name)
print(f"Found {len(network_interactions)} protein-protein interactions")
# Generate output filename
input_path = Path(args.interactions_file)
output_name = input_path.stem.replace('_significant_interactions', '')
output_dir = Path(args.output_dir)
output_dir.mkdir(parents=True, exist_ok=True)
# Save results
enrichment_file = output_dir / f"{output_name}_network_enrichment.tsv"
interactions_file = output_dir / f"{output_name}_network_interactions.tsv"
enrichment_results.to_csv(enrichment_file, sep='\t')
network_interactions.to_csv(interactions_file, sep='\t')
print(f"\nResults saved:")
print(f" Enrichment: {enrichment_file}")
print(f" Interactions: {interactions_file}")
if __name__ == '__main__':
main()

332
app_network/network_enrich_offline.py Normal file
View File

@@ -0,0 +1,332 @@
#!/usr/bin/env python3
"""
Offline network enrichment and interaction analysis using local STRING-DB files.
Replicates the NETWORK_ENRICHMENT Nextflow process without internet connection.
"""
import pandas as pd
import argparse
from pathlib import Path
from scipy import stats
import numpy as np
def load_string_data(string_db_dir):
"""Load all required STRING-DB files."""
string_db_dir = Path(string_db_dir)
print("Loading STRING-DB files...")
# Load alias mapping (ENST -> ENSP)
aliases = pd.read_csv(
string_db_dir / "9606.protein.aliases.enst.v12.0.tsv",
sep='\t',
comment='#',
names=['string_protein_id', 'alias', 'source']
)
enst_to_ensp = aliases[aliases['source'] == 'Ensembl_transcript'].set_index('alias')['string_protein_id'].to_dict()
# Load protein info (for preferred names)
info = pd.read_csv(
string_db_dir / "9606.protein.info.v12.0.txt",
sep='\t',
comment='#',
names=['string_protein_id', 'preferred_name', 'protein_size', 'annotation']
)
ensp_to_name = info.set_index('string_protein_id')['preferred_name'].to_dict()
# Load protein links - USE DETAILED FILE
links = pd.read_csv(
string_db_dir / "9606.protein.links.detailed.v12.0.txt",
sep=' '
)
# Load enrichment terms
# Note: STRING files usually don't have headers, or have specific comment lines.
# We ensure we capture string_protein_id, category, term, description
enrichment = pd.read_csv(
string_db_dir / "9606.protein.enrichment.terms.v12.0.txt",
sep='\t',
comment='#',
names=['string_protein_id', 'category', 'term', 'description']
)
print(f"Loaded {len(enst_to_ensp)} ENST->ENSP mappings")
print(f"Loaded {len(links)} protein-protein interactions")
print(f"Loaded {len(enrichment)} enrichment annotations")
return enst_to_ensp, ensp_to_name, links, enrichment
def perform_enrichment_analysis(query_proteins, enrichment_df, ensp_to_name, ensp_to_input_map):
"""
Perform enrichment analysis similar to STRING-DB API.
Uses Fisher's exact test for each term.
"""
results = []
query_set = set(query_proteins)
n_query = len(query_set)
print(f"Analyzing enrichment for {n_query} proteins...")
# Group by category to calculate background size per category
for category, cat_group in enrichment_df.groupby('category'):
# Background: Total unique proteins annotated in this category
category_universe = set(cat_group['string_protein_id'])
background_size = len(category_universe)
# Now iterate over terms within this category
for term, group in cat_group.groupby('term'):
term_proteins = set(group['string_protein_id'])
# Intersection: proteins in both query and term
intersection = query_set & term_proteins
n_intersection = len(intersection)
if n_intersection == 0:
continue
# Background term count
n_term_background = len(term_proteins)
# Fisher's exact test
# Contingency table:
# In term Not in term
# In query a b
# Not in query c d
a = n_intersection
b = n_query - a
c = n_term_background - a
d = background_size - n_term_background - b
# Ensure no negative values (safety check)
if c < 0 or d < 0:
continue
# One-sided test for enrichment
oddsratio, pvalue = stats.fisher_exact([[a, b], [c, d]], alternative='greater')
# Get description (take first)
description = group['description'].iloc[0]
# Get input genes (map ENSP back to ENST input)
intersection_list = sorted(list(intersection))
# Reconstruct the 'inputGenes' list using the original ENST IDs
# If an ENSP maps to multiple ENSTs in the input, we list them all
input_genes_list = []
for ensp in intersection_list:
if ensp in ensp_to_input_map:
# Append the ENST that mapped to this ENSP
input_genes_list.append(ensp_to_input_map[ensp])
else:
input_genes_list.append(ensp)
input_genes = ','.join(input_genes_list)
preferred_names = ','.join([ensp_to_name.get(p, p.split('.')[-1]) for p in intersection_list])
results.append({
'category': category,
'term': term,
'number_of_genes': n_intersection,
'number_of_genes_in_background': n_term_background,
'ncbiTaxonId': 9606,
'inputGenes': input_genes,
'preferredNames': preferred_names,
'p_value': pvalue,
'description': description
})
if not results:
return pd.DataFrame()
# Create DataFrame and calculate FDR
results_df = pd.DataFrame(results)
# Benjamini-Hochberg FDR correction
results_df = results_df.sort_values('p_value')
n_tests = len(results_df)
results_df['fdr'] = results_df['p_value'] * n_tests / (np.arange(1, n_tests + 1))
results_df['fdr'] = results_df['fdr'].clip(upper=1.0)
# Sort by p-value
results_df = results_df.sort_values('p_value').reset_index(drop=True)
# Reorder columns to match API output
# API Order: category, term, number_of_genes, number_of_genes_in_background, ncbiTaxonId, inputGenes, preferredNames, p_value, fdr, description
cols = [
'category', 'term', 'number_of_genes', 'number_of_genes_in_background',
'ncbiTaxonId', 'inputGenes', 'preferredNames', 'p_value', 'fdr', 'description'
]
results_df = results_df[cols]
return results_df
def get_network_interactions(query_proteins, links_df, ensp_to_name):
"""
Extract network interactions for query proteins.
Converts combined_score to normalized scores similar to STRING API.
"""
query_set = set(query_proteins)
# Filter links where both proteins are in query set
interactions = links_df[
links_df['protein1'].isin(query_set) &
links_df['protein2'].isin(query_set)
].copy()
if len(interactions) == 0:
return pd.DataFrame()
# Normalize scores (STRING files are integers 0-1000, API is float 0-1)
score_cols = ['combined_score', 'neighborhood', 'fusion', 'cooccurence',
'coexpression', 'experimental', 'database', 'textmining']
target_cols = ['score', 'nscore', 'fscore', 'pscore',
'ascore', 'escore', 'dscore', 'tscore']
for src, tgt in zip(score_cols, target_cols):
if src in interactions.columns:
interactions[tgt] = interactions[src] / 1000.0
else:
interactions[tgt] = 0.0
# Add preferred names
interactions['preferredName_A'] = interactions['protein1'].map(
lambda x: ensp_to_name.get(x, x.split('.')[-1])
)
interactions['preferredName_B'] = interactions['protein2'].map(
lambda x: ensp_to_name.get(x, x.split('.')[-1])
)
# Rename columns to match STRING API output
interactions = interactions.rename(columns={
'protein1': 'stringId_A',
'protein2': 'stringId_B'
})
interactions['ncbiTaxonId'] = 9606
# Select and order columns to match original output
column_order = [
'stringId_A', 'stringId_B', 'preferredName_A', 'preferredName_B',
'ncbiTaxonId', 'score', 'nscore', 'fscore', 'pscore',
'ascore', 'escore', 'dscore', 'tscore'
]
interactions = interactions[column_order].reset_index(drop=True)
return interactions
def main():
parser = argparse.ArgumentParser(
description='Offline network enrichment analysis using local STRING-DB files'
)
parser.add_argument(
'interactions_file',
type=str,
help='Input TSV file with significant interactions (conplex output)'
)
parser.add_argument(
'--string-db-dir',
type=str,
default='/data/bugra/digital_trials/app_network',
help='Directory containing STRING-DB files'
)
parser.add_argument(
'--threshold',
type=float,
default=0.65,
help='ConPlex score threshold for protein network'
)
parser.add_argument(
'--max-proteins',
type=int,
default=450,
help='Maximum number of proteins to analyze'
)
parser.add_argument(
'--output-dir',
type=str,
default='.',
help='Output directory for results'
)
args = parser.parse_args()
# Load STRING-DB data
enst_to_ensp, ensp_to_name, links, enrichment = load_string_data(args.string_db_dir)
# Load interaction data
print(f"\nLoading interaction data from {args.interactions_file}...")
interaction_data = pd.read_csv(args.interactions_file, sep='\t')
interaction_data = interaction_data.sort_values('conplex_score', ascending=False)
# Remove duplicates and limit
# Replicates Nextflow logic: drops duplicates on transcript BEFORE limit
interaction_data = interaction_data.drop_duplicates('transcipt')
if interaction_data.shape[0] > args.max_proteins:
print(f"Limiting to top {args.max_proteins} proteins")
interaction_data = interaction_data.iloc[:args.max_proteins]
# Filter by threshold
filtered_data = interaction_data[interaction_data['conplex_score'] > args.threshold]
print(f"Found {len(filtered_data)} proteins above threshold {args.threshold}")
# Map ENST to ENSP and keep track of mapping for output
enst_list = filtered_data['transcipt'].tolist()
ensp_list = []
ensp_to_input_map = {} # Map ENSP back to ENST for output generation
for enst in enst_list:
ensp = enst_to_ensp.get(enst)
if ensp:
ensp_list.append(ensp)
# We map ENSP back to the ENST. If multiple ENSTs map to one ENSP,
# this simple dict keeps the last one.
# However, since input is deduped on transcript, this is mostly 1-to-1
# for the query set.
ensp_to_input_map[ensp] = enst
print(f"Mapped {len(ensp_list)} ENST IDs to ENSP IDs")
if len(ensp_list) == 0:
print("ERROR: No valid ENSP mappings found!")
return
# Perform enrichment analysis
print("\nPerforming enrichment analysis...")
enrichment_results = perform_enrichment_analysis(ensp_list, enrichment, ensp_to_name, ensp_to_input_map)
print(f"Found {len(enrichment_results)} enriched terms")
# Get network interactions
print("\nExtracting network interactions...")
network_interactions = get_network_interactions(ensp_list, links, ensp_to_name)
print(f"Found {len(network_interactions)} protein-protein interactions")
# Generate output filename
input_path = Path(args.interactions_file)
output_name = input_path.stem.replace('_significant_interactions', '')
output_dir = Path(args.output_dir)
output_dir.mkdir(parents=True, exist_ok=True)
# Save results
enrichment_file = output_dir / f"{output_name}_network_enrichment.tsv"
interactions_file = output_dir / f"{output_name}_network_interactions.tsv"
enrichment_results.to_csv(enrichment_file, sep='\t', index=False)
network_interactions.to_csv(interactions_file, sep='\t', index=False)
print(f"\nResults saved:")
print(f" Enrichment: {enrichment_file}")
print(f" Interactions: {interactions_file}")
if __name__ == '__main__':
main()

145
conplex.py Executable file
View File

@@ -0,0 +1,145 @@
import argparse
import pandas as pd
import os
import numpy as np
import re
import subprocess
import sys
def parse_fasta_seq(fasta_file):
try:
with open(fasta_file, 'r') as file:
return [line.strip() for line in file if not line.startswith('>')]
except Exception as e:
raise ValueError(f"Error parsing FASTA file: {fasta_file}") from e
def parse_fasta_name(fasta_file):
try:
with open(fasta_file, 'r') as file:
return [line.strip()[1:] for line in file if line.startswith('>')]
except Exception as e:
raise ValueError(f"Error parsing FASTA file: {fasta_file}") from e
def create_tsv_frags(fastas, smis, screening_batch_size):
protein_sequence_list = parse_fasta_seq(fastas)
protein_name_list = parse_fasta_name(fastas)
full_df = pd.read_csv(smis, delimiter='\t', names=['smiles', 'chem_id'])
#splits = int(np.ceil((len(protein_sequence_list))/screening_batch_size))
#protein_sequence_list = np.array_split(protein_sequence_list, splits)
#protein_name_list = np.array_split(protein_name_list, splits)
try:
[full_df.assign(protein_id = [protein_id]*full_df.shape[0]).assign(protein_sequence = [protein_sequence]*full_df.shape[0])[['protein_id', 'chem_id', 'protein_sequence', 'smiles']].to_csv(f"{protein_id}.tsv", sep='\t', header=False, index=False) for protein_id, protein_sequence in zip(protein_name_list,protein_sequence_list)]
tsv_files = [f"{protein_id}.tsv" for protein_id in protein_name_list]
return tsv_files
except Exception as e:
print(f"Failed to process files: {e}")
raise
def screen_frags(tsv_files):
#[subprocess.run(["conplex-dti", "predict","--data-file", tsv_file,"--model-path", "/home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt","--outfile", f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv"]) for tsv_file in tsv_files]
[subprocess.run(["conplex-dti", "predict","--data-file", tsv_file,"--model-path", "/home/omic/ConPLex/models/Run_best_model_epoch46.pt","--outfile", f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv"]) for tsv_file in tsv_files]
scores_files = [f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv" for tsv_file in tsv_files]
#scores_files = []
#for tsv_file in tsv_files:
#base_name = os.path.splitext(os.path.basename(tsv_file))[0]
#scores_file = f"{base_name}_scores.tsv"
#subprocess.run([
# "conplex-dti", "predict",
# "--data-file", tsv_file,
# "--model-path", "/home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt",
# "--outfile", f"{base_name}_results.tsv"
#])
#with open(scores_file, 'w') as f:
# f.write("chem_id\tprotein_id\tscore\n")
#with open(f"{base_name}_results.tsv", 'r') as results_file, open(f"{base_name}_temp.tsv", 'w') as temp_file:
# for line in results_file:
# fields = line.strip().split('\t')
# temp_file.write('\t'.join(fields) + '\n')
#merged_df = pd.read_csv(f"{base_name}_temp.tsv", sep='\t', names=['chem_id', 'protein_id', 'score'])
#tsv_df = pd.read_csv(tsv_file, sep='\t', names=['protein_id', 'chem_id', 'sequence', 'smiles'])
#merged_df = merged_df.merge(tsv_df[['chem_id', 'smiles']], on='chem_id')
#merged_df.to_csv(scores_file, sep='\t', index=False)
#os.remove(f"{base_name}_temp.tsv")
#scores_files.append(scores_file)
return scores_files
def collect_frags(scores_files, fasta_file, outdir, split_write_df = 'no'):
def concatenate_dataframes(file_list):
df_list = []
header = None
for i, file in enumerate(file_list):
if os.path.getsize(file) > 0:
if i == 0:
df = pd.read_csv(file, sep='\t', index_col=None)
if df.columns[0] == 'chem_id':
header = df.columns
else:
df = pd.read_csv(file, sep='\t', index_col=None, header=None)
df.columns = ['chem_id', 'protein_id', 'score', 'smiles']
else:
df = pd.read_csv(file, sep='\t', index_col=None, header=None)
if header is not None:
df.columns = header
df_list.append(df)
else:
print(f"Skipping empty file: {file}")
if df_list:
concatenated_df = pd.concat(df_list, ignore_index=True)
return concatenated_df
else:
return pd.DataFrame()
scores_df = concatenate_dataframes(scores_files)
if not scores_df.empty:
score_column_index = 2 if 'score' not in scores_df.columns else 'score'
scores_df[score_column_index] = pd.to_numeric(scores_df[score_column_index], errors='coerce')
scores_df = scores_df.dropna(subset=[score_column_index])
sorted_scores_df = scores_df.sort_values(by=score_column_index, ascending=False)
if 'score' not in scores_df.columns:
sorted_scores_df.columns = ['chem_id', 'protein_id', 'score', 'hit', 'smiles']
base_name = os.path.splitext(os.path.basename(fasta_file))[0]
all_scores_file = os.path.join(outdir, f"{base_name}_all_scores.tsv")
sorted_scores_df.to_csv(all_scores_file, sep='\t', index=False, header=True)
else:
print("No score files found or all score files are empty.")
with open(fasta_file, 'r') as fasta:
fasta_lines = fasta.readlines()
fasta_sequence = fasta_lines[1].strip() if len(fasta_lines) > 1 else ''
if not scores_df.empty:
df = sorted_scores_df
header = df.columns.tolist()
if split_write_df == 'yes':
for index, row in df.iterrows():
row_df = pd.DataFrame([row], columns=header)
csv_filename = f"{row['complex_name'].replace(' ', '-')}_hit.csv"
row_df.to_csv(os.path.join(outdir, csv_filename), index=False)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--fastas", required=True, help="Path to the FASTA file.")
parser.add_argument("--smis", required=True, help="Path to the SMILES file.")
parser.add_argument("--screening_batch_size", type=int, default=100000, help="Batch size for screening.")
parser.add_argument("--outdir", default="output", help="Output directory.")
parser.add_argument("--split_write_df", default="no", help="Write all complexes in separate files")
args = parser.parse_args()
tsv_files = create_tsv_frags(args.fastas, args.smis, args.screening_batch_size)
scores_files = screen_frags(tsv_files)
#collect_frags(scores_files, args.fastas, args.outdir, args.split_write_df)

71
digital-trial/Dockerfile_biotransformer Normal file
View File

@@ -0,0 +1,71 @@
FROM debian:bullseye-slim
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
default-jre \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
# main conda env (biotransformer)
RUN conda create -n biotransformer
ENV PATH="$PATH:/opt/conda/envs/biotransformer/bin"
RUN echo "source activate biotransformer" >> ~/.bashrc
RUN conda clean --all -f -y
# Install RDKit
RUN conda install -y -n biotransformer -c conda-forge rdkit
WORKDIR /home/omic
# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/get/6432cf887ed7.zip && \
# unzip 6432cf887ed7.zip && \
# rm 6432cf887ed7.zip && \
# mv wishartlab-biotransformer3.0jar-6432cf887ed7 biotransformer
# RUN git clone https://github.com/Wishartlab-openscience/Biotransformer.git && \
# mv Biotransformer biotransformer
RUN git clone https://bitbucket.org/wishartlab/biotransformer3.0jar biotransformer && mv biotransformer/BioTransformer3.0_20230525.jar biotransformer/biotransformer
WORKDIR /home/omic/biotransformer
# RUN wget https://bitbucket.org/wishartlab/biotransformer3.0jar/raw/6432cf887ed70c7c943c2dfeb60298ccdc788d7d/BioTransformer3.0_20230525.jar && \
# mv BioTransformer3.0_20230525.jar biotransformer && \
# chmod +x biotransformer
ENV PATH="$PATH:/home/omic/biotransformer"
# Create a symlink from /home/omic/biotransformer/database to /home/omic/biotransformer/btkb
RUN ln -s /home/omic/biotransformer/database /home/omic/biotransformer/btkb
## Test
# RUN java -jar biotransformer -multiThread "2 example.csv 36000 3 1 true"
#Download The Human Metabolome Database smiles
RUN wget https://hmdb.ca/system/downloads/current/structures.zip
RUN unzip structures.zip
#install pandas and requests
RUN conda install -y -n biotransformer -c conda-forge pandas requests

127
digital-trial/Dockerfile_conplex Normal file
View File

@@ -0,0 +1,127 @@
ARG CUDA=11.7
FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Add the NVIDIA GPG key directly
RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
RUN apt-get -y update && \
apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (conplex)
RUN conda create -n conplex-dti python=3.9
ENV PATH "$PATH:/opt/conda/envs/conplex-dti/bin"
RUN echo "source activate conplex-dti" >> ~/.bashrc
RUN conda clean --all -f -y
# main conda env (secse)
#RUN conda create --name secse -c conda-forge parallel tqdm biopandas openbabel chemprop xlrd=2 pandarallel python=3.9 perl=5.32
#RUN conda install -y -n secse -c conda-forge pandas=1.3.5
#RUN conda install -y -n secse -c conda-forge rdkit=2022.03.5
#RUN echo "conda activate secse" >> ~/.bashrc
#ENV PATH="$PATH:/opt/conda/envs/secse/bin"
#ARG PATH="$PATH:/opt/conda/envs/secse/bin"
RUN git clone https://github.com/samsledje/ConPLex.git
WORKDIR /home/omic/ConPLex
# Install conplex
RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install conplex-dti
RUN conplex-dti --help
# Package into python script for running in nextflow
COPY conplex.py /home/omic/ConPLex/conplex.py
RUN chmod +x /home/omic/ConPLex/conplex.py
# Install pretrained models
RUN mkdir -p /home/omic/ConPLex/models
RUN wget --no-check-certificate -O /home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt https://cb.csail.mit.edu/cb/conplex/data/models/BindingDB_ExperimentalValidModel.pt
# Test
RUN conplex-dti predict --data-file /home/omic/ConPLex/tests/toy_predict.tsv --model-path /home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt --outfile ./results.tsv
#copy protein reference trascipt fasta file
COPY ensemble_reference.fasta .
COPY MANE_referent_transcipt_reference.fasta .
COPY MANE_all_transcipts.csv .
COPY get_round_2.py .
RUN chmod +x /home/omic/ConPLex/get_round_2.py
#new model weights
COPY Run_best_model_epoch46.pt /home/omic/ConPLex/models/
# Fix predict.py not working on single protein-ligand complex
#COPY predict.py /home/omic/ConPLex/conplex_dti/cli/predict.py
#COPY predict.py /opt/conda/envs/conplex-dti/lib/python3.9/site-packages/conplex_dti/cli/predict.py
#RUN chmod +x /home/omic/ConPLex/conplex_dti/cli/predict.py
#RUN chmod +x /opt/conda/envs/conplex-dti/lib/python3.9/site-packages/conplex_dti/cli/predict.py
# Clone secse
#RUN git clone https://github.com/KeenThera/SECSE.git
#RUN mv /home/omic/ConPLex/SECSE/secse /home/omic/ConPLex/secse && rm -r /home/omic/ConPLex/SECSE && rm -r /home/omic/ConPLex/secse/scoring
#COPY secse/scoring /home/omic/ConPLex/secse/scoring
#COPY secse/grow_processes.py /home/omic/ConPLex/secse/scoring/grow_processes.py
#RUN chmod +x /home/omic/ConPLex/secse/grow_processes.py
#RUN chmod +x /home/omic/ConPLex/secse/scoring/ranking.py
#RUN chmod +x /home/omic/ConPLex/secse/growing/mutation/mutation.py
# Add missing boost
#RUN conda install -n secse -c conda-forge boost
# Install CREM for chemical growth
#RUN git clone https://github.com/DrrDom/crem.git
#RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install crem pandas numpy
#WORKDIR /home/omic/ConPLex
#RUN chmod -R +x /home/omic/ConPLex
#ENV PATH="$PATH:/opt/conda/envs/secse/bin:/home/omic/ConPLex/secse"
#ENV SECSE="/home/omic/ConPLex/secse"
#ENV PYTHONPATH="PYTHONPATH=/home/omic/ConPLex/secse:/home/omic/ConPLex:/home/omic/ConPLex/crem"
#ARG PYTHONPATH="PYTHONPATH=/home/omic/ConPLex/secse:/home/omic/ConPLex:/home/omic/ConPLex/crem"
# Package into python script for running in nextflow
#COPY conplex.py /home/omic/ConPLex/conplex.py
#RUN chmod +x /home/omic/ConPLex/conplex.py
#Mutation file
#RUN /opt/conda/envs/conplex-dti/bin/python3 -m pip install crem
#RUN wget https://www.dropbox.com/s/4r48ohopechsd59/replacements02_sa2.db.gz?dl=0
#RUN mv replacements02_sa2.db.gz?dl=0 replacements02_sa2.db.gz
#RUN gzip -d replacements02_sa2.db.gz
#COPY fragment_mutations.py /home/omic/ConPLex/fragment_mutations.py
#RUN chmod +x /home/omic/ConPLex/fragment_mutations.py

60
digital-trial/Dockerfile_tissue Executable file
View File

@@ -0,0 +1,60 @@
ARG CUDA=11.7
FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
USER root
SHELL ["/bin/bash", "-c"]
WORKDIR /home
RUN mkdir -p /home/omic
WORKDIR /home/omic
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y && apt-get install -y --no-install-recommends \
build-essential \
cmake \
curl \
git \
wget \
ca-certificates \
hmmer \
kalign \
tzdata \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Add the NVIDIA GPG key directly
RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
RUN apt-get -y update && \
apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& bash miniconda.sh -b -p /opt/conda \
&& rm miniconda.sh \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
&& echo "conda activate base" >> ~/.bashrc \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& /opt/conda/bin/conda clean -afy
ENV PATH /opt/conda/bin:$PATH
RUN conda update -y -n base -c defaults conda
# main conda env (tissue)
RUN conda create -n tissue python=3.9
ENV PATH "$PATH:/opt/conda/envs/tissue/bin"
RUN echo "source activate tissue" >> ~/.bashrc
RUN conda clean --all -f -y
# Install packages
RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
RUN /opt/conda/envs/tissue/bin/python3 -m pip install pandas numpy
# Package into python script for running in nextflow
COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
RUN chmod +x /home/omic/drug_tissue_distribution.py
# copy reference file
COPY HPA_normal_ihc_data.tsv .
COPY MANE_all_transcipts.csv .

5
digital-trial/Note.txt Normal file
View File

@@ -0,0 +1,5 @@
Add options for metabolites not existing and process failed
Remove unnecessary data while process is running, take up too much memory
ncbiproteins_seq_exist.csv is replaced with ncbiproteins_seq_exist_reduce.csv so it will be able to fit to gitlab

217
digital-trial/Phase1-2proteins.tsv Normal file
View File

@@ -0,0 +1,217 @@
MoleculeType Uniprot Symbol
Phase1 P22760 AADAC
Phase1 P08684 CYP3A4
Phase1 Q96SQ9 CYP2S1
Phase1 P10635 CYP2D6
Phase1 Q8TAV3 CYP2W1
Phase1 Q9HB55 CYP3A43
Phase1 Q5TCH4 CYP4A22
Phase1 Q6NT55 CYP4F22
Phase1 P13584 CYP4B1
Phase1 Q02928 CYP4A11
Phase1 P78329 CYP4F2
Phase1 Q08477 CYP4F3
Phase1 Q9HBI6 CYP4F11
Phase1 Q7Z449 CYP2U1
Phase1 Q9UNU6 CYP8B1
Phase1 Q16647 PTGIS
Phase1 P98187 CYP4F8
Phase1 P24557 TBXAS1
Phase1 Q9HCS2 CYP4F12
Phase1 P22680 CYP7A1
Phase1 O75881 CYP7B1
Phase1 P19793 RXRA
Phase1 Q15788 NCOA1
Phase1 Q96RI1 NR1H4
Phase1 Q15596 NCOA2
Phase1 P19099 CYP11B2
Phase1 P11511 CYP19A1
Phase1 Q16678 CYP1B1
Phase1 A9YTQ3 AHRR
Phase1 P27540 ARNT
Phase1 Q9HBZ2 ARNT2
Phase1 P35869 AHR
Phase1 P08686 CYP21A2
Phase1 P10109 FDX1
Phase1 Q6P4F2 FDX2
Phase1 P05108 CYP11A1
Phase1 P22570 FDXR
Phase1 P15538 CYP11B1
Phase1 P01189 POMC
Phase1 Q9NYL5 CYP39A1
Phase1 Q16850 CYP51A1
Phase1 Q6ZWL3 CYP4V2
Phase1 Q02318 CYP27A1
Phase1 Q9Y6A2 CYP46A1
Phase1 P20853 CYP2A7
Phase1 P20813 CYP2B6
Phase1 Q16696 CYP2A13
Phase1 P24903 CYP2F1
Phase1 P51589 CYP2J2
Phase1 P05181 CYP2E1
Phase1 P11509 CYP2A6
Phase1 P33260 CYP2C18
Phase1 P11712 CYP2C9
Phase1 P33261 CYP2C19
Phase1 P10632 CYP2C8
Phase1 P20815 CYP3A5
Phase1 P24462 CYP3A7
Phase1 P05177 CYP1A2
Phase1 P04798 CYP1A1
Phase1 P16435 POR
Phase1 Q6V0L0 CYP26C1
Phase1 Q9NR63 CYP26B1
Phase1 O43174 CYP26A1
Phase1 Q6VVX0 CYP2R1
Phase1 Q07973 CYP24A1
Phase1 O15528 CYP27B1
Phase1 Q9NUB1 ACSS1
Phase1 Q9NR19 ACSS2
Phase1 P07327 ADH1A
Phase1 P00325 ADH1B
Phase1 P08319 ADH4
Phase1 P00326 ADH1C
Phase1 P28332 ADH6
Phase1 P40394 ADH7
Phase1 P05091 ALDH2
Phase1 P00352 ALDH1A1
Phase1 P11766 ADH5
Phase1 P30837 ALDH1B1
Phase1 Q86WA6 BPHL
Phase1 P23219 PTGS1
Phase1 P19801 AOC1
Phase1 P31513 FMO3
Phase1 Q01740 FMO1
Phase1 Q99518 FMO2
Phase1 Q969Z3 MTARC2
Phase1 P00387 CYB5R3
Phase1 Q5VT66 MTARC1
Phase1 O43169 CYB5B
Phase1 Q6QHF9 PAOX
Phase1 Q9NWM0-3 SMOX
Phase1 P27338 MAOB
Phase1 P21397 MAOA
Phase1 Q15185 PTGES3
Phase1 P08238 HSP90AB1
Phase1 O00170 AIP
Phase1 P16083 NQO2
Phase1 P23141 CES1
Phase1 O00748 CES2
Phase1 P30838 ALDH3A1
Phase1 P07099 EPHX1
Phase1 Q6UWW8 CES3
Phase1 Q96DG6 CMBL
Phase1 O75106 AOC2
Phase1 O75828 CBR3
Phase1 Q16853 AOC3
Phase2 P18440 NAT1
Phase2 P11245 NAT2
Phase2 P05177 CYP1A2
Phase2 P23526 AHCY
Phase2 Q9HBK9 AS3MT
Phase2 Q99707 MTR
Phase2 Q9UBK8 MTRR
Phase2 P21964 COMT
Phase2 P78417 GSTO1
Phase2 P40261 NNMT
Phase2 Q9Y5N5 N6AMT1
Phase2 Q9UI30 TRMT112
Phase2 P51580 TPMT
Phase2 Q00266 MAT1A
Phase2 P31153 MAT2A
Phase2 Q9NZL9 MAT2B
Phase2 Q68CK6 ACSM2B
Phase2 Q08AH1 ACSM1
Phase2 Q8WU03 GLYATL2
Phase2 Q5SZD4 GLYATL3
Phase2 Q969I3 GLYATL1
Phase2 Q6IB77 GLYAT
Phase2 P0C7M7 ACSM4
Phase2 Q08AH3 ACSM2A
Phase2 Q6NUN0 ACSM5
Phase2 P50225 SULT1A1
Phase2 O00204-1 SULT2B1
Phase2 P50226 SULT1A2
Phase2 O75897 SULT1C4
Phase2 Q9BR01 SULT4A1
Phase2 O00204-2 SULT2B1
Phase2 P49888 SULT1E1
Phase2 Q96IU4 ABHD14B
Phase2 O00338 SULT1C2
Phase2 P0DMM9 SULT1A3
Phase2 Q06520 SULT2A1
Phase2 O43704 SULT1B1
Phase2 Q6IMI4 SULT6B1
Phase2 Q9NX62 BPNT2
Phase2 Q8TB61 SLC35B2
Phase2 Q9H1N7 SLC35B3
Phase2 P50443 SLC26A2
Phase2 Q9H2B4 SLC26A1
Phase2 O43252 PAPSS1
Phase2 O95340 PAPSS2
Phase2 P0DMN0 SULT1A4
Phase2 O95861 BPNT1
Phase2 O60704 TPST2
Phase2 O60507 TPST1
Phase2 Q9NZ53 PODXL2
Phase2 O75223 GGCT
Phase2 Q96KP4 CNDP2
Phase2 Q6P531 GGT6
Phase2 P36269 GGT5
Phase2 A6NGU5 GGT3P
Phase2 Q9UJ14 GGT7
Phase2 P19440 GGT1
Phase2 P48637 GSS
Phase2 O14841 OPLAH
Phase2 P48506 GCLC
Phase2 P48507 GCLM
Phase2 Q8WUX2 CHAC2
Phase2 Q9BUX1 CHAC1
Phase2 P0CG29 GSTT2
Phase2 Q7RTV2 GSTA5
Phase2 O15217 GSTA4
Phase2 O60760 HPGDS
Phase2 P09211 GSTP1
Phase2 P0CG30 GSTT2B
Phase2 Q9H4Y5 GSTO2
Phase2 P21266 GSTM3
Phase2 P30711 GSTT1
Phase2 P09488 GSTM1
Phase2 Q16772 GSTA3
Phase2 Q03013 GSTM4
Phase2 O43708 GSTZ1
Phase2 P09210 GSTA2
Phase2 P08263 GSTA1
Phase2 P28161 GSTM2
Phase2 P46439 GSTM5
Phase2 Q9Y2Q3 GSTK1
Phase2 P10620 MGST1
Phase2 O14880 MGST3
Phase2 Q99735 MGST2
Phase2 P10768 ESD
Phase2 P14550 AKR1A1
Phase2 P0DTE4 UGT2A1
Phase2 P0DTE5 UGT2A1
Phase2 Q9BY64 UGT2B28
Phase2 P35504 UGT1A5
Phase2 P36537 UGT2B10
Phase2 O75310 UGT2B11
Phase2 Q9HAW7 UGT1A7
Phase2 O75795 UGT2B17
Phase2 P16662 UGT2B7
Phase2 Q9HAW9 UGT1A8
Phase2 Q6NUS8 UGT3A1
Phase2 P35503 UGT1A3
Phase2 O60656 UGT1A9
Phase2 P54855 UGT2B15
Phase2 P06133 UGT2B4
Phase2 P22310 UGT1A4
Phase2 Q6UWM9 UGT2A3
Phase2 Q3SY77 UGT3A2
Phase2 P22309 UGT1A1
Phase2 P19224 UGT1A6
Phase2 Q9NUJ1 ABHD10
Phase2 Q9NTN3 SLC35D1
Phase2 Q16851 UGP2
Phase2 O60701 UGDH
Phase2 Q9HAW8 UGT1A10
1 MoleculeType Uniprot Symbol
2 Phase1 P22760 AADAC
3 Phase1 P08684 CYP3A4
4 Phase1 Q96SQ9 CYP2S1
5 Phase1 P10635 CYP2D6
6 Phase1 Q8TAV3 CYP2W1
7 Phase1 Q9HB55 CYP3A43
8 Phase1 Q5TCH4 CYP4A22
9 Phase1 Q6NT55 CYP4F22
10 Phase1 P13584 CYP4B1
11 Phase1 Q02928 CYP4A11
12 Phase1 P78329 CYP4F2
13 Phase1 Q08477 CYP4F3
14 Phase1 Q9HBI6 CYP4F11
15 Phase1 Q7Z449 CYP2U1
16 Phase1 Q9UNU6 CYP8B1
17 Phase1 Q16647 PTGIS
18 Phase1 P98187 CYP4F8
19 Phase1 P24557 TBXAS1
20 Phase1 Q9HCS2 CYP4F12
21 Phase1 P22680 CYP7A1
22 Phase1 O75881 CYP7B1
23 Phase1 P19793 RXRA
24 Phase1 Q15788 NCOA1
25 Phase1 Q96RI1 NR1H4
26 Phase1 Q15596 NCOA2
27 Phase1 P19099 CYP11B2
28 Phase1 P11511 CYP19A1
29 Phase1 Q16678 CYP1B1
30 Phase1 A9YTQ3 AHRR
31 Phase1 P27540 ARNT
32 Phase1 Q9HBZ2 ARNT2
33 Phase1 P35869 AHR
34 Phase1 P08686 CYP21A2
35 Phase1 P10109 FDX1
36 Phase1 Q6P4F2 FDX2
37 Phase1 P05108 CYP11A1
38 Phase1 P22570 FDXR
39 Phase1 P15538 CYP11B1
40 Phase1 P01189 POMC
41 Phase1 Q9NYL5 CYP39A1
42 Phase1 Q16850 CYP51A1
43 Phase1 Q6ZWL3 CYP4V2
44 Phase1 Q02318 CYP27A1
45 Phase1 Q9Y6A2 CYP46A1
46 Phase1 P20853 CYP2A7
47 Phase1 P20813 CYP2B6
48 Phase1 Q16696 CYP2A13
49 Phase1 P24903 CYP2F1
50 Phase1 P51589 CYP2J2
51 Phase1 P05181 CYP2E1
52 Phase1 P11509 CYP2A6
53 Phase1 P33260 CYP2C18
54 Phase1 P11712 CYP2C9
55 Phase1 P33261 CYP2C19
56 Phase1 P10632 CYP2C8
57 Phase1 P20815 CYP3A5
58 Phase1 P24462 CYP3A7
59 Phase1 P05177 CYP1A2
60 Phase1 P04798 CYP1A1
61 Phase1 P16435 POR
62 Phase1 Q6V0L0 CYP26C1
63 Phase1 Q9NR63 CYP26B1
64 Phase1 O43174 CYP26A1
65 Phase1 Q6VVX0 CYP2R1
66 Phase1 Q07973 CYP24A1
67 Phase1 O15528 CYP27B1
68 Phase1 Q9NUB1 ACSS1
69 Phase1 Q9NR19 ACSS2
70 Phase1 P07327 ADH1A
71 Phase1 P00325 ADH1B
72 Phase1 P08319 ADH4
73 Phase1 P00326 ADH1C
74 Phase1 P28332 ADH6
75 Phase1 P40394 ADH7
76 Phase1 P05091 ALDH2
77 Phase1 P00352 ALDH1A1
78 Phase1 P11766 ADH5
79 Phase1 P30837 ALDH1B1
80 Phase1 Q86WA6 BPHL
81 Phase1 P23219 PTGS1
82 Phase1 P19801 AOC1
83 Phase1 P31513 FMO3
84 Phase1 Q01740 FMO1
85 Phase1 Q99518 FMO2
86 Phase1 Q969Z3 MTARC2
87 Phase1 P00387 CYB5R3
88 Phase1 Q5VT66 MTARC1
89 Phase1 O43169 CYB5B
90 Phase1 Q6QHF9 PAOX
91 Phase1 Q9NWM0-3 SMOX
92 Phase1 P27338 MAOB
93 Phase1 P21397 MAOA
94 Phase1 Q15185 PTGES3
95 Phase1 P08238 HSP90AB1
96 Phase1 O00170 AIP
97 Phase1 P16083 NQO2
98 Phase1 P23141 CES1
99 Phase1 O00748 CES2
100 Phase1 P30838 ALDH3A1
101 Phase1 P07099 EPHX1
102 Phase1 Q6UWW8 CES3
103 Phase1 Q96DG6 CMBL
104 Phase1 O75106 AOC2
105 Phase1 O75828 CBR3
106 Phase1 Q16853 AOC3
107 Phase2 P18440 NAT1
108 Phase2 P11245 NAT2
109 Phase2 P05177 CYP1A2
110 Phase2 P23526 AHCY
111 Phase2 Q9HBK9 AS3MT
112 Phase2 Q99707 MTR
113 Phase2 Q9UBK8 MTRR
114 Phase2 P21964 COMT
115 Phase2 P78417 GSTO1
116 Phase2 P40261 NNMT
117 Phase2 Q9Y5N5 N6AMT1
118 Phase2 Q9UI30 TRMT112
119 Phase2 P51580 TPMT
120 Phase2 Q00266 MAT1A
121 Phase2 P31153 MAT2A
122 Phase2 Q9NZL9 MAT2B
123 Phase2 Q68CK6 ACSM2B
124 Phase2 Q08AH1 ACSM1
125 Phase2 Q8WU03 GLYATL2
126 Phase2 Q5SZD4 GLYATL3
127 Phase2 Q969I3 GLYATL1
128 Phase2 Q6IB77 GLYAT
129 Phase2 P0C7M7 ACSM4
130 Phase2 Q08AH3 ACSM2A
131 Phase2 Q6NUN0 ACSM5
132 Phase2 P50225 SULT1A1
133 Phase2 O00204-1 SULT2B1
134 Phase2 P50226 SULT1A2
135 Phase2 O75897 SULT1C4
136 Phase2 Q9BR01 SULT4A1
137 Phase2 O00204-2 SULT2B1
138 Phase2 P49888 SULT1E1
139 Phase2 Q96IU4 ABHD14B
140 Phase2 O00338 SULT1C2
141 Phase2 P0DMM9 SULT1A3
142 Phase2 Q06520 SULT2A1
143 Phase2 O43704 SULT1B1
144 Phase2 Q6IMI4 SULT6B1
145 Phase2 Q9NX62 BPNT2
146 Phase2 Q8TB61 SLC35B2
147 Phase2 Q9H1N7 SLC35B3
148 Phase2 P50443 SLC26A2
149 Phase2 Q9H2B4 SLC26A1
150 Phase2 O43252 PAPSS1
151 Phase2 O95340 PAPSS2
152 Phase2 P0DMN0 SULT1A4
153 Phase2 O95861 BPNT1
154 Phase2 O60704 TPST2
155 Phase2 O60507 TPST1
156 Phase2 Q9NZ53 PODXL2
157 Phase2 O75223 GGCT
158 Phase2 Q96KP4 CNDP2
159 Phase2 Q6P531 GGT6
160 Phase2 P36269 GGT5
161 Phase2 A6NGU5 GGT3P
162 Phase2 Q9UJ14 GGT7
163 Phase2 P19440 GGT1
164 Phase2 P48637 GSS
165 Phase2 O14841 OPLAH
166 Phase2 P48506 GCLC
167 Phase2 P48507 GCLM
168 Phase2 Q8WUX2 CHAC2
169 Phase2 Q9BUX1 CHAC1
170 Phase2 P0CG29 GSTT2
171 Phase2 Q7RTV2 GSTA5
172 Phase2 O15217 GSTA4
173 Phase2 O60760 HPGDS
174 Phase2 P09211 GSTP1
175 Phase2 P0CG30 GSTT2B
176 Phase2 Q9H4Y5 GSTO2
177 Phase2 P21266 GSTM3
178 Phase2 P30711 GSTT1
179 Phase2 P09488 GSTM1
180 Phase2 Q16772 GSTA3
181 Phase2 Q03013 GSTM4
182 Phase2 O43708 GSTZ1
183 Phase2 P09210 GSTA2
184 Phase2 P08263 GSTA1
185 Phase2 P28161 GSTM2
186 Phase2 P46439 GSTM5
187 Phase2 Q9Y2Q3 GSTK1
188 Phase2 P10620 MGST1
189 Phase2 O14880 MGST3
190 Phase2 Q99735 MGST2
191 Phase2 P10768 ESD
192 Phase2 P14550 AKR1A1
193 Phase2 P0DTE4 UGT2A1
194 Phase2 P0DTE5 UGT2A1
195 Phase2 Q9BY64 UGT2B28
196 Phase2 P35504 UGT1A5
197 Phase2 P36537 UGT2B10
198 Phase2 O75310 UGT2B11
199 Phase2 Q9HAW7 UGT1A7
200 Phase2 O75795 UGT2B17
201 Phase2 P16662 UGT2B7
202 Phase2 Q9HAW9 UGT1A8
203 Phase2 Q6NUS8 UGT3A1
204 Phase2 P35503 UGT1A3
205 Phase2 O60656 UGT1A9
206 Phase2 P54855 UGT2B15
207 Phase2 P06133 UGT2B4
208 Phase2 P22310 UGT1A4
209 Phase2 Q6UWM9 UGT2A3
210 Phase2 Q3SY77 UGT3A2
211 Phase2 P22309 UGT1A1
212 Phase2 P19224 UGT1A6
213 Phase2 Q9NUJ1 ABHD10
214 Phase2 Q9NTN3 SLC35D1
215 Phase2 Q16851 UGP2
216 Phase2 O60701 UGDH
217 Phase2 Q9HAW8 UGT1A10

42
digital-trial/README.md Normal file
View File

@@ -0,0 +1,42 @@
# Digital Trial Pipeline
## v1 steps
| Step | Status | Model | Input | Output | Notes |
| ---- | ------ | ----- | ----- | ------ | ----- |
|1. Metabolite Prediction | done | biotransformer | SMILES | DRUG_out.txt | intermediate step |
|2. Drug & metabolite - screening against patient proteome | done | ConPlex | patient.fasta from digital patient step 3 (vcf2prot); "DRUG_out.txt" | "patientID_DRUG_significant_interactions.tsv" | intermediate step - pairs are sorted by scores and filtered for next step
|3. Biological processes/Pathway enrichment analysis | done | stringDB API | "patientID_DRUG_significant_interactions.tsv" | DRUG_patientID_network_enrichment.tsv; DRUG_patientID_network_interactions.tsv | biological processes/pathways for proteins that bind to the drug or metabolites - to use ML model to summarise output
|4. Drug localization | | | | |
### Pipeline steps descriptions and tasks
1. Metabolite Prediction
- predicted metabolites of input drug
- filtered out intermediate metabolites and excluded from subsequent steps
2. Drug/Metabolite screen against patient proteome
- columns 2 & 3 being a pair (SMILES-ENST#) and column 4 with corresponding score for the pair in each row
- UI tasks
- [ ] allow user to input target [Ensembl ID] of test drug and we show score of interaction as main interactions; add following description:
#####
| Score | Interaction probability |
| > 0.9 | Excellent |
| 0.8 - 0.9 | Acceptable |
| < 0.8 | Highly unlikely |
- [ ] add a slider for adjusting the cutoff score (set default cutoff on slider to 0.75)
- [ ] show the significant interactions as table for top 20 drugs/metabolites against proteins ordered by scores below the main interaction
3. Biological processes/Pathway enrichment
- Is the drug strongly and specifically interacting with the target and/or do we have a lot of drug or metabolite off-target effects
- [ ] create ML model to create summary description using "XXX_network_enrichment.tsv"
4. Drug localization
- which organs/tissues are the interacting proteins usually localised, Human Protein Atlas tissue-enhanced protein lists for tissue proportion estimate. Heat map of proteins of interest expressed in each tissue.
- [ ] get list of protein expressed in which tissue from HPA and upload to gitlab
___________________________________
## v2 planned steps
5. Drug clearance
- mutations in Phase1/2 proteins

145
digital-trial/conplex.py Executable file
View File

@@ -0,0 +1,145 @@
import argparse
import pandas as pd
import os
import numpy as np
import re
import subprocess
import sys
def parse_fasta_seq(fasta_file):
try:
with open(fasta_file, 'r') as file:
return [line.strip() for line in file if not line.startswith('>')]
except Exception as e:
raise ValueError(f"Error parsing FASTA file: {fasta_file}") from e
def parse_fasta_name(fasta_file):
try:
with open(fasta_file, 'r') as file:
return [line.strip()[1:] for line in file if line.startswith('>')]
except Exception as e:
raise ValueError(f"Error parsing FASTA file: {fasta_file}") from e
def create_tsv_frags(fastas, smis, screening_batch_size):
protein_sequence_list = parse_fasta_seq(fastas)
protein_name_list = parse_fasta_name(fastas)
full_df = pd.read_csv(smis, delimiter='\t', names=['smiles', 'chem_id'])
#splits = int(np.ceil((len(protein_sequence_list))/screening_batch_size))
#protein_sequence_list = np.array_split(protein_sequence_list, splits)
#protein_name_list = np.array_split(protein_name_list, splits)
try:
[full_df.assign(protein_id = [protein_id]*full_df.shape[0]).assign(protein_sequence = [protein_sequence]*full_df.shape[0])[['protein_id', 'chem_id', 'protein_sequence', 'smiles']].to_csv(f"{protein_id}.tsv", sep='\t', header=False, index=False) for protein_id, protein_sequence in zip(protein_name_list,protein_sequence_list)]
tsv_files = [f"{protein_id}.tsv" for protein_id in protein_name_list]
return tsv_files
except Exception as e:
print(f"Failed to process files: {e}")
raise
def screen_frags(tsv_files):
#[subprocess.run(["conplex-dti", "predict","--data-file", tsv_file,"--model-path", "/home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt","--outfile", f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv"]) for tsv_file in tsv_files]
[subprocess.run(["conplex-dti", "predict","--data-file", tsv_file,"--model-path", "/home/omic/ConPLex/models/Run_best_model_epoch46.pt","--outfile", f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv"]) for tsv_file in tsv_files]
scores_files = [f"{os.path.splitext(os.path.basename(tsv_file))[0]}_results.tsv" for tsv_file in tsv_files]
#scores_files = []
#for tsv_file in tsv_files:
#base_name = os.path.splitext(os.path.basename(tsv_file))[0]
#scores_file = f"{base_name}_scores.tsv"
#subprocess.run([
# "conplex-dti", "predict",
# "--data-file", tsv_file,
# "--model-path", "/home/omic/ConPLex/models/ConPLex_v1_BindingDB.pt",
# "--outfile", f"{base_name}_results.tsv"
#])
#with open(scores_file, 'w') as f:
# f.write("chem_id\tprotein_id\tscore\n")
#with open(f"{base_name}_results.tsv", 'r') as results_file, open(f"{base_name}_temp.tsv", 'w') as temp_file:
# for line in results_file:
# fields = line.strip().split('\t')
# temp_file.write('\t'.join(fields) + '\n')
#merged_df = pd.read_csv(f"{base_name}_temp.tsv", sep='\t', names=['chem_id', 'protein_id', 'score'])
#tsv_df = pd.read_csv(tsv_file, sep='\t', names=['protein_id', 'chem_id', 'sequence', 'smiles'])
#merged_df = merged_df.merge(tsv_df[['chem_id', 'smiles']], on='chem_id')
#merged_df.to_csv(scores_file, sep='\t', index=False)
#os.remove(f"{base_name}_temp.tsv")
#scores_files.append(scores_file)
return scores_files
def collect_frags(scores_files, fasta_file, outdir, split_write_df = 'no'):
def concatenate_dataframes(file_list):
df_list = []
header = None
for i, file in enumerate(file_list):
if os.path.getsize(file) > 0:
if i == 0:
df = pd.read_csv(file, sep='\t', index_col=None)
if df.columns[0] == 'chem_id':
header = df.columns
else:
df = pd.read_csv(file, sep='\t', index_col=None, header=None)
df.columns = ['chem_id', 'protein_id', 'score', 'smiles']
else:
df = pd.read_csv(file, sep='\t', index_col=None, header=None)
if header is not None:
df.columns = header
df_list.append(df)
else:
print(f"Skipping empty file: {file}")
if df_list:
concatenated_df = pd.concat(df_list, ignore_index=True)
return concatenated_df
else:
return pd.DataFrame()
scores_df = concatenate_dataframes(scores_files)
if not scores_df.empty:
score_column_index = 2 if 'score' not in scores_df.columns else 'score'
scores_df[score_column_index] = pd.to_numeric(scores_df[score_column_index], errors='coerce')
scores_df = scores_df.dropna(subset=[score_column_index])
sorted_scores_df = scores_df.sort_values(by=score_column_index, ascending=False)
if 'score' not in scores_df.columns:
sorted_scores_df.columns = ['chem_id', 'protein_id', 'score', 'hit', 'smiles']
base_name = os.path.splitext(os.path.basename(fasta_file))[0]
all_scores_file = os.path.join(outdir, f"{base_name}_all_scores.tsv")
sorted_scores_df.to_csv(all_scores_file, sep='\t', index=False, header=True)
else:
print("No score files found or all score files are empty.")
with open(fasta_file, 'r') as fasta:
fasta_lines = fasta.readlines()
fasta_sequence = fasta_lines[1].strip() if len(fasta_lines) > 1 else ''
if not scores_df.empty:
df = sorted_scores_df
header = df.columns.tolist()
if split_write_df == 'yes':
for index, row in df.iterrows():
row_df = pd.DataFrame([row], columns=header)
csv_filename = f"{row['complex_name'].replace(' ', '-')}_hit.csv"
row_df.to_csv(os.path.join(outdir, csv_filename), index=False)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--fastas", required=True, help="Path to the FASTA file.")
parser.add_argument("--smis", required=True, help="Path to the SMILES file.")
parser.add_argument("--screening_batch_size", type=int, default=100000, help="Batch size for screening.")
parser.add_argument("--outdir", default="output", help="Output directory.")
parser.add_argument("--split_write_df", default="no", help="Write all complexes in separate files")
args = parser.parse_args()
tsv_files = create_tsv_frags(args.fastas, args.smis, args.screening_batch_size)
scores_files = screen_frags(tsv_files)
#collect_frags(scores_files, args.fastas, args.outdir, args.split_write_df)

39
digital-trial/drug_tissue_distribution.py Normal file
View File

@@ -0,0 +1,39 @@
import argparse
import pandas as pd
import numpy as np
def get_tissue_distribution(file_name):
#load protein expression per tissue
HPA = pd.read_csv('/home/omic/HPA_normal_ihc_data.tsv', sep = '\t')
#load enst symbol mapping data
MANE_all_transcipts = pd.read_csv('/home/omic/MANE_all_transcipts.csv')
#load interaction data
significant_interactions = pd.read_csv(file_name, sep = '\t')
#filter out tissues with low confidence
HPA = HPA[(HPA['Level'] == 'Medium') | (HPA['Level'] == 'High')]
#get protrin symbols from siginificant interactions
prot_enst = [i.split('_')[0] for i in pd.unique(significant_interactions['transcipt'])]
prot_symbol = [MANE_all_transcipts[MANE_all_transcipts['transcipt'] == i]['symbol'].iloc[0] for i in prot_enst]
prot_symbol = pd.unique(prot_symbol)
#get protein expression per tissue
tissue_per_prot_symbol = [list(pd.unique(HPA[HPA['Gene name'] == i]['Tissue'])) for i in prot_symbol]
#transform list do array
tissue_per_prot_symbol_array = np.array([[i in j for i in pd.unique(HPA['Tissue'])] for j in tissue_per_prot_symbol])
tissue_per_prot_symbol_pd = pd.DataFrame(tissue_per_prot_symbol_array)
tissue_per_prot_symbol_pd.columns = pd.unique(HPA['Tissue'])
tissue_per_prot_symbol_pd = tissue_per_prot_symbol_pd.set_index(prot_symbol)
#save
save_name = file_name.split('significant_interactions.tsv')[0] + 'tissue_distribution.tsv'
tissue_per_prot_symbol_pd.to_csv(save_name, sep = '\t')
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Get tissue distribution from *significant_interactions.tsv.")
parser.add_argument("--file_name", required=True, help="file_name")
args = parser.parse_args()
get_tissue_distribution(args.file_name)

78
digital-trial/get_round_2.py Executable file
View File

@@ -0,0 +1,78 @@
import argparse
import pandas as pd
import numpy as np
import subprocess
from itertools import chain
seq_exist = pd.read_csv('/home/omic/ConPLex/MANE_all_transcipts.csv')
def get_round_2(threshold, workdir, round):
#get output names
#get patient fasta name
fasta_name = subprocess.check_output([f'find {workdir} -name \*_variants_transcript_id_mutations.fasta' ], shell = True)
fasta_name = str(fasta_name).split('/')[-1].split('_variants_transcript_id_mutations.fasta')[0]
#get test drug
drug_name = subprocess.check_output([f'find {workdir} -name \*.csv' ], shell = True)
drug_name = [x for x in str(drug_name).split('/') if "round_1.csv" not in x][-1].split('.csv')[0]
name_out = drug_name + '_' + fasta_name
#get all work dir conplex files
#res_list = subprocess.check_output([f'ls {workdir}/*_results.tsv'], shell = True)
res_list = subprocess.check_output([f'find {workdir} -name \*_results.tsv' ], shell = True)
round_1_score_list = str(res_list).split('\'')[1].split('\\n')[:-1]
#read 1. round
transcipts_1 = [pd.read_csv(i, sep = '\t', header=None).sort_values([2], ascending=False) for i in round_1_score_list]
#get poition of drag interaction vs all metabolites
drug_pos = [[n for n, j in enumerate(list(i[0])) if j[:4] == 'drug'] for i in transcipts_1]
#drug score
drug_0_score = pd.concat([i[i[0] =='drug_0'] for i in transcipts_1]).rename({0:'Drug', 1:'Transcript', 2:'Score'}, axis = 1)
#filter all below threshold
transcipts_1 = [i[i[2] > threshold] for i in transcipts_1]
#save transcipt_conplex above threshold to one file
if round == 2:
inter_import = pd.concat(transcipts_1, ignore_index=True).rename({0:'drug/metabolite',1:'transcipt',2:'conplex_score'},axis = 1)
#add drug
test_smiles = pd.read_csv(f'{workdir}/smiles.smi', sep = '\t', header=None)
smi_ = [test_smiles[test_smiles[1] == i].iloc[0][0] for i in list(inter_import['drug/metabolite'])]
inter_import['smile'] = smi_
inter_import[['drug/metabolite','smile','transcipt','conplex_score']].to_csv(f'{workdir}/{name_out}_significant_interactions.tsv',sep = '\t',index = False)
drug_0_score.to_csv(f'{workdir}/{name_out}_drug_scores.tsv',sep = '\t',index = False)
transcipts_1 = pd.DataFrame([(j.split('/')[-1].split('_results')[0], i.shape[0], i[2].mean(), k[0]) for i,j, k in zip(transcipts_1, round_1_score_list, drug_pos) if i.shape[0] != 0])
#chack if any interaction is is above threshold for first roud
if round == 1:
if transcipts_1.shape == (0,0):
transcipts_1.to_csv(f'{workdir}/round_1.csv', index = False)
with open(f'{workdir}/round_1.fasta', 'w') as f:
f.write("all_data_is_filtered_out\n")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
transcipts_1 = transcipts_1.rename({0:'transcipt_name',1:'number_of_iteracting_compounds', 2:'mean_binding_above_threshold', 3:'drug_position'}, axis='columns')
transcipts_1['if_drug_above_threshold'] = transcipts_1.iloc[:,1] > transcipts_1.iloc[:,3]
#if protein is mutated it has _2 in name, removes it
transcipt_names = [i.split('_')[0] for i in list(transcipts_1['transcipt_name'])]
transcipts_1['protein_name'] = [[seq_exist[seq_exist['transcipt'] == i].iloc[0]['symbol']][0] for i in transcipt_names]
#save data on first round
transcipts_1.to_csv(f'{workdir}/round_{round}.csv', index = False)
#get fasta for second round
if round == 1:
#get all transcipts of proteins above threshold
name_2_filttered = list(transcipts_1['protein_name'])
transcipts_2 = [list(seq_exist[seq_exist['symbol'] == i]['transcipt']) for i in name_2_filttered]
transcipts_2 = list(chain(*transcipts_2))
transcipts_2 = list(np.unique((transcipts_2)))
#filter out transcripts already ran through complex
transcipts_2 = list(np.array(transcipts_2)[[i not in list(transcipts_1['transcipt_name']) for i in transcipts_2]])
fasta_new = [['>'+i, seq_exist[seq_exist['transcipt'] == i]['seq'].iloc[0]] for i in transcipts_2]
fasta_new = list(chain(*fasta_new))
#write fasta to run
with open(f'{workdir}/round_2.fasta', 'w') as f:
for line in fasta_new:
f.write(f"{line}\n")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--threshold", required=True, type=float, help="Threshold for 1. round.of conplex scores")
parser.add_argument("--workdir", required=True, help="workdir")
parser.add_argument("--round", required=True, type=int, help="Round 1 or 2")
args = parser.parse_args()
get_round_2(args.threshold, args.workdir, args.round)

220
digital-trial/main_biotransformer.nf Normal file
View File

@@ -0,0 +1,220 @@
nextflow.enable.dsl=2
process SUPER_TRANSFORMER {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Predicting Biotransformation Using the Human Super Transformer:
# This command predicts the biotransformation of molecules from an SDF input (example.csv) using the human super transformer (superbio) and annotates the metabolites with names and database IDs (from PubChem).
java -jar /home/omic/biotransformer/biotransformer -k pred -b superbio -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -a
"""
}
process HUMAN_TRANSFORMER {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/sdf", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
set -e
workdir=\$(pwd)
cd /home/omic/biotransformer
# Function to get available memory percentage
get_available_mem_percent() {
free | awk '/Mem:/ {print int(\$7/\$2 * 100)}'
}
# Function to log memory usage
log_memory() {
local pid=\$1
echo "MEMLOG: Timestamp,BioTransformer Memory (MB),Available System Memory (%)" >&2
while kill -0 \$pid 2>/dev/null; do
local biotrans_mem=\$(ps -o rss= -p \$pid | awk '{print \$1/1024}')
local avail_mem=\$(get_available_mem_percent)
echo "MEMLOG: \$(date '+%Y-%m-%d %H:%M:%S'),\$biotrans_mem,\$avail_mem" >&2
if [ \$avail_mem -lt 5 ]; then
echo "MEMLOG: Available memory below 5%. Terminating process." >&2
kill -15 \$pid
wait \$pid
echo 'PROCESS TERMINATED DUE TO LOW MEMORY' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
exit 1
fi
sleep 1800 # Sleep for 30 minutes
done
}
# Calculate max Java heap size (90% of available memory)
max_heap=\$(free -g | awk '/Mem:/ {print int(\$7 * 0.9)}')
# Start the biotransformer process
java -Xmx"\${max_heap}g" -jar /home/omic/biotransformer/biotransformer -a -k pred -b superbio -isdf "\$workdir/${smiles_csv.simpleName}.csv" -ocsv "\${workdir}/${smiles_csv.simpleName}_out.csv" -osdf "\${workdir}/${smiles_csv.simpleName}.sdf" -s 100 &
biotrans_pid=\$!
# Start memory logging in the background
log_memory \$biotrans_pid &
log_pid=\$!
# Wait for the biotransformer process to finish
wait \$biotrans_pid
status=\$?
# Stop the logging process
kill \$log_pid 2>/dev/null || true
if [ ! -s "\${workdir}/${smiles_csv.simpleName}_out.csv" ]; then
if [ \$status -ne 0 ] && [ ! -f "\${workdir}/${smiles_csv.simpleName}_out.csv" ]; then
echo 'PROCESS FAILED' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
else
echo 'NO METABOLITES' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
fi
fi
"""
}
process METABOLITES_BY_MASS {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/graphs", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Identifying Metabolites with Specific Masses:
# This command identifies all human metabolites of compounds in example.csv with masses 292.0946 Da and 304.0946 Da (max depth = 2), with a mass tolerance of 0.01 Da. It provides annotations when available.
java -jar /home/omic/biotransformer/biotransformer -k cid -b allHuman -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -s 2 -m "292.0946;304.0946" -t 0.01 -a
"""
}
process ORDERED_SEQUENCE {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/screening", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Simulating an Ordered Sequence of Metabolism:
# This command simulates an ordered sequence of metabolism for compounds in example.csv, starting with two steps of CYP450 oxidation, followed by one step of conjugation. The output is saved in an SDF file (output.sdf).
java -jar /home/omic/biotransformer/biotransformer -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -k pred -q "cyp450:2; phaseII:1"
"""
}
process GET_FINAL_METABOLITES {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/screening", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}.txt"
script:
"""
#!/opt/conda/envs/biotransformer/bin/python
from rdkit import Chem
import numpy as np
import pandas as pd
import requests
#load biotransformet ouput
biotransformer = pd.read_csv('$smiles_csv')
#check if metabolites exist
if biotransformer.shape[0] == 0:
with open('${smiles_csv.simpleName}.txt', 'w') as f:
f.write(f"NO_METABOLITES\\n")
else:
metabolite_id = biotransformer['Metabolite ID']
#get only metabolites that are not precursors for next metabolisam step
last_step_metabolites = biotransformer[[i not in list(biotransformer['Precursor ID']) for i in metabolite_id]]
last_step_metabolites = last_step_metabolites.drop_duplicates()
#get only "active" ones
InChIKey = last_step_metabolites['InChIKey']
InChIKey = pd.unique(InChIKey)
#look if metabolite is in chembl
chembl = []
for i in InChIKey:
curl_commend = f"https://www.ebi.ac.uk/chembl/api/data/molecule/{i}"
c = requests.get(curl_commend)
if c.status_code == 200:
#compund exists in chembl
chembl.append(True)
else:
#compund does not exists in chembl
chembl.append(False)
ChEMBL_bool = pd.DataFrame([InChIKey, chembl]).T.rename({0:'InChIKey',1:'in_ChEMBL'}, axis = 1)
last_step_metabolites = last_step_metabolites.merge(ChEMBL_bool, how='inner', on='InChIKey')
#if in PUBCHEM
last_step_metabolites['in_PUBCHEM'] = ~last_step_metabolites['PUBCHEM_CID'].isna()
##logic
#if metabolite is not in PUBCHEM pass it to next step. We don't know if it's "active"
#has to be in ChEMBL and PUBCHEM to have "activity"
mask = (last_step_metabolites['in_PUBCHEM'] == False) | (np.sum(last_step_metabolites[['in_ChEMBL','in_PUBCHEM']], 1) == 2)
#filtered metabolites
last_step_metabolites = last_step_metabolites[mask]
#convert biotransformer smi to canonical smi and eliminate nonsense structures
metabolite_smi = list(np.unique(last_step_metabolites['SMILES']))
metabolite_smi = [Chem.CanonSmiles(i) for i in metabolite_smi if Chem.MolFromSmiles(i) != None]
#final metabolites
metabolite_smi_filteres = np.array(metabolite_smi)
#save smi
with open('${smiles_csv.simpleName}.txt', 'w') as f:
for n, line in enumerate(metabolite_smi_filteres):
f.write(f"{line}\\tmetabol_{n}\\n")
"""
}

123
digital-trial/main_conplex.nf Normal file
View File

@@ -0,0 +1,123 @@
nextflow.enable.dsl=2
process CONPLEX {
container "${params.container_conplex}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
debug true
maxForks 5
// scratch true //deletes workdir after successful completion
input:
path smi_drug
path smi_metabolite
path mut_fasta
output:
path "*drug_scores.tsv", emit: drug
path "*significant_interactions.tsv", emit: interactions
script:
"""
workdir=`pwd`
#concat mutated and reference fasta files. If it has name with _2 its mutated.
#after test is don retrun this
cat $mut_fasta /home/omic/ConPLex/MANE_referent_transcipt_reference.fasta > \$workdir/all_protein.fasta
### Test
#head -n 100 /home/omic/ConPLex/MANE_referent_transcipt_reference.fasta > \$workdir/test.fasta
#cat $mut_fasta \$workdir/test.fasta > \$workdir/all_protein.fasta
###
. activate conplex-dti
#transform smi for conplex
python3 -c "
import sys
from rdkit import Chem
import numpy as np
import pandas as pd
def converter(drug_csv, outname):
#open file to write drug/matabolite smi
out_file = open(outname + '.txt', 'w')
#load drug csv; only has drug in separate lines
drug_smi_list = np.array(pd.read_csv(drug_csv)['SMILES']).tolist()
#original drugs are anotated with drug_{}
for n, smi in enumerate(drug_smi_list):
out_file.write('{}\\tdrug_{}\\n'.format(smi, n))
out_file.close()
converter('$smi_drug', 'drag')
"
#concatinate drag and metabolites
cat drag.txt $smi_metabolite > \$workdir/smiles.smi
#conplex predicition 1. round
python3 /home/omic/ConPLex/conplex.py --fastas \$workdir/all_protein.fasta --smis \$workdir/smiles.smi --screening_batch_size ${params.screening_batch_size} --outdir \$workdir --split_write_df 'no'
#### this part is use to test all alternative transcripts (this part can be skipped for now, cuz we will use it for tissue specific analysis later)
##get fasta for 2. round transcripts for proteins above threshold
#python3 /home/omic/ConPLex/get_round_2.py --threshold ${params.threshold} --workdir \$workdir --round 1
##conplex all transcipt for protrin above threshold
#python3 /home/omic/ConPLex/conplex.py --fastas \$workdir/round_2.fasta --smis \$workdir/smiles.smi --screening_batch_size ${params.screening_batch_size} --outdir \$workdir --split_write_df 'no'
####
#get data for second run
python3 /home/omic/ConPLex/get_round_2.py --threshold ${params.threshold} --workdir \$workdir --round 2
"""
}
process NETWORK_ENRICHMENT {
container "${params.container_conplex}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
debug true
maxForks 5
input:
path interactions
output:
path "*_network_enrichment.tsv", emit: network_enrichment
path "*_network_interactions.tsv", emit: network_interactions
script:
"""
#!/opt/conda/envs/conplex-dti/bin/python
import pandas as pd
import requests
interaction_data = pd.read_csv('$interactions', sep = '\\t')
interaction_data = interaction_data.sort_values('conplex_score', ascending=False)
#get list of enst above threshold
protein_network_list = '%0d'.join(list(pd.unique(interaction_data[interaction_data['conplex_score'] > ${params.protein_network_threshold}]['transcipt'])))
#get urls
url_network = f'https://string-db.org/api/tsv/network?identifiers={protein_network_list}&species=9606'
url_enrichment = f'https://string-db.org/api/tsv/enrichment?identifiers={protein_network_list}&species=9606'
#get enrichment dataframe
r = requests.get(url_enrichment)
lines = r.text.split('\\n') # pull the text from the response object and split based on new lines
data = [l.split('\\t') for l in lines] # split each line into its components based on tabs
enrichment_df = pd.DataFrame(data[1:-1], columns = data[0]) # convert to dataframe using the first row as the column names; drop empty, final row
#get protein interaction dataframe
r = requests.get(url_network)
lines = r.text.split('\\n') # pull the text from the response object and split based on new lines
data = [l.split('\\t') for l in lines] # split each line into its components based on tabs
# convert to dataframe using the first row as the column names; drop empty, final row
interactions_df = pd.DataFrame(data[1:-1], columns = data[0])
# dataframe with the preferred names of the two proteins and the score of the interaction
#interactions_df = interactions_df[['preferredName_A', 'preferredName_B', 'score']]
#output name
output_name = '$interactions'.split('/')[-1].split('_significant_interactions.tsv')[0]
#save
enrichment_df.to_csv(f'{output_name }_network_enrichment.tsv',sep='\\t')
interactions_df.to_csv(f'{output_name }_network_interactions.tsv',sep='\\t')
"""
}

22
digital-trial/main_tissue.nf Executable file
View File

@@ -0,0 +1,22 @@
nextflow.enable.dsl=2
process TISSUE_DISTRIBUTION {
container "${params.container_tissue}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/tissue_distribution", mode: 'copy'
debug true
input:
path interaction
output:
path "*tissue_distribution.tsv", emit: tissue_dist
script:
"""
. activate tissue
python3 /home/omic/drug_tissue_distribution.py --file_name ${interaction}
"""
}

15
digital-trial/nextflow.config Normal file
View File

@@ -0,0 +1,15 @@
manifest {
name = 'Digital Trial'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/tools/digital-trial.git'
description = 'Digital drug protein interactions'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
}
docker {
enabled = true
temp = 'auto'
}

192
digital-trial/params.json Normal file
View File

@@ -0,0 +1,192 @@
{
"params": {
"// GENERAL PARAMETERS": {},
"outdir": {
"type": "folder",
"description": "Output directory for results",
"default": "/mnt/OmicNAS/private/old/gabe/digital_trials",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": [
"/mnt/OmicNAS/private/old/gabe/digital_trials",
"/path/to/custom/output"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where all pipeline results will be stored"
},
"project_name": {
"type": "string",
"description": "Project identifier",
"default": "test",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.project_name",
"examples": [
"test",
"production",
"drug_metabolism_study"
],
"pattern": ".*",
"validation": {},
"notes": "Identifier for the digital trials project"
},
"containerOptions": {
"type": "string",
"description": "Container runtime options",
"default": "--gpus all --rm -v /mnt:/mnt",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions",
"examples": [
"--gpus all --rm -v /mnt:/mnt",
"--rm -v /data:/data"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for GPU usage and volume mounts"
},
"// BIOTRANSFORMER PARAMETERS": {},
"container_biotransformer": {
"type": "string",
"description": "BioTransformer container image",
"default": "biotransformer:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_biotransformer",
"examples": [
"biotransformer:latest",
"biotransformer:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for BioTransformer module"
},
"ligands": {
"type": "folder",
"description": "Path to input ligands directory",
"default": "/Workspace/next/registry/pipelines/digital_trials/input",
"required": true,
"pipeline_io": "input",
"var_name": "params.ligands",
"examples": [
"/Workspace/next/registry/pipelines/digital_trials/input",
"/path/to/ligands"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing CSV files with ligand data for metabolic transformation"
},
"mode": {
"type": "string",
"description": "BioTransformer operation mode",
"default": "HUMAN",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.mode",
"examples": [
"HUMAN",
"SUPER",
"MASS",
"ORDERED"
],
"pattern": "^(HUMAN|SUPER|MASS|ORDERED)$",
"enum": [
"HUMAN",
"SUPER",
"MASS",
"ORDERED"
],
"validation": {},
"notes": "IMPORTANT: Use HUMAN mode as it's the only fully implemented option that returns expected metabolism to the last step"
},
"// CONPLEX PARAMETERS": {},
"container_conplex": {
"type": "string",
"description": "CONPLEX container image",
"default": "conplex_dig_pat:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_conplex",
"examples": [
"conplex_dig_pat:latest",
"conplex_dig_pat:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for CONPLEX module"
},
"mutated_protein_fasta": {
"type": "folder",
"description": "Path to mutated protein FASTA files directory",
"default": "/Workspace/next/registry/pipelines/digital_trials/input",
"required": true,
"pipeline_io": "input",
"var_name": "params.mutated_protein_fasta",
"examples": [
"/Workspace/next/registry/pipelines/digital_trials/input",
"/path/to/protein/fasta/files"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing FASTA files with mutated protein sequences"
},
"threshold": {
"type": "number",
"description": "Binding affinity threshold for interactions",
"default": 0.7,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.threshold",
"examples": [
0.5,
0.7,
0.9
],
"pattern": "^\\d+(\\.\\d+)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"notes": "Threshold value for determining significant binding interactions"
},
"screening_batch_size": {
"type": "integer",
"description": "Batch size for virtual screening",
"default": 100000,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.screening_batch_size",
"examples": [
10000,
100000,
1000000
],
"pattern": "^\\d+$",
"validation": {
"min": 1
},
"notes": "Batch size for virtual screening (100k is ideal to optimize performance)"
},
"protein_network_threshold": {
"type": "number",
"description": "Threshold for protein network analysis",
"default": 0.95,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.protein_network_threshold",
"examples": [
0.9,
0.95,
0.99
],
"pattern": "^\\d+(\\.\\d+)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"notes": "Threshold value for protein-protein interaction network construction"
}
}
}

61
digital-trial/test.nf Normal file
View File

@@ -0,0 +1,61 @@
nextflow.enable.dsl=2
//BIOTRANSFORMER
params.container_biotransformer = 'biotransformer:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
params.project_name = 'test'
params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
//CONPLEX
params.container_conplex = 'conplex_dig_pat:latest'
params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input'
params.threshold = 0.8 //0.5 //0.7
params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
params.protein_network_threshold = 0.95
//TISSUE DISTRIBUTION
params.container_tissue = 'tissue:latest'
//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX } from './main_conplex.nf'
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
//TISSUE_DISTRIBUTION
include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
workflow {
//BIOTRANSFORMER
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
switch (params.mode) {
case 'SUPER':
SUPER_TRANSFORMER(lig_ch)
break
case 'HUMAN':
HUMAN_TRANSFORMER(lig_ch)
break
case 'MASS':
METABOLITES_BY_MASS(lig_ch)
break
case 'ORDERED':
ORDERED_SEQUENCE(lig_ch)
break
default:
println("Invalid mode specified: ${params.mode}")
}
GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
//CONPLEX
pat_fasta = Channel.fromPath("${params.mutated_protein_fasta}/*.fasta")
CONPLEX(lig_ch, GET_FINAL_METABOLITES.out, pat_fasta)
NETWORK_ENRICHMENT(CONPLEX.out.interactions)
//TISSUE DISTRIBUTION
TISSUE_DISTRIBUTION(CONPLEX.out.interactions)
}

49
digital-trial/test.nf.save Normal file
View File

@@ -0,0 +1,49 @@
nextflow.enable.dsl=2
//BIOTRANSFORMER
params.container_biotransformer = 'biotransformer:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
params.project_name = 'test'
params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
//CONPLEX
params.container_conplex= 'conplex_dig_pat'
params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input/*.fasta'
params.threshold = 0.2 //0.75
params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX } from './main_conplex.nf'
workflow {
//BIOTRANSFORMER
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
switch (params.mode) {
case 'SUPER':
SUPER_TRANSFORMER(lig_ch)
break
case 'HUMAN':
HUMAN_TRANSFORMER(lig_ch)
break
case 'MASS':
METABOLITES_BY_MASS(lig_ch)
break
case 'ORDERED':
ORDERED_SEQUENCE(lig_ch)
break
default:
println("Invalid mode specified: ${params.mode}")
}
GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
//CONPLEX
}

239
digital_patient_extract_metrics.py Normal file
View File

@@ -0,0 +1,239 @@
import pandas as pd
import numpy as np
import argparse
#get data framw with ENST ids and tissue specific expression
human_protein_atlas = '/home/omic/HPA_normal_ihc_data.tsv'
mane = '/home/omic/MANE_all_transcipts.csv'
#extrect enst with hight expression per tissue and match to enst ids
HPA_normal_ihc_data = pd.read_csv(human_protein_atlas, sep = '\t')
MANE_all_transcipts = pd.read_csv(mane)
#change name to merge
HPA_normal_ihc_data = HPA_normal_ihc_data.rename({'Gene':'Ensembl_Gene'}, axis=1)
#merge dfs
HPA_normal_ihc_data = MANE_all_transcipts.merge(HPA_normal_ihc_data, left_on='Ensembl_Gene', right_on='Ensembl_Gene')
#drop not needed colums
HPA_normal_ihc_data = HPA_normal_ihc_data.drop(['Unnamed: 0', 'seq', 'Ensembl_Gene'], axis=1)
#get only hight expressed proteins
HPA_normal_hight = HPA_normal_ihc_data[HPA_normal_ihc_data['Level'] == 'High']
def get_n_metabolites(file):
"""
Get number of metabolites for a drug
input metabolite file from GET_FINAL_METABOLITES
"""
with open(file, 'r') as f:
first_line = f.readline().strip()
if first_line == 'NO_METABOLITES' or first_line == '':
return 0
metabol = pd.read_csv(file, sep = '\t', header=None)
return metabol.shape[0]
def get_conplex_metric(file_drug, file_all_interactions, target):
"""
Get merrics of interest in dataframe and a list of ENTSs with durg/metabolite interactions
with high expression based on Human Protein Atlas
input files from CONPLEX (first for drug interaction only, second for all interaction above threshold)
and traget ids from pipeline input csv file
"""
#drug target interaction
drug_interactions = pd.read_csv(file_drug, sep = '\t')
#drug target protein ents
ensts = target
scors = []
for enst in ensts:
scor = drug_interactions[drug_interactions['Transcript'] == enst]['Score']
scors.append(scor)
# mean_drug_scor = avg(scors)
mean_drug_scor = 0
max_drug_scor = 0
if len(scors) > 0:
mean_drug_scor = pd.concat(scors).mean() # 0 if empty
max_drug_scor = pd.concat(scors).max() # 0 if empty
#drug/metabolite target interaction — only 'transcipt' and 'conplex_score' are
# referenced below (the 'smile' and 'drug/metabolite' columns are the bulk of the
# 5+ GB file). Skipping them cuts memory ~10x and prevents OOM in 5 GB pods.
drug_interactions = pd.read_csv(file_all_interactions, sep = '\t', usecols=['transcipt', 'conplex_score'])
n_significant_int = len(drug_interactions)
# Handle empty DataFrame case
if n_significant_int == 0:
df = pd.DataFrame([max_drug_scor, mean_drug_scor, np.nan, np.nan, 0, 0, 0, 0, np.nan]).T.rename(
{0:'max_drug_scor',1:'mean_drug_scor',2:'max_target_scor',3:'mean_target_scor',
4:'n_significant_int',5:'n_unique_proteins_above_target_interaction',
6:'n_interactions_above_target_interaction',7:'n_enst_with_hight_expression',
8:'mean_scor_with_hight_expression'}, axis = 1)
return df, [], drug_interactions
#drug target protein ents
ensts = target
scors = []
for enst in ensts:
scor = drug_interactions[drug_interactions['transcipt'] == enst]['conplex_score']
scors.append(scor)
mean_target_scor = 0
max_target_scor = 0
if len(scors) > 0:
mean_target_scor = pd.concat(scors).mean() # 0 if empty
max_target_scor = pd.concat(scors).max() # 0 if empty
if np.isnan(max_target_scor):
pass
else:
drug_interactions = drug_interactions[drug_interactions['conplex_score'] >= max_target_scor].sort_values('conplex_score',ascending=False)
n_unique_proteins_above_target_interaction = pd.unique(drug_interactions['transcipt']).shape[0]
n_interactions_above_target_interaction = drug_interactions.shape[0]
uniq_enst = pd.unique(drug_interactions['transcipt'])
#get only ensts with hight expression
uniq_enst_hight = list(set(pd.unique(HPA_normal_hight['transcipt'])).intersection(uniq_enst))
enst_with_hight_expression = len(uniq_enst_hight)
#sort based on a conplex score
drug_interactions = drug_interactions[[i in uniq_enst_hight for i in drug_interactions['transcipt']]]
if len(drug_interactions) > 0:
mean_scor_with_hight_expression = drug_interactions['conplex_score'].mean()
hight_expression_enst_per_drug = pd.unique(drug_interactions['transcipt'])
else:
mean_scor_with_hight_expression = np.nan
hight_expression_enst_per_drug = []
df = pd.DataFrame([max_drug_scor, mean_drug_scor, max_target_scor, mean_target_scor, n_significant_int,n_unique_proteins_above_target_interaction,n_interactions_above_target_interaction,enst_with_hight_expression, mean_scor_with_hight_expression]).T.rename({0:'max_drug_scor',1:'mean_drug_scor',2:'max_target_scor',3:'mean_target_scor',4:'n_significant_int',5:'n_unique_proteins_above_target_interaction',6:'n_interactions_above_target_interaction',7:'n_enst_with_hight_expression',8:'mean_scor_with_hight_expression'}, axis = 1)
return df, hight_expression_enst_per_drug, drug_interactions
#look at tissue interactions specificly
def get_number_of_interacting_prot_per_tissue(names, hight_expression_enst_per_drug, drug_interactions, n_of_interactions = None):
'''
Tissue specific interactions, only for high expressed proteins
input:
names; drug id, list
hight_expression_enst_per_drug; ensts with interaction of interest, make sure if follows names order and enst orderd by importance based on highest conplex score, lisf of list
drug_interactions; significant interactions filtered
n_of_interactions; n proteins to analyse ,default None use all proteins, use when there is no drug target interaction, interger
output:
number and min_max of tissue highly exprest proteins in interaction with a drug/metabolites, pandas df
'''
n_interactions = []
min_max_df = []
list_of_tissue_ids = [['Heart muscle'],\
['Rectum', 'Gallbladder', 'Esophagus', 'Stomach', 'Small intestine', 'Duodenum', 'Colon', 'Salivary gland'],\
['Breast', 'Lactating breast', 'Cervix', 'Fallopian tube', 'Ovary', 'Placenta', 'Endometrium', 'Vagina'],\
['Testis', 'Prostate', 'Epididymis', 'Seminal vesicle'],\
['Liver'],\
['Kidney', 'Urinary bladder'],\
['Cerebral cortex', 'Cerebellum', 'Caudate', 'Hippocampus', 'Hypothalamus', 'Dorsal raphe', 'Choroid plexus', 'Pituitary gland', 'Substantia nigra'],\
['Adrenal gland', 'Pancreas', 'Parathyroid gland', 'Thyroid gland'],\
['Appendix', 'Lymph node', 'Spleen', 'Thymus', 'Tonsil'],\
['Bone marrow'],\
['Bronchus', 'Lung', 'Nasopharynx', 'Oral mucosa'],\
['Eye', 'Retina'],\
['Skeletal muscle', 'Cartilage'],\
['Adipose tissue', 'Hair', 'Skin', 'Smooth muscle', 'Soft tissue', 'Sole of foot']]
list_of_tissue_names = ['heart', 'gasrto_intestin', 'female_tissues', 'male_tissues', 'liver', 'kidney', 'brain', 'endocrine', 'immune',\
'hematopoietic', 'respiratory', 'sensory', 'musculoskeletal', 'others']
for t_id, t_name in zip(list_of_tissue_ids, list_of_tissue_names):
HPA_normal_hight_tis = HPA_normal_hight[[i in t_id for i in HPA_normal_hight['Tissue']]]
tis = [HPA_normal_hight_tis[[i in j[:n_of_interactions] for i in HPA_normal_hight_tis['transcipt']]] for j in hight_expression_enst_per_drug]
tis = [i.drop_duplicates('transcipt') for i in tis]
# Calculate highly expressed proteins once to use in both branches
num_highly_expressed = len(HPA_normal_hight_tis.drop_duplicates('transcipt'))
# Handle empty drug_interactions case
if len(drug_interactions) == 0 or len(tis[0]) == 0:
min_max_df.append(pd.DataFrame([names, [np.nan], [np.nan], [np.nan], [num_highly_expressed], [0.0], [np.nan]])\
.T.rename({0:'Drug_ID',
1:f'max_{t_name}_interaction',
2:f'min_{t_name}_interaction',
3:f'mean_{t_name}_interaction',
4:f'n_high_protein_in_{t_name}',
5:f'share_affected_{t_name}',
6:f'weighted_score_{t_name}'}, axis = 1))
else:
#get max and min conplex sores for tissue specific ents !!! only for one drug ate a time not for a list (n_interactions is for a list)
inter = drug_interactions[drug_interactions['transcipt'].isin(tis[0]['transcipt'])].sort_values('conplex_score', ascending=False)
# Calculate new metrics based on `inter`
num_affected = inter.shape[0]
share_affected = num_affected / num_highly_expressed if num_highly_expressed > 0 else 0.0
mean_score = inter['conplex_score'].mean()
weighted_score = share_affected * mean_score
min_max_df.append(pd.DataFrame([names, [inter['conplex_score'].max()], [inter['conplex_score'].min()], [mean_score], [num_highly_expressed], [share_affected], [weighted_score]])\
.T.rename({0:'Drug_ID',
1:f'max_{t_name}_interaction',
2:f'min_{t_name}_interaction',
3:f'mean_{t_name}_interaction',
4:f'n_high_protein_in_{t_name}',
5:f'share_affected_{t_name}',
6:f'weighted_score_{t_name}'}, axis = 1))
#get number of interactions for tissue specific ents
n_interactions.append(pd.DataFrame([names, [len(i) for i in tis]]).T.rename({0:'Drug_ID',1:f'n_enst_{t_name}_above_target_interaction'}, axis = 1))
#merge interaction data
df_n_interactions = n_interactions[0]
for d in n_interactions[1:]:
df_n_interactions = df_n_interactions.merge(d, on='Drug_ID')
#merge min max data
df_min_max_df = min_max_df[0]
for d in min_max_df[1:]:
df_min_max_df = df_min_max_df.merge(d, on='Drug_ID')
n_interactions = df_n_interactions.merge(df_min_max_df, left_on='Drug_ID', right_on='Drug_ID')
return n_interactions
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Calculate biological metrics.")
parser.add_argument("--metabolites", required=True, help="Path to the metabolites file.")
parser.add_argument("--conplex_all_interactions", required=True, help="Path to the conplex_significant_interaction file.")
parser.add_argument("--conplex_drug", required=True, help="Path to the conplex_significant_interaction_drug_only file.")
parser.add_argument("--target", required=True, help="PATH to file csv with drug targets in ENST formet separated by space.")
args = parser.parse_args()
drug_name = args.metabolites.split('/')[-1].split('_out.txt')[0]
n_metabolites = get_n_metabolites(args.metabolites)
#get target
target = pd.read_csv(args.target, header=None)[2:]
if len(target) == 2:
target = list(target.iloc[-1])
target = target[0].split(' ')
else:
target = []
df_1, target_ents, drug_interactions = get_conplex_metric(args.conplex_drug, args.conplex_all_interactions, target)
#if no target interaction use only 200 unique proteins with highest interactions per tissue
if df_1['max_target_scor'].isna()[0]:
target_interaction = 0
df_2 = get_number_of_interacting_prot_per_tissue([drug_name], [target_ents], drug_interactions, n_of_interactions = 200)
else:
target_interaction = 1
df_2 = get_number_of_interacting_prot_per_tissue([drug_name], [target_ents], drug_interactions)
df = pd.concat([df_2, df_1], axis=1)
df['target_interaction_found'] = target_interaction
df['n_metabolites'] = n_metabolites
df.to_csv(f'{drug_name}_biological_properties.tsv', sep = '\t', index=False)

21
docker-compose.yml Normal file
View File

@@ -0,0 +1,21 @@
version: '3.8'
services:
tissue:
build:
context: .
dockerfile: Dockerfile_tissue
image: harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.1.1
chembl:
build:
context: .
dockerfile: Dockerfile_chembl
image: harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0
network:
build:
context: .
dockerfile: Dockerfile_network
image: harbor.cluster.omic.ai/omic/digitaltrials/network:1.0.0
volumes:
- /data/bugra/digital_trials/work/48/1e78bc2c0d60c8f0e72800d6226604:/workdir
- /data/:/data

67
drug_tissue_distribution.py Normal file
View File

@@ -0,0 +1,67 @@
from pathlib import Path
import argparse
import pandas as pd
import numpy as np
def get_tissue_distribution(file_name):
# Convert to Path object
file_path = Path(file_name)
# Load interaction data — only the 'transcipt' column is referenced downstream
# (the bulk of the file is the 'smile' column we never use). Skipping it cuts
# memory ~30x on metabolite-heavy drugs (11 GB file -> ~400 MB resident).
significant_interactions = pd.read_csv(file_path, sep='\t', usecols=['transcipt'])
# Check if data exists
if len(significant_interactions) == 0:
print(f"No significant interactions found in {file_name}. Creating empty output.")
tissue_per_prot_symbol_pd = pd.DataFrame()
save_name = str(file_path.parent / (file_path.stem.replace('_significant_interactions', '_tissue_distribution') + '.tsv'))
tissue_per_prot_symbol_pd.to_csv(save_name, sep='\t')
print(f"Saved empty tissue distribution to: {save_name}")
return
# Load protein expression per tissue
HPA = pd.read_csv('/home/omic/HPA_normal_ihc_data.tsv', sep='\t')
# Load enst symbol mapping data
MANE_all_transcipts = pd.read_csv('/home/omic/MANE_all_transcipts.csv')
# Filter out tissues with low confidence
HPA = HPA[(HPA['Level'] == 'Medium') | (HPA['Level'] == 'High')]
# Get protein symbols from significant interactions
prot_enst = [i.split('_')[0] for i in significant_interactions['transcipt'].unique()]
# Safely map to symbols, skipping missing ones
prot_symbol = []
for i in prot_enst:
matches = MANE_all_transcipts[MANE_all_transcipts['transcipt'] == i]
if not matches.empty:
prot_symbol.append(matches['symbol'].iloc[0])
else:
print(f"Warning: Transcript {i} not found in MANE mapping. Skipping.")
prot_symbol = pd.unique(prot_symbol)
# Get unique tissues
unique_tissues = HPA['Tissue'].unique()
# Get protein expression per tissue
tissue_per_prot_symbol = [list(HPA[HPA['Gene name'] == i]['Tissue'].unique()) for i in prot_symbol]
# Transform list to array
tissue_per_prot_symbol_array = np.array([[tissue in gene_tissues for tissue in unique_tissues] for gene_tissues in tissue_per_prot_symbol])
tissue_per_prot_symbol_pd = pd.DataFrame(tissue_per_prot_symbol_array, columns=unique_tissues, index=prot_symbol)
# Save
save_name = str(file_path.parent / (file_path.stem.replace('_significant_interactions', '_tissue_distribution') + '.tsv'))
tissue_per_prot_symbol_pd.to_csv(save_name, sep='\t')
print(f"Saved tissue distribution to: {save_name}")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Get tissue distribution from *significant_interactions.tsv.")
parser.add_argument("--file_name", required=True, help="file_name")
args = parser.parse_args()
get_tissue_distribution(args.file_name)

78
get_round_2.py Executable file
View File

@@ -0,0 +1,78 @@
import argparse
import pandas as pd
import numpy as np
import subprocess
from itertools import chain
seq_exist = pd.read_csv('/home/omic/ConPLex/MANE_all_transcipts.csv')
def get_round_2(threshold, workdir, round):
#get output names
#get patient fasta name
fasta_name = subprocess.check_output([f'find {workdir} -name \*_variants_transcript_id_mutations.fasta' ], shell = True)
fasta_name = str(fasta_name).split('/')[-1].split('_variants_transcript_id_mutations.fasta')[0]
#get test drug
drug_name = subprocess.check_output([f'find {workdir} -name \*.csv' ], shell = True)
drug_name = [x for x in str(drug_name).split('/') if "round_1.csv" not in x][-1].split('.csv')[0]
name_out = drug_name + '_' + fasta_name
#get all work dir conplex files
#res_list = subprocess.check_output([f'ls {workdir}/*_results.tsv'], shell = True)
res_list = subprocess.check_output([f'find {workdir} -name \*_results.tsv' ], shell = True)
round_1_score_list = str(res_list).split('\'')[1].split('\\n')[:-1]
#read 1. round
transcipts_1 = [pd.read_csv(i, sep = '\t', header=None).sort_values([2], ascending=False) for i in round_1_score_list]
#get poition of drag interaction vs all metabolites
drug_pos = [[n for n, j in enumerate(list(i[0])) if j[:4] == 'drug'] for i in transcipts_1]
#drug score
drug_0_score = pd.concat([i[i[0] =='drug_0'] for i in transcipts_1]).rename({0:'Drug', 1:'Transcript', 2:'Score'}, axis = 1)
#filter all below threshold
transcipts_1 = [i[i[2] > threshold] for i in transcipts_1]
#save transcipt_conplex above threshold to one file
if round == 2:
inter_import = pd.concat(transcipts_1, ignore_index=True).rename({0:'drug/metabolite',1:'transcipt',2:'conplex_score'},axis = 1)
#add drug
test_smiles = pd.read_csv(f'{workdir}/smiles.smi', sep = '\t', header=None)
smi_ = [test_smiles[test_smiles[1] == i].iloc[0][0] for i in list(inter_import['drug/metabolite'])]
inter_import['smile'] = smi_
inter_import[['drug/metabolite','smile','transcipt','conplex_score']].to_csv(f'{workdir}/{name_out}_significant_interactions.tsv',sep = '\t',index = False)
drug_0_score.to_csv(f'{workdir}/{name_out}_drug_scores.tsv',sep = '\t',index = False)
transcipts_1 = pd.DataFrame([(j.split('/')[-1].split('_results')[0], i.shape[0], i[2].mean(), k[0]) for i,j, k in zip(transcipts_1, round_1_score_list, drug_pos) if i.shape[0] != 0])
#chack if any interaction is is above threshold for first roud
if round == 1:
if transcipts_1.shape == (0,0):
transcipts_1.to_csv(f'{workdir}/round_1.csv', index = False)
with open(f'{workdir}/round_1.fasta', 'w') as f:
f.write("all_data_is_filtered_out\n")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
transcipts_1 = transcipts_1.rename({0:'transcipt_name',1:'number_of_iteracting_compounds', 2:'mean_binding_above_threshold', 3:'drug_position'}, axis='columns')
transcipts_1['if_drug_above_threshold'] = transcipts_1.iloc[:,1] > transcipts_1.iloc[:,3]
#if protein is mutated it has _2 in name, removes it
transcipt_names = [i.split('_')[0] for i in list(transcipts_1['transcipt_name'])]
transcipts_1['protein_name'] = [[seq_exist[seq_exist['transcipt'] == i].iloc[0]['symbol']][0] for i in transcipt_names]
#save data on first round
transcipts_1.to_csv(f'{workdir}/round_{round}.csv', index = False)
#get fasta for second round
if round == 1:
#get all transcipts of proteins above threshold
name_2_filttered = list(transcipts_1['protein_name'])
transcipts_2 = [list(seq_exist[seq_exist['symbol'] == i]['transcipt']) for i in name_2_filttered]
transcipts_2 = list(chain(*transcipts_2))
transcipts_2 = list(np.unique((transcipts_2)))
#filter out transcripts already ran through complex
transcipts_2 = list(np.array(transcipts_2)[[i not in list(transcipts_1['transcipt_name']) for i in transcipts_2]])
fasta_new = [['>'+i, seq_exist[seq_exist['transcipt'] == i]['seq'].iloc[0]] for i in transcipts_2]
fasta_new = list(chain(*fasta_new))
#write fasta to run
with open(f'{workdir}/round_2.fasta', 'w') as f:
for line in fasta_new:
f.write(f"{line}\n")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--threshold", required=True, type=float, help="Threshold for 1. round.of conplex scores")
parser.add_argument("--workdir", required=True, help="workdir")
parser.add_argument("--round", required=True, type=int, help="Round 1 or 2")
args = parser.parse_args()
get_round_2(args.threshold, args.workdir, args.round)

15
k8s/README.md Normal file
View File

@@ -0,0 +1,15 @@
# access the current workspace
kubectl exec -it -n bioinformatics $(kubectl get pod -l app=digital-trials-nextflow -n bioinformatics | grep Run | awk '{ print $1 }') -- bash
nextflow run main.nf -profile k8s
# DEPRECATE: cleanup error pods in bioinformatics
kubectl get pod -n bioinformatics | grep -E "Pending|Error" | awk '{print $1}' | xargs -P 10 -I {} kubectl delete pod -n bioinformatics {}
# sync data (/data/bugra/similarity-search/utility/vec_db/nf_fingerptint) from node to workspace
kubectl delete -f k8s/job-copy-node-to-pvc.yaml; kubectl apply -f k8s/job-copy-node-to-pvc.yaml
# run the actual nextflow jobs
kubectl apply -f k8s/job-nextflow-digital-trials.yaml
# [WARNING] destroy the curent nextflow job
kubectl delete -f k8s/job-nextflow-digital-trials.yaml

73
k8s/deployment-worksplace.yaml Normal file
View File

@@ -0,0 +1,73 @@
apiVersion: apps/v1
kind: Deployment
metadata:
name: digital-trials-nextflow
namespace: bioinformatics
spec:
progressDeadlineSeconds: 600
replicas: 1
revisionHistoryLimit: 10
selector:
matchLabels:
app: digital-trials-nextflow
strategy:
rollingUpdate:
maxSurge: 25%
maxUnavailable: 25%
type: RollingUpdate
template:
metadata:
creationTimestamp: null
labels:
app: digital-trials-nextflow
spec:
containers:
- command:
- sleep
- infinity
image: nextflow/nextflow:25.04.6
imagePullPolicy: IfNotPresent
name: nextflow
workingDir: /mnt/dreamdock-data/digital_trials
resources:
limits:
cpu: "2"
memory: 4Gi
requests:
cpu: "1"
memory: 2Gi
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /mnt/ZINC-22
name: zinc-22-volume
- mountPath: /mnt/dreamdock-data
name: dreamdock-volume
dnsPolicy: ClusterFirst
restartPolicy: Always
schedulerName: default-scheduler
securityContext: {}
serviceAccount: nextflow-sa
serviceAccountName: nextflow-sa
terminationGracePeriodSeconds: 30
volumes:
- name: zinc-22-volume
hostPath:
path: /mnt/ZINC-22
type: Directory
- name: dreamdock-volume
persistentVolumeClaim:
claimName: dreamdock-data
# ---
# apiVersion: v1
# kind: PersistentVolumeClaim
# metadata:
# name: digital-trials-data
# namespace: bioinformatics
# spec:
# accessModes:
# - ReadWriteMany
# resources:
# requests:
# storage: 6000Gi
# storageClassName: truenas-nfs

54
k8s/job-copy-node-to-pvc.yaml Normal file
View File

@@ -0,0 +1,54 @@
apiVersion: batch/v1
kind: Job
metadata:
name: job-data-copy-digital-trials-node-to-pvc
namespace: bioinformatics
spec:
backoffLimit: 6
completionMode: NonIndexed
completions: 1
manualSelector: false
parallelism: 1
suspend: false
template:
spec:
containers:
- args:
- |
apk add --no-cache rsync
mkdir -p /target
rsync -av --exclude .git/ --exclude .git-old/ --exclude work/ /source/ /target/digital_trials/
command:
- /bin/sh
- -c
image: alpine
imagePullPolicy: Always
name: data-copy
resources: {}
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /source
name: k8s-node
- mountPath: /target
name: pvc-volume
dnsPolicy: ClusterFirst
nodeSelector:
kubernetes.io/hostname: k8s-node23
restartPolicy: Never
schedulerName: default-scheduler
securityContext: {}
terminationGracePeriodSeconds: 30
tolerations:
- effect: NoExecute
key: omic-app
operator: Equal
value: similarity-search
volumes:
- name: pvc-volume
persistentVolumeClaim:
claimName: dreamdock-data
- hostPath:
path: /data/bugra/digital_trials ## CHANGE ME
type: ""
name: k8s-node

52
k8s/job-nextflow-digital-trials.yaml Normal file
View File

@@ -0,0 +1,52 @@
apiVersion: batch/v1
kind: Job
metadata:
name: job-nextflow-digital-trials
namespace: bioinformatics
spec:
backoffLimit: 1
completionMode: NonIndexed
completions: 1
manualSelector: false
parallelism: 1
podReplacementPolicy: TerminatingOrFailed
suspend: false
template:
spec:
containers:
- command:
- /bin/bash
- -c
- cd /mnt/dreamdock-data/digital_trials && nextflow run main.nf -profile k8s ## CHANGE ME
image: nextflow/nextflow:25.04.6
imagePullPolicy: IfNotPresent
name: nextflow
resources:
limits:
cpu: "4"
memory: 8Gi
requests:
cpu: "2"
memory: 4Gi
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts: ## CHANGE ME
- mountPath: /mnt/ZINC-22
name: zinc-22-volume
- mountPath: /mnt/dreamdock-data
name: dreamdock-volume
dnsPolicy: ClusterFirst
restartPolicy: Never
schedulerName: default-scheduler
securityContext: {}
serviceAccount: nextflow-sa
serviceAccountName: nextflow-sa
terminationGracePeriodSeconds: 30
volumes: ## CHANGE ME
- name: zinc-22-volume
hostPath:
path: /mnt/ZINC-22
type: Directory
- name: dreamdock-volume
persistentVolumeClaim:
claimName: dreamdock-data

169
main.nf Normal file
View File

@@ -0,0 +1,169 @@
nextflow.enable.dsl=2
// params.container_biotransformer = 'harbor.cluster.omic.ai/omic/digitaltrials/biotransformer:latest'
// params.container_conplex = 'harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat:latest'
// params.container_tissue = 'harbor.cluster.omic.ai/omic/digitaltrials/tissue:latest'
// params.container_preprocess = 'harbor.cluster.omic.ai/omic/metabolite-screen:project'
// params.container_mass_screen = 'harbor.cluster.omic.ai/omic/metabolite-screen:adaptive'
// params.container_chembl = 'harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0'
params.container_biotransformer = 'harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5'
params.container_conplex = 'harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3'
params.container_tissue = 'harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.1.2'
params.container_preprocess = 'harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17'
params.container_mass_screen = 'harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.2.0'
params.container_chembl = 'harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0'
params.containerOptions = '--rm' // '--gpus all --rm -v /mnt:/mnt'
//BIOTRANSFORMER
params.project_name = 'test'
//params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
params.bt_initial_memory = 5 // GB - starting memory for biotransformer
params.bt_growth_memory = 15 // GB - additional memory per retry
params.bt_max_retries = 10
params.bt_fail_action = 'ignore' // 'terminate' or 'ignore'
params.bt_max_forks = 0 // 0 = unlimited, set to N to limit concurrency
//CONPLEX
params.keep_enst = 'false' //'true' //'false' //to keep individual protein data created by conplex step
params.conplex_initial_memory = 5 // GB - starting memory for conplex
params.conplex_growth_memory = 15 // GB - additional memory per retry
params.conplex_max_retries = 1
params.conplex_fail_action = 'ignore' // 'terminate' or 'ignore'
// params.mutated_protein_csv = '/Workspace/next/registry/pipelines/digital_trials/MANE_all_transcipts.csv'
params.threshold = 0.65 //0.65 //0.8 //0.5 //0.7
// params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
params.protein_network_threshold = 0.65 //0.65 //threshold for stirng input
// NETWORK_ENRICHMENT (string-db) — Python-level urllib3 Retry handles 429/5xx blips first
// so most rate-limit failures are absorbed without spawning a Nextflow retry workdir.
params.string_max_forks = 5 // 0 = unlimited; cap below string-db's ~10 req/s throttle
params.string_max_retries = 1 // Nextflow-level fallback retries (kept low — Python retries are the primary defense)
params.string_fail_action = 'ignore' // 'terminate' or 'ignore' after max retries exhausted
params.string_initial_memory = 1 // GB - starting memory; the script reads only transcipt+conplex_score columns
params.string_growth_memory = 2 // GB - additional memory per retry attempt
// TISSUE_DISTRIBUTION + BIO_METRICS (tissue container) — both scripts now use
// usecols= on significant_interactions.tsv so a 5+ GB input only loads the
// 'transcipt' (and 'conplex_score' for BIO_METRICS) column.
params.tissue_initial_memory = 5 // GB
params.tissue_growth_memory = 5 // GB per retry attempt
params.tissue_max_retries = 2
params.tissue_fail_action = 'ignore'
params.bio_initial_memory = 5 // GB
params.bio_growth_memory = 5 // GB per retry attempt
params.bio_max_retries = 2
params.bio_fail_action = 'ignore'
//TISSUE DISTRIBUTION / BIO PROP
// ========================================= ALL RELEVANT FILEPATHS IN THIS SECTION ===================================================
// Defaults below are the PVC mount paths used for local/k8s execution. WES overrides
// ligands/outdir via experiment_params (it translates s3:// URIs to PVC mount paths).
params.outdir = '/omic/eureka/digital-trial/output'
// Ligand CSVs staged in the eureka workspace (s3://omic/eureka/digital-trial/input/ligands/)
params.ligands = '/omic/eureka/digital-trial/input/ligands'
// Intentionally empty: no *.fasta here means PREPROCESS_PROTEIN is never scheduled and
// the pipeline screens against the prebuilt protein_zarr below. Do NOT point this at a
// directory containing .fasta files — params.container_preprocess is pinned to a digest
// that no longer exists in Harbor, so the process would fail on image pull.
params.mutated_protein_fasta = '/mnt/dreamdock-data/digital_trials/input/blank'
// Prebuilt reference data on the dreamdock-data PVC (verified present on k8s-node23)
params.protein_zarr = '/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr' // 7.5 MB
params.chembl_db = '/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db' // 9.2 GB
// =====================================================================================================================================
//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
// include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES_STATIC } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX as CONPLEX_ALL } from './main_conplex.nf'
include { PREPROCESS_PROTEIN } from './main_conplex.nf'
include { MERGE_DRUG } from './main_conplex.nf'
include { MERGE_INTERACTIONS } from './main_conplex.nf'
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
//TISSUE_DISTRIBUTION / BIO_PROP
include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
include { BIO_METRICS } from './main_tissue.nf'
workflow {
//BIOTRANSFORMER
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
switch (params.mode) {
case 'SUPER':
SUPER_TRANSFORMER(lig_ch)
break
case 'HUMAN':
HUMAN_TRANSFORMER(lig_ch)
break
case 'MASS':
METABOLITES_BY_MASS(lig_ch)
break
case 'ORDERED':
ORDERED_SEQUENCE(lig_ch)
break
default:
println("Invalid mode specified: ${params.mode}")
}
chembl_ch = Channel.fromPath(params.chembl_db).collect()
// GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out) // TODO: LOCALIZE
GET_FINAL_METABOLITES_STATIC(HUMAN_TRANSFORMER.out, chembl_ch)
//CONPLEX
protein_fasta = Channel
.fromPath("${params.mutated_protein_fasta}/*.fasta")
.collect()
// protein_csv = file(params.mutated_protein_csv)
protein_zarr = PREPROCESS_PROTEIN(protein_fasta).collect().map { it[0] }
pre_protein_zarr = Channel.fromPath(params.protein_zarr)
// Merge both zarr channels into a single list
merged_zarr = protein_zarr.concat(pre_protein_zarr).collect()
lig_with_id = lig_ch.map { csv ->
[csv.simpleName, csv]
}
metabolite_with_id = GET_FINAL_METABOLITES_STATIC.out.map { txt ->
def name = txt.simpleName.replaceAll(/_out$/, '')
[name, txt]
}
// Join on the identifier and remove it
matched_ch = lig_with_id
.join(metabolite_with_id)
// .map { id, ligand, metabolite -> [ligand, metabolite] }
// DEBUG_MATCH(matched_ch, merged_zarr)
CONPLEX_ALL(matched_ch, merged_zarr)
conplex_drug_ch = CONPLEX_ALL.out.map { id, drug, interactions -> drug }
conplex_interactions_ch = CONPLEX_ALL.out.map { id, drug, interactions -> interactions }
NETWORK_ENRICHMENT(conplex_interactions_ch) // TODO: Localize this (use human only)
//TISSUE DISTRIBUTION
TISSUE_DISTRIBUTION(conplex_interactions_ch)
biometric_ch = matched_ch.join(CONPLEX_ALL.out)
// BIO_METRICS(GET_FINAL_METABOLITES.out,conplex_interactions_ch,conplex_drug_ch,lig_ch)
BIO_METRICS(biometric_ch)
}

392
main_biotransformer.nf Executable file
View File

@@ -0,0 +1,392 @@
nextflow.enable.dsl=2
process SUPER_TRANSFORMER {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Predicting Biotransformation Using the Human Super Transformer:
# This command predicts the biotransformation of molecules from an SDF input (example.csv) using the human super transformer (superbio) and annotates the metabolites with names and database IDs (from PubChem).
java -jar /home/omic/biotransformer/biotransformer -k pred -b superbio -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -a
"""
}
process HUMAN_TRANSFORMER {
memory { params.bt_initial_memory.toFloat().GB + (task.attempt - 1) * params.bt_growth_memory.toFloat().GB }
errorStrategy { task.attempt <= params.bt_max_retries.toInteger() ? 'retry' : params.bt_fail_action }
maxRetries params.bt_max_retries.toInteger()
maxForks params.bt_max_forks.toInteger() ?: null
container "${params.container_biotransformer}"
// containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/1_biotransformer", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
// maxForks 5
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
set -e
workdir=\$(pwd)
cd /home/omic/biotransformer
# Function to get available memory percentage
get_available_mem_percent() {
free | awk '/Mem:/ {print int(\$7/\$2 * 100)}'
}
# Function to log memory usage
log_memory() {
local pid=\$1
echo "MEMLOG: Timestamp,BioTransformer Memory (MB),Available System Memory (%)" >&2
while kill -0 \$pid 2>/dev/null; do
local biotrans_mem=\$(ps -o rss= -p \$pid | awk '{print \$1/1024}')
local avail_mem=\$(get_available_mem_percent)
echo "MEMLOG: \$(date '+%Y-%m-%d %H:%M:%S'),\$biotrans_mem,\$avail_mem" >&2
if [ \$avail_mem -lt 5 ]; then
echo "MEMLOG: Available memory below 5%. Terminating process." >&2
kill -15 \$pid
wait \$pid
echo 'PROCESS TERMINATED DUE TO LOW MEMORY' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
exit 1
fi
sleep 1800 # Sleep for 30 minutes
done
}
# Calculate max Java heap size (90% of available memory)
# max_heap=\$(free -g | awk '/Mem:/ {print int(\$7 * 0.9)}')
#remove unnecessary data to run biotransformer
head -n 2 "\$workdir/${smiles_csv.simpleName}.csv" > "\$workdir/${smiles_csv.simpleName}_run.csv"
get_container_mem_bytes() {
if [ -f /sys/fs/cgroup/memory/memory.limit_in_bytes ]; then
cat /sys/fs/cgroup/memory/memory.limit_in_bytes
elif [ -f /sys/fs/cgroup/memory.max ]; then
# cgroup v2; "max" means no limit
val=\$(cat /sys/fs/cgroup/memory.max)
if [ "\$val" = "max" ]; then
# fall back to host MemTotal
awk '/MemTotal:/ {print \$2 * 1024}' /proc/meminfo
else
echo "\$val"
fi
else
# fallback to host MemTotal
awk '/MemTotal:/ {print \$2 * 1024}' /proc/meminfo
fi
}
container_mem_bytes=\$(get_container_mem_bytes)
# 95% of container memory, in MB (integer)
heap_mb=\$(awk -v m="\$container_mem_bytes" 'BEGIN { printf "%d", (m*0.95)/(1024*1024) }')
echo "Using Java heap: \${heap_mb}m (95% of container limit)" >&2
java -Xmx"\${heap_mb}m" -jar /home/omic/biotransformer/biotransformer \
-a -k pred -b superbio \
-isdf "\$workdir/${smiles_csv.simpleName}_run.csv" \
-ocsv "\${workdir}/${smiles_csv.simpleName}_out.csv" \
-osdf "\${workdir}/${smiles_csv.simpleName}.sdf" \
-s 100
biotrans_pid=\$!
# Start memory logging in the background
log_memory \$biotrans_pid &
log_pid=\$!
# Wait for the biotransformer process to finish
wait \$biotrans_pid
status=\$?
# Stop the logging process
kill \$log_pid 2>/dev/null || true
if [ ! -s "\${workdir}/${smiles_csv.simpleName}_out.csv" ]; then
if [ \$status -ne 0 ] && [ ! -f "\${workdir}/${smiles_csv.simpleName}_out.csv" ]; then
echo 'PROCESS FAILED' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
else
echo 'NO METABOLITES' > "\${workdir}/${smiles_csv.simpleName}_out.csv"
fi
fi
"""
}
process METABOLITES_BY_MASS {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/graphs", mode: 'copy'
debug true
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Identifying Metabolites with Specific Masses:
# This command identifies all human metabolites of compounds in example.csv with masses 292.0946 Da and 304.0946 Da (max depth = 2), with a mass tolerance of 0.01 Da. It provides annotations when available.
java -jar /home/omic/biotransformer/biotransformer -k cid -b allHuman -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -s 2 -m "292.0946;304.0946" -t 0.01 -a
"""
}
process ORDERED_SEQUENCE {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/screening", mode: 'copy'
debug true
errorStrategy 'ignore'
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}_out.csv"
script:
"""
#!/bin/bash
workdir=`pwd`
cd /home/omic/biotransformer
## Simulating an Ordered Sequence of Metabolism:
# This command simulates an ordered sequence of metabolism for compounds in example.csv, starting with two steps of CYP450 oxidation, followed by one step of conjugation. The output is saved in an SDF file (output.sdf).
java -jar /home/omic/biotransformer/biotransformer -isdf \$workdir/${smiles_csv.simpleName}.csv -ocsv \${workdir}/${smiles_csv.simpleName}_out.csv -osdf \${workdir}/${smiles_csv.simpleName}.sdf -k pred -q "cyp450:2; phaseII:1"
"""
}
process GET_FINAL_METABOLITES {
container "${params.container_biotransformer}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/screening", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
// maxForks 1
// errorStrategy 'ignore'
errorStrategy { task.attempt <= 10 ? 'retry' : 'ignore' }
maxRetries 10
input:
path smiles_csv
output:
path "${smiles_csv.simpleName}.txt"
script:
"""
#!/opt/conda/envs/biotransformer/bin/python
from rdkit import Chem
import numpy as np
import pandas as pd
import requests
#load biotransformet ouput
biotransformer = pd.read_csv('$smiles_csv')
#check if metabolites exist
if biotransformer.shape[0] == 0:
with open('${smiles_csv.simpleName}.txt', 'w') as f:
f.write(f"NO_METABOLITES\\n")
else:
metabolite_id = biotransformer['Metabolite ID']
#get only metabolites that are not precursors for next metabolisam step
last_step_metabolites = biotransformer[[i not in list(biotransformer['Precursor ID']) for i in metabolite_id]]
last_step_metabolites = last_step_metabolites.drop_duplicates()
#get only "active" ones
InChIKey = last_step_metabolites['InChIKey']
InChIKey = pd.unique(InChIKey)
#look if metabolite is in chembl
chembl = []
for i in InChIKey:
curl_commend = f"https://www.ebi.ac.uk/chembl/api/data/molecule/{i}"
c = requests.get(curl_commend)
if c.status_code == 200:
#compund exists in chembl
chembl.append(True)
else:
#compund does not exists in chembl
chembl.append(False)
ChEMBL_bool = pd.DataFrame([InChIKey, chembl]).T.rename({0:'InChIKey',1:'in_ChEMBL'}, axis = 1)
last_step_metabolites = last_step_metabolites.merge(ChEMBL_bool, how='inner', on='InChIKey')
#if in PUBCHEM
last_step_metabolites['in_PUBCHEM'] = ~last_step_metabolites['PUBCHEM_CID'].isna()
##logic
#if metabolite is not in PUBCHEM pass it to next step. We don't know if it's "active"
#has to be in ChEMBL and PUBCHEM to have "activity"
mask = (last_step_metabolites['in_PUBCHEM'] == False) | (np.sum(last_step_metabolites[['in_ChEMBL','in_PUBCHEM']], 1) == 2)
#filtered metabolites
last_step_metabolites = last_step_metabolites[mask]
#check for empty smile positions
last_step_metabolites = last_step_metabolites.reset_index()
if last_step_metabolites['SMILES'].isnull().any():
for i in range(len(last_step_metabolites)):
if pd.isna(last_step_metabolites.at[i, 'SMILES']):
last_step_metabolites.at[i, 'SMILES'] = Chem.MolToSmiles(Chem.MolFromInchi(last_step_metabolites.at[i, 'InChI']))
#convert biotransformer smi to canonical smi and eliminate nonsense structures
metabolite_smi = list(np.unique(last_step_metabolites['SMILES']))
metabolite_smi = [Chem.CanonSmiles(i) for i in metabolite_smi if Chem.MolFromSmiles(i) != None]
#final metabolites
metabolite_smi_filteres = np.array(metabolite_smi)
#save smi
with open('${smiles_csv.simpleName}.txt', 'w') as f:
if len(metabolite_smi_filteres) == 0:
f.write(f"NO_METABOLITES\\n")
else:
for n, line in enumerate(metabolite_smi_filteres):
f.write(f"{line}\\tmetabol_{n}\\n")
"""
}
process GET_FINAL_METABOLITES_STATIC {
memory 1.GB
container "${params.container_chembl}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/1b_final_metabolites", mode: 'copy'
errorStrategy { task.attempt <= 10 ? 'retry' : 'ignore' }
maxRetries 10
input:
path smiles_csv
path chembl_db // Add ChEMBL SQLite database as input
output:
path "${smiles_csv.simpleName}.txt"
script:
"""
#!/opt/conda/bin/python
from rdkit import Chem
import numpy as np
import pandas as pd
import sqlite3
# Connect to ChEMBL database
conn = sqlite3.connect('file:$chembl_db?mode=ro&immutable=1', uri=True)
# conn = sqlite3.connect('$chembl_db')
cursor = conn.cursor()
# Load biotransformer output
biotransformer = pd.read_csv('$smiles_csv')
# Check if metabolites exist
if biotransformer.shape[0] == 0:
with open('${smiles_csv.simpleName}.txt', 'w') as f:
f.write(f"NO_METABOLITES\\n")
else:
# metabolite_id = biotransformer['Metabolite ID']
# # Get only metabolites that are not precursors for next metabolism step
# last_step_metabolites = biotransformer[[i not in list(biotransformer['Precursor ID']) for i in metabolite_id]]
# last_step_metabolites = last_step_metabolites.drop_duplicates()
# Get metabolite IDs that are NOT precursors for other metabolites
metabolite_id = biotransformer['Metabolite ID']
precursor_ids = set(biotransformer['Precursor ID'].dropna()) # Remove NaN values
final_metabolite_mask = ~metabolite_id.isin(precursor_ids)
# Filter to get only final metabolites
last_step_metabolites = biotransformer[final_metabolite_mask].copy()
last_step_metabolites = last_step_metabolites.drop_duplicates()
# Get only "active" ones
InChIKey = last_step_metabolites['InChIKey']
InChIKey = pd.unique(InChIKey)
# Look if metabolite is in ChEMBL using local database
chembl = []
for inchikey in InChIKey:
# Query ChEMBL SQLite database for the InChIKey
# The standard InChIKey is stored in COMPOUND_STRUCTURES table
cursor.execute(\"""
SELECT COUNT(*)
FROM COMPOUND_STRUCTURES
WHERE STANDARD_INCHI_KEY = ?
LIMIT 1
\""", (inchikey,))
result = cursor.fetchone()
chembl.append(result[0] > 0)
# ChEMBL_bool = pd.DataFrame([InChIKey, chembl]).T.rename({0:'InChIKey',1:'in_ChEMBL'}, axis=1)
ChEMBL_bool = pd.DataFrame({
'InChIKey': InChIKey,
'in_ChEMBL': chembl
})
last_step_metabolites = last_step_metabolites.merge(ChEMBL_bool, how='inner', on='InChIKey')
# If in PUBCHEM
last_step_metabolites['in_PUBCHEM'] = ~last_step_metabolites['PUBCHEM_CID'].isna()
# Logic
# If metabolite is not in PUBCHEM pass it to next step. We don't know if it's "active"
# Has to be in ChEMBL and PUBCHEM to have "activity"
mask = (last_step_metabolites['in_PUBCHEM'] == False) | (np.sum(last_step_metabolites[['in_ChEMBL','in_PUBCHEM']], 1) == 2)
# Filtered metabolites
last_step_metabolites = last_step_metabolites[mask]
# Check for empty smile positions
last_step_metabolites = last_step_metabolites.reset_index()
if last_step_metabolites['SMILES'].isnull().any():
for i in range(len(last_step_metabolites)):
if pd.isna(last_step_metabolites.at[i, 'SMILES']):
last_step_metabolites.at[i, 'SMILES'] = Chem.MolToSmiles(Chem.MolFromInchi(last_step_metabolites.at[i, 'InChI']))
# Convert biotransformer smi to canonical smi and eliminate nonsense structures
metabolite_smi = list(np.unique(last_step_metabolites['SMILES']))
metabolite_smi = [Chem.CanonSmiles(i) for i in metabolite_smi if Chem.MolFromSmiles(i) != None]
# Final metabolites
metabolite_smi_filteres = np.array(metabolite_smi)
# Save smi
with open('${smiles_csv.simpleName}.txt', 'w') as f:
if len(metabolite_smi_filteres) == 0:
f.write(f"NO_METABOLITES\\n")
else:
for n, line in enumerate(metabolite_smi_filteres):
f.write(f"{line}\\tmetabol_{n}\\n")
# Close database connection
conn.close()
"""
}

239
main_conplex.nf Normal file
View File

@@ -0,0 +1,239 @@
#!/usr/bin/env nextflow
process CONPLEX {
//debug true
publishDir "${params.outdir}/${params.project_name}/2_conplex", mode: 'copy'
memory { params.conplex_initial_memory.toInteger().GB + (task.attempt - 1) * params.conplex_growth_memory.toInteger().GB }
errorStrategy { task.attempt <= params.conplex_max_retries.toInteger() ? 'retry' : params.conplex_fail_action }
maxRetries params.conplex_max_retries.toInteger()
container "${params.container_mass_screen}"
// containerOptions "--rm --gpus all"
// maxForks 1
// errorStrategy 'ignore'
afterScript "if [[ ${params.keep_enst} == 'false' ]]; then find . -name '*_results.zarr' -type d -exec rm -rf {} + 2>/dev/null || true; fi"
input:
tuple(
val( id ),
path( input_drug, arity: '1') , // CSV file with SMILES column
path( input_metabol, arity: '1') // TSV file with SMILES and metabolite IDs
)
path input_zarr, arity: '1..*' // ZARR DB holding all the protein vectors and their names
output:
tuple(
val ( id ),
path( "*drug_scores.tsv"),
path( "*significant_interactions.tsv")
)
script:
"""
set -e
# Set up trap to clean up on any exit (success, failure, or signal)
if [[ ${params.keep_enst} == 'false' ]]; then
trap 'find \$PWD -name "*_results.zarr" -type d -exec rm -rf {} + 2>/dev/null || true' EXIT
fi
#remove unnecessary data to run conplex
head -n 2 ${input_drug} > run.csv
# Convert drug CSV and metabolite TSV to smiles.smi format
python /app/convert.py run.csv ${input_metabol} -o smiles.smi
# Run screening for each zarr database
for zarr_dir in ${input_zarr}; do
python /app/screen.py -i smiles.smi -z "\${zarr_dir}"
done
# Process results and generate final outputs
python /app/get_round_2.py --threshold ${params.threshold} --workdir \$PWD --round 2 --drug-csv ${input_drug}
"""
}
process MERGE_DRUG {
//debug true
memory '10 GB'
container "${params.container_mass_screen}"
// maxForks 1
// errorStrategy 'ignore'
input:
path 'inputs/drug_*.tsv', arity: '1..*'
output:
path "patient_0_drug_scores.tsv"
script:
"""
#!/opt/conda/bin/python
import pandas as pd
from pathlib import Path
inputs_dir = Path("inputs")
tsv_files = sorted(inputs_dir.glob("drug_*.tsv"))
dfs = [pd.read_csv(f, sep="\\t") for f in tsv_files]
df_out = pd.concat(dfs, ignore_index=True)
df_out.to_csv("patient_0_drug_scores.tsv", sep="\\t", index=False)
"""
}
process MERGE_INTERACTIONS {
//debug true
memory '10 GB'
container "${params.container_mass_screen}"
// maxForks 1
// errorStrategy 'ignore'
input:
path 'inputs/interaction_*.tsv'
output:
path "patient_0_significant_interactions.tsv"
script:
"""
#!/opt/conda/bin/python
import pandas as pd
from pathlib import Path
inputs_dir = Path("inputs")
tsv_files = sorted(inputs_dir.glob("interaction_*.tsv"))
dfs = [pd.read_csv(f, sep="\\t") for f in tsv_files]
df_out = pd.concat(dfs, ignore_index=True)
df_out.to_csv("patient_0_significant_interactions.tsv", sep="\\t", index=False)
"""
}
process NETWORK_ENRICHMENT {
memory { params.string_initial_memory.toInteger().GB + (task.attempt - 1) * params.string_growth_memory.toInteger().GB }
container "${params.container_conplex}"
// containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/3_string", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
maxForks params.string_max_forks.toInteger() ?: null
errorStrategy { task.attempt <= params.string_max_retries.toInteger() ? 'retry' : params.string_fail_action }
maxRetries params.string_max_retries.toInteger()
input:
path interactions
output:
path "*_network_enrichment.tsv", emit: network_enrichment
path "*_network_interactions.tsv", emit: network_interactions
script:
"""
#!/opt/conda/envs/conplex-dti/bin/python
import sys
import pandas as pd
import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry
# Read ONLY the columns we use. The 'smile' column in significant_interactions.tsv
# is the bulk of the file (long SMILES strings × millions of rows for metabolite-heavy
# drugs → ~2 GB on disk), and we never reference it here. Dropping it on read cuts
# the in-memory DataFrame from ~2 GB to ~350 MB on worst-case drugs and prevents OOM.
interaction_data = pd.read_csv('$interactions', sep='\\t', usecols=['transcipt', 'conplex_score'])
interaction_data = interaction_data.sort_values('conplex_score', ascending=False)
# string-db accepts at most 450 identifiers per call.
interaction_data = interaction_data.drop_duplicates('transcipt')
if interaction_data.shape[0] > 450:
interaction_data = interaction_data.iloc[:450]
proteins = list(pd.unique(
interaction_data[interaction_data['conplex_score'] > ${params.protein_network_threshold}]['transcipt']
))
output_name = '$interactions'.split('/')[-1].split('_significant_interactions.tsv')[0]
# Empty-identifier early exit: nothing to enrich; write empty outputs so the
# task succeeds without hitting string-db (which would otherwise return an
# error for an empty identifier list and trip a Nextflow retry).
if not proteins:
print(f"NETWORK_ENRICHMENT: no proteins above threshold for {output_name}", flush=True)
pd.DataFrame().to_csv(f'{output_name}_network_enrichment.tsv', sep='\\t')
pd.DataFrame().to_csv(f'{output_name}_network_interactions.tsv', sep='\\t')
sys.exit(0)
# urllib3 Retry handles 429 / 5xx / connection blips transparently at the
# adapter layer — no exception reaches user code, and Nextflow does not see a
# task failure. backoff_factor=2 produces delays 2,4,8,16,32 s (capped at
# Retry.BACKOFF_MAX), respecting any Retry-After header string-db sends.
# This absorbs the common rate-limit case WITHOUT spawning a fresh workdir,
# which would just get throttled the same way.
session = requests.Session()
session.mount('https://', HTTPAdapter(max_retries=Retry(
total=5,
backoff_factor=2,
status_forcelist=[429, 500, 502, 503, 504],
)))
def fetch(url, kind):
r = session.get(url, timeout=60)
r.raise_for_status()
if not r.text.strip():
raise RuntimeError(f"{kind}: 200 but empty body from string-db")
lines = r.text.split('\\n')
data = [l.split('\\t') for l in lines]
if not data or not data[0]:
raise RuntimeError(f"{kind}: malformed response (no header row)")
return pd.DataFrame(data[1:-1], columns=data[0])
protein_network_list = '%0d'.join(proteins)
url_network = f'https://string-db.org/api/tsv/network?identifiers={protein_network_list}&species=9606'
url_enrichment = f'https://string-db.org/api/tsv/enrichment?identifiers={protein_network_list}&species=9606'
enrichment_df = fetch(url_enrichment, 'enrichment')
interactions_df = fetch(url_network, 'network')
enrichment_df.to_csv(f'{output_name}_network_enrichment.tsv', sep='\\t')
interactions_df.to_csv(f'{output_name}_network_interactions.tsv', sep='\\t')
"""
}
process PREPROCESS_PROTEIN {
memory '10 GB'
accelerator 1
container "${params.container_preprocess}"
label 'gpu_process'
// containerOptions "--rm --gpus all"
// errorStrategy 'ignore'
input:
path("input_*.fasta", arity: '1..*')
output:
path "mutated.zarr"
script:
"""
set -e
cat input_*.fasta > merged.fasta
python /app/project.py merged.fasta mutated.zarr
"""
}

125
main_conplex.nf.old Executable file
View File

@@ -0,0 +1,125 @@
nextflow.enable.dsl=2
process CONPLEX {
container "${params.container_conplex}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
maxForks 5
// scratch true //deletes workdir after successful completion
input:
path smi_drug
path smi_metabolite
path mut_fasta
output:
path "*drug_scores.tsv", emit: drug
path "*significant_interactions.tsv", emit: interactions
script:
"""
workdir=`pwd`
#concat mutated and reference fasta files. If it has name with _2 its mutated.
#after test is don retrun this
cat $mut_fasta /home/omic/ConPLex/MANE_referent_transcipt_reference.fasta > \$workdir/all_protein.fasta
### Test
#head -n 100 /home/omic/ConPLex/MANE_referent_transcipt_reference.fasta > \$workdir/test.fasta
#cat $mut_fasta \$workdir/test.fasta > \$workdir/all_protein.fasta
###
. activate conplex-dti
#transform smi for conplex
python3 -c "
import sys
from rdkit import Chem
import numpy as np
import pandas as pd
def converter(drug_csv, outname):
#open file to write drug/matabolite smi
out_file = open(outname + '.txt', 'w')
#load drug csv; only has drug in separate lines
drug_smi_list = np.array(pd.read_csv(drug_csv)['SMILES']).tolist()
#original drugs are anotated with drug_{}
for n, smi in enumerate(drug_smi_list):
out_file.write('{}\\tdrug_{}\\n'.format(smi, n))
out_file.close()
converter('$smi_drug', 'drag')
"
#concatinate drag and metabolites
cat drag.txt $smi_metabolite > \$workdir/smiles.smi
#conplex predicition 1. round
python3 /home/omic/ConPLex/conplex.py --fastas \$workdir/all_protein.fasta --smis \$workdir/smiles.smi --screening_batch_size ${params.screening_batch_size} --outdir \$workdir --split_write_df 'no'
#### this part is use to test all alternative transcripts (this part can be skipped for now, cuz we will use it for tissue specific analysis later)
##get fasta for 2. round transcripts for proteins above threshold
#python3 /home/omic/ConPLex/get_round_2.py --threshold ${params.threshold} --workdir \$workdir --round 1
##conplex all transcipt for protrin above threshold
#python3 /home/omic/ConPLex/conplex.py --fastas \$workdir/round_2.fasta --smis \$workdir/smiles.smi --screening_batch_size ${params.screening_batch_size} --outdir \$workdir --split_write_df 'no'
####
#get data for second run
python3 /home/omic/ConPLex/get_round_2.py --threshold ${params.threshold} --workdir \$workdir --round 2
"""
}
process NETWORK_ENRICHMENT {
container "${params.container_conplex}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/receptors", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
maxForks 5
input:
path interactions
output:
path "*_network_enrichment.tsv", emit: network_enrichment
path "*_network_interactions.tsv", emit: network_interactions
script:
"""
#!/opt/conda/envs/conplex-dti/bin/python
import pandas as pd
import requests
interaction_data = pd.read_csv('$interactions', sep = '\\t')
interaction_data = interaction_data.sort_values('conplex_score', ascending=False)
#get list of enst above threshold
protein_network_list = '%0d'.join(list(pd.unique(interaction_data[interaction_data['conplex_score'] > ${params.protein_network_threshold}]['transcipt'])))
#get urls
url_network = f'https://string-db.org/api/tsv/network?identifiers={protein_network_list}&species=9606'
url_enrichment = f'https://string-db.org/api/tsv/enrichment?identifiers={protein_network_list}&species=9606'
#get enrichment dataframe
r = requests.get(url_enrichment)
lines = r.text.split('\\n') # pull the text from the response object and split based on new lines
data = [l.split('\\t') for l in lines] # split each line into its components based on tabs
enrichment_df = pd.DataFrame(data[1:-1], columns = data[0]) # convert to dataframe using the first row as the column names; drop empty, final row
#get protein interaction dataframe
r = requests.get(url_network)
lines = r.text.split('\\n') # pull the text from the response object and split based on new lines
data = [l.split('\\t') for l in lines] # split each line into its components based on tabs
# convert to dataframe using the first row as the column names; drop empty, final row
interactions_df = pd.DataFrame(data[1:-1], columns = data[0])
# dataframe with the preferred names of the two proteins and the score of the interaction
#interactions_df = interactions_df[['preferredName_A', 'preferredName_B', 'score']]
#output name
output_name = '$interactions'.split('/')[-1].split('_significant_interactions.tsv')[0]
#save
enrichment_df.to_csv(f'{output_name }_network_enrichment.tsv',sep='\\t')
interactions_df.to_csv(f'{output_name }_network_interactions.tsv',sep='\\t')
"""
}

57
main_tissue.nf Executable file
View File

@@ -0,0 +1,57 @@
nextflow.enable.dsl=2
process TISSUE_DISTRIBUTION {
memory { params.tissue_initial_memory.toInteger().GB + (task.attempt - 1) * params.tissue_growth_memory.toInteger().GB }
container "${params.container_tissue}"
// containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
// // Temporarily disabled debug prints
// debug true
errorStrategy { task.attempt <= params.tissue_max_retries.toInteger() ? 'retry' : params.tissue_fail_action }
maxRetries params.tissue_max_retries.toInteger()
input:
path interaction
output:
path "*tissue_distribution.tsv", emit: tissue_dist
script:
"""
# . activate tissue
python /home/omic/drug_tissue_distribution.py --file_name ${interaction}
"""
}
process BIO_METRICS {
memory { params.bio_initial_memory.toInteger().GB + (task.attempt - 1) * params.bio_growth_memory.toInteger().GB }
container "${params.container_tissue}"
// containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
// debug true
errorStrategy { task.attempt <= params.bio_max_retries.toInteger() ? 'retry' : params.bio_fail_action }
maxRetries params.bio_max_retries.toInteger()
input:
tuple (
val(id),
path( target),
path( metabolites),
path( conplex_drug),
path( conplex_all_interactions),
)
output:
path "*_biological_properties.tsv", emit: bio_prop
script:
"""
# . activate tissue
python /home/omic/digital_patient_extract_metrics.py --metabolites ${metabolites} --conplex_all_interactions ${conplex_all_interactions} --conplex_drug ${conplex_drug} --target ${target}
"""
}

90
nextflow.config Executable file
View File

@@ -0,0 +1,90 @@
manifest {
name = 'Digital Trial'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/tools/digital-trial.git'
description = 'Digital drug protein interactions'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
}
docker {
enabled = true
temp = 'auto'
remove = true
}
process {
withLabel: 'gpu_process' {
containerOptions = '--gpus all --rm'
pod = [
[nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
]
}
withLabel: 'cpu_process' {
containerOptions = '--rm'
}
}
profiles {
// Minimal k8s profile: WES injects its own profile.config via -C, which supplies the
// executor, namespace, service account, workDir and PVC mounts. Anything set here that
// WES also sets is either overridden or conflicts, so keep this deliberately sparse.
//
// NOTE: the dreamdock-data PVC must be mounted by the WES-side profile for
// params.protein_zarr and params.chembl_db (/mnt/dreamdock-data/...) to resolve.
k8s {
process.executor = 'k8s'
}
// Full standalone k8s profile for running this pipeline directly (not via WES),
// e.g. `nextflow run main.nf -profile k8s_standalone` from a pod on the cluster.
k8s_standalone {
process.executor = 'k8s'
process.namespace = 'bioinformatics'
process.debug = true
workDir = "/mnt/dreamdock-data/digital_trials/workdir"
executor {
queueSize = 0 // Increase to desired concurrency
// submitRateLimit = '1 sec' // Recommended to prevent K8s API timeouts
}
k8s {
serviceAccount = 'nextflow-sa'
namespace = 'bioinformatics'
storageClaimName = 'dreamdock-data'
storageMountPath = '/mnt/dreamdock-data'
pullPolicy = 'IfNotPresent'
cleanup = true // delete pods after Ctrl+C or finished?
imagePullSecrets = 'omic-registry-secret'
// RUN AS DIFFERENT USERS
// securityContext = [fsGroup: 1000]
// securityContext = [
// runAsUser: 1000,
// fsGroup: 1000,
// runAsNonRoot: true
// ]
}
// Pod-level customization
process.pod = [
[env: 'NXF_DEBUG', value: '0'],
[label: 'omic-app', value: 'dreamdock'],
[imagePullSecret: 'gitlab-registry-secret'],
// [nodeSelector: [gpu: 'yes', 'gpu-type': 'rtx-3090']],
[hostPath: '/mnt/ZINC-22/', mountPath: '/mnt/ZINC-22/']
// [volumeClaim: 'conplex-index-builder-data', mountPath: '/mnt/conplex-index/']
// [privileged: true],
]
}
}

69
nextflow.config.old Executable file
View File

@@ -0,0 +1,69 @@
manifest {
name = 'Dream Dock'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/pipelines/dreamdock'
description = 'Small drug creation based on a protein target'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
}
docker {
enabled = true
temp = 'auto'
}
profiles {
k8s {
process.executor = 'k8s'
process.namespace = 'bioinformatics'
process.debug = true
workDir = "/mnt/dreamdock-data/work"
k8s {
serviceAccount = 'nextflow-sa'
namespace = 'bioinformatics'
storageClaimName = 'dreamdock-data'
storageMountPath = '/mnt/dreamdock-data'
pullPolicy = 'IfNotPresent'
cleanup = true // delete pods after Ctrl+C or finished?
// RUN AS DIFFERENT USERS
// securityContext = [fsGroup: 1000]
// securityContext = [
// runAsUser: 1000,
// fsGroup: 1000,
// runAsNonRoot: true
// ]
}
// Use container image
// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
// Pod-level customization
process.pod = [
[env: 'NXF_DEBUG', value: '0'],
[label: 'omic-app', value: 'dreamdock'],
[imagePullSecret: 'gitlab-registry-secret'],
[hostPath: '/mnt/ZINC-22/', mountPath: '/mnt/ZINC-22/'],
[nodeSelector: [gpu: 'yes', 'gpu-type': 'rtx-3090']],
[volumeClaim: 'conplex-index-builder-data', mountPath: '/mnt/conplex-index/']
//[nodeSelector: [gpu: 'yes', 'kubernetes.io/hostname': 'k8s-node25']],
// [privileged: true],
]
}
docker {
// Docker/Singularity configuration
docker {
enabled = true
runOptions = '--rm'
}
}
}

94
nf_metabol_screen_adaptive/.nextflow.log Normal file
View File

@@ -0,0 +1,94 @@
Jul-21 03:07:10.282 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf
Jul-21 03:07:10.349 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.2
Jul-21 03:07:10.366 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.2,nf-wave@1.12.1
Jul-21 03:07:10.387 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-21 03:07:10.388 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-21 03:07:10.390 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-21 03:07:10.399 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-21 03:07:10.415 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-21 03:07:10.417 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-21 03:07:10.442 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-21 03:07:10.445 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@759d81f3] - activable => nextflow.secret.LocalSecretsProvider@759d81f3
Jul-21 03:07:10.450 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jul-21 03:07:10.819 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-21 03:07:10.830 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [confident_euler] DSL2 - revision: b00b655f5b
Jul-21 03:07:10.831 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-21 03:07:10.831 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Session UUID: 5e2c3d52-6405-43b3-a203-f96c06488e9b
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Run name: confident_euler
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Executor pool size: 20
Jul-21 03:07:10.878 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-21 03:07:10.883 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-21 03:07:10.901 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.2 build 5947
Created: 13-05-2025 21:58 UTC (14:58 PDT)
System: Linux 6.8.0-52-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 17.0.15+6-Ubuntu-0ubuntu122.04
Encoding: UTF-8 (UTF-8)
Process: 3902257@alien [127.0.1.1]
CPUs: 20 - Mem: 62.6 GB (836.3 MB) - Swap: 2 GB (96.4 MB)
Jul-21 03:07:10.924 [main] DEBUG nextflow.Session - Work-dir: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-21 03:07:10.925 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/bin
Jul-21 03:07:10.935 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-21 03:07:10.946 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-21 03:07:10.967 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-21 03:07:10.993 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-21 03:07:11.002 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000
Jul-21 03:07:11.051 [main] DEBUG nextflow.Session - Session start
Jul-21 03:07:11.055 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/execution_trace.txt
Jul-21 03:07:11.178 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-21 03:07:11.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-21 03:07:11.315 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-21 03:07:11.320 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-21 03:07:11.324 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=62.6 GB; capacity=20; pollInterval=100ms; dumpInterval=5m
Jul-21 03:07:11.327 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-21 03:07:11.348 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'METABOLITE_SCREEN': maxForks=0; fair=false; array=0
Jul-21 03:07:11.396 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-21 03:07:11.397 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-21 03:07:11.398 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-21 03:07:11.399 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_9d98cafae0c3b8e5: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/test.nf
Script_c8d2b32ed0aeeac9: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/main.nf
Jul-21 03:07:11.399 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-21 03:07:11.399 [main] DEBUG nextflow.Session - Session await
Jul-21 03:07:11.552 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-21 03:07:11.554 [Task submitter] INFO nextflow.Session - [f9/21c381] Submitted process > METABOLITE_SCREEN
Jul-21 03:07:11.590 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 127; error: -; workDir: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9]
Jul-21 03:07:11.591 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-21 03:07:11.600 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=METABOLITE_SCREEN; work-dir=/dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9
error [nextflow.exception.ProcessFailedException]: Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Jul-21 03:07:11.615 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'METABOLITE_SCREEN'
Caused by:
Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Command executed:
set -e
python /app/screen.py -i metabolites-rev.tsv -z protein_seq.zarr
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 3: python: command not found
Work dir:
/dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jul-21 03:07:11.621 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-21 03:07:11.628 [TaskFinalizer-1] DEBUG nextflow.Session - Session aborted -- Cause: Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Jul-21 03:07:11.643 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-21 03:07:11.643 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-21 03:07:11.648 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=18ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-21 03:07:11.648 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-21 03:07:11.649 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-21 03:07:12.149 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-21 03:07:12.189 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-21 03:07:12.197 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

67
nf_metabol_screen_adaptive/.nextflow.log.1 Normal file
View File

@@ -0,0 +1,67 @@
Jul-15 07:43:54.338 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-15 07:43:54.407 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.3
Jul-15 07:43:54.418 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4
Jul-15 07:43:54.443 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-15 07:43:54.443 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-15 07:43:54.445 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-15 07:43:54.452 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-15 07:43:54.463 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-15 07:43:54.464 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-15 07:43:54.479 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-15 07:43:54.481 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@17ca8b92] - activable => nextflow.secret.LocalSecretsProvider@17ca8b92
Jul-15 07:43:54.484 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-15 07:43:54.738 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-15 07:43:54.752 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-15 07:43:54.763 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [boring_faggin] DSL2 - revision: b00b655f5b
Jul-15 07:43:54.764 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-15 07:43:54.764 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-15 07:43:54.796 [main] DEBUG nextflow.Session - Session UUID: 063177a9-1ffb-407e-a41d-e6a1184c5dd1
Jul-15 07:43:54.796 [main] DEBUG nextflow.Session - Run name: boring_faggin
Jul-15 07:43:54.797 [main] DEBUG nextflow.Session - Executor pool size: 32
Jul-15 07:43:54.803 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-15 07:43:54.807 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-15 07:43:54.825 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.3 build 5933
Created: 16-12-2024 15:34 UTC (07:34 PDT)
System: Linux 6.8.0-58-generic
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3458331@bigbertha [127.0.1.1]
CPUs: 32 - Mem: 61.9 GB (4.3 GB) - Swap: 8 GB (128 KB)
Jul-15 07:43:54.842 [main] DEBUG nextflow.Session - Work-dir: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-15 07:43:54.842 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/bin
Jul-15 07:43:54.848 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-15 07:43:54.853 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-15 07:43:54.872 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-15 07:43:54.877 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jul-15 07:43:55.002 [main] DEBUG nextflow.Session - Session start
Jul-15 07:43:55.003 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/execution_trace.txt
Jul-15 07:43:55.083 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-15 07:43:55.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-15 07:43:55.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-15 07:43:55.199 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-15 07:43:55.204 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=61.9 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jul-15 07:43:55.205 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-15 07:43:55.246 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-15 07:43:55.247 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-15 07:43:55.247 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-15 07:43:55.247 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_9d98cafae0c3b8e5: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/test.nf
Script_c8d2b32ed0aeeac9: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/./main.nf
Jul-15 07:43:55.247 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-15 07:43:55.247 [main] DEBUG nextflow.Session - Session await
Jul-15 07:43:55.334 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-15 07:43:55.336 [Task submitter] INFO nextflow.Session - [5b/95e3bb] Submitted process > METABOLITE_SCREEN
Jul-15 07:44:05.790 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugrasWorkspace3/metabolite-screen-alt/nf_metabol_screen_adaptive/work/5b/95e3bb5e9a086140ca514eab04dd78]
Jul-15 07:44:05.791 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-15 07:44:06.031 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-15 07:44:06.090 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-15 07:44:06.090 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-15 07:44:06.091 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-15 07:44:06.094 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=2.8s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-15 07:44:06.094 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-15 07:44:06.095 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-15 07:44:06.349 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-15 07:44:06.431 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-15 07:44:06.436 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-15 07:44:06.436 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

80
nf_metabol_screen_adaptive/.nextflow.log.2 Normal file
View File

@@ -0,0 +1,80 @@
Jul-11 04:23:14.724 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf -bg -with-tower 'http://nucleus.omic.ai:8000/api'
Jul-11 04:23:14.779 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.3
Jul-11 04:23:14.789 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4
Jul-11 04:23:14.808 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-11 04:23:14.808 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-11 04:23:14.810 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-11 04:23:14.820 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-11 04:23:14.831 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-11 04:23:14.832 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-11 04:23:14.849 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-11 04:23:14.851 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@26a94fa5] - activable => nextflow.secret.LocalSecretsProvider@26a94fa5
Jul-11 04:23:14.853 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-11 04:23:15.119 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-11 04:23:15.133 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-11 04:23:15.145 [main] INFO nextflow.cli.CmdRun - Launching `test.nf` [admiring_magritte] DSL2 - revision: 5f66a2b283
Jul-11 04:23:15.145 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-11 04:23:15.146 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.9.3]
Jul-11 04:23:15.146 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.9.3
Jul-11 04:23:15.150 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.9.3' resolved
Jul-11 04:23:15.150 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.9.3'
Jul-11 04:23:15.165 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.9.3
Jul-11 04:23:15.195 [main] DEBUG nextflow.Session - Session UUID: 8abf60bb-5459-4d36-9886-d8f0064971ac
Jul-11 04:23:15.195 [main] DEBUG nextflow.Session - Run name: admiring_magritte
Jul-11 04:23:15.195 [main] DEBUG nextflow.Session - Executor pool size: 32
Jul-11 04:23:15.200 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-11 04:23:15.203 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-11 04:23:15.205 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-11 04:23:15.205 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-11 04:23:15.206 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-11 04:23:15.243 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-11 04:23:15.269 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.3 build 5933
Created: 16-12-2024 15:34 UTC (07:34 PDT)
System: Linux 6.8.0-58-generic
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 2298940@bigbertha [127.0.1.1]
CPUs: 32 - Mem: 61.9 GB (882.4 MB) - Swap: 8 GB (972 KB)
Jul-11 04:23:15.288 [main] DEBUG nextflow.Session - Work-dir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-11 04:23:15.288 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/bin
Jul-11 04:23:15.295 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-11 04:23:15.301 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-11 04:23:15.309 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jul-11 04:23:15.438 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-11 04:23:15.444 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jul-11 04:23:15.651 [main] DEBUG nextflow.Session - Session start
Jul-11 04:23:15.653 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/execution_trace.txt
Jul-11 04:23:15.656 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Seqera Platform observer -- endpoint=http://nucleus.omic.ai:8000/api; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250
Jul-11 04:23:15.893 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-11 04:23:15.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-11 04:23:15.973 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-11 04:23:15.975 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-11 04:23:15.979 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=61.9 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jul-11 04:23:15.980 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-11 04:23:16.020 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-11 04:23:16.140 [main] INFO io.seqera.tower.plugin.TowerClient - Monitor the execution with Seqera Platform using this URL: http://localhost:8000/watch/J8JA6yEb
Jul-11 04:23:16.141 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-11 04:23:16.141 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-11 04:23:16.141 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c8d2b32ed0aeeac9: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/./main.nf
Script_85e5efa6aea507c6: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/test.nf
Jul-11 04:23:16.141 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-11 04:23:16.141 [main] DEBUG nextflow.Session - Session await
Jul-11 04:23:16.243 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-11 04:23:16.245 [Task submitter] INFO nextflow.Session - [cf/a7b064] Submitted process > METABOLITE_SCREEN
Jul-11 04:23:34.062 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work/cf/a7b0643787b68bed3189f63698ed53]
Jul-11 04:23:34.063 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-11 04:23:34.299 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-11 04:23:34.362 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-11 04:23:34.362 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-11 04:23:34.364 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-11 04:23:34.366 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=7.7s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-11 04:23:34.366 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-11 04:23:34.367 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-11 04:23:34.614 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-11 04:23:34.743 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-11 04:23:34.748 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.9.3'
Jul-11 04:23:34.748 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Jul-11 04:23:34.749 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-11 04:23:34.749 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

67
nf_metabol_screen_adaptive/.nextflow.log.3 Normal file
View File

@@ -0,0 +1,67 @@
Jul-10 05:08:04.417 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-10 05:08:04.464 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.3
Jul-10 05:08:04.474 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4
Jul-10 05:08:04.515 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-10 05:08:04.516 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-10 05:08:04.517 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-10 05:08:04.523 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-10 05:08:04.533 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-10 05:08:04.534 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-10 05:08:04.549 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-10 05:08:04.551 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@17ca8b92] - activable => nextflow.secret.LocalSecretsProvider@17ca8b92
Jul-10 05:08:04.556 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-10 05:08:04.812 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-10 05:08:04.827 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-10 05:08:04.834 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [drunk_swartz] DSL2 - revision: 8594c93ec6
Jul-10 05:08:04.834 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-10 05:08:04.835 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-10 05:08:04.859 [main] DEBUG nextflow.Session - Session UUID: 925b41d5-7b1c-4ed9-b34c-88420509e2e8
Jul-10 05:08:04.859 [main] DEBUG nextflow.Session - Run name: drunk_swartz
Jul-10 05:08:04.859 [main] DEBUG nextflow.Session - Executor pool size: 32
Jul-10 05:08:04.863 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-10 05:08:04.866 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 05:08:04.878 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.3 build 5933
Created: 16-12-2024 15:34 UTC (07:34 PDT)
System: Linux 6.8.0-58-generic
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 324567@bigbertha [127.0.1.1]
CPUs: 32 - Mem: 61.9 GB (4 GB) - Swap: 8 GB (5.6 MB)
Jul-10 05:08:04.889 [main] DEBUG nextflow.Session - Work-dir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-10 05:08:04.889 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/bin
Jul-10 05:08:04.894 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-10 05:08:04.899 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-10 05:08:04.921 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-10 05:08:04.926 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jul-10 05:08:05.053 [main] DEBUG nextflow.Session - Session start
Jul-10 05:08:05.054 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/execution_trace.txt
Jul-10 05:08:05.123 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-10 05:08:05.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-10 05:08:05.213 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-10 05:08:05.216 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-10 05:08:05.220 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=61.9 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jul-10 05:08:05.221 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-10 05:08:05.260 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-10 05:08:05.261 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-10 05:08:05.261 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-10 05:08:05.261 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c8d2b32ed0aeeac9: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/./main.nf
Script_041bcf7aceb7d897: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/test.nf
Jul-10 05:08:05.261 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-10 05:08:05.261 [main] DEBUG nextflow.Session - Session await
Jul-10 05:08:05.359 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-10 05:08:05.360 [Task submitter] INFO nextflow.Session - [0a/8843c6] Submitted process > METABOLITE_SCREEN
Jul-10 05:08:37.851 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work/0a/8843c652f011dbd021cd836c526d44]
Jul-10 05:08:37.852 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 05:08:38.827 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-10 05:08:38.852 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-10 05:08:38.852 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-10 05:08:38.853 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-10 05:08:38.857 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=13.6s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-10 05:08:38.857 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-10 05:08:38.858 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-10 05:08:39.681 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-10 05:08:39.893 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-10 05:08:39.897 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-10 05:08:39.897 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

67
nf_metabol_screen_adaptive/.nextflow.log.4 Normal file
View File

@@ -0,0 +1,67 @@
Jul-10 05:06:57.796 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-10 05:06:57.858 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.3
Jul-10 05:06:57.870 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4
Jul-10 05:06:57.889 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-10 05:06:57.890 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-10 05:06:57.891 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-10 05:06:57.899 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-10 05:06:57.909 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-10 05:06:57.911 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/nextflow.config
Jul-10 05:06:57.927 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-10 05:06:57.929 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@17ca8b92] - activable => nextflow.secret.LocalSecretsProvider@17ca8b92
Jul-10 05:06:57.931 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-10 05:06:58.207 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-10 05:06:58.222 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-10 05:06:58.232 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [nice_lagrange] DSL2 - revision: 8594c93ec6
Jul-10 05:06:58.233 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-10 05:06:58.233 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-10 05:06:58.266 [main] DEBUG nextflow.Session - Session UUID: 63ec0e24-1334-45e4-a396-bb1b7734bb1c
Jul-10 05:06:58.266 [main] DEBUG nextflow.Session - Run name: nice_lagrange
Jul-10 05:06:58.266 [main] DEBUG nextflow.Session - Executor pool size: 32
Jul-10 05:06:58.271 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-10 05:06:58.274 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 05:06:58.292 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.3 build 5933
Created: 16-12-2024 15:34 UTC (07:34 PDT)
System: Linux 6.8.0-58-generic
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 318707@bigbertha [127.0.1.1]
CPUs: 32 - Mem: 61.9 GB (5.9 GB) - Swap: 8 GB (692 KB)
Jul-10 05:06:58.308 [main] DEBUG nextflow.Session - Work-dir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-10 05:06:58.309 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/bin
Jul-10 05:06:58.314 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-10 05:06:58.319 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-10 05:06:58.338 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-10 05:06:58.344 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jul-10 05:06:58.461 [main] DEBUG nextflow.Session - Session start
Jul-10 05:06:58.463 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/execution_trace.txt
Jul-10 05:06:58.544 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-10 05:06:58.620 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-10 05:06:58.620 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-10 05:06:58.623 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-10 05:06:58.627 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=61.9 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jul-10 05:06:58.628 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-10 05:06:58.667 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-10 05:06:58.668 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-10 05:06:58.668 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-10 05:06:58.668 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_c8d2b32ed0aeeac9: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/./main.nf
Script_041bcf7aceb7d897: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/test.nf
Jul-10 05:06:58.668 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-10 05:06:58.668 [main] DEBUG nextflow.Session - Session await
Jul-10 05:06:58.759 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-10 05:06:58.761 [Task submitter] INFO nextflow.Session - [b1/b3e41f] Submitted process > METABOLITE_SCREEN
Jul-10 05:07:34.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugrasWorkspace3/metabolite-screen/nf_metabol_screen_adaptive/work/b1/b3e41f08bc233c93e7ac82702bb856]
Jul-10 05:07:34.617 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-10 05:07:35.660 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-10 05:07:35.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-10 05:07:35.716 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-10 05:07:35.718 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-10 05:07:35.721 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=15.9s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-10 05:07:35.721 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-10 05:07:35.722 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-10 05:07:35.973 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-10 05:07:36.099 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-10 05:07:36.104 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-10 05:07:36.104 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

69
nf_metabol_screen_adaptive/.nextflow.log.5 Normal file
View File

@@ -0,0 +1,69 @@
Jul-03 12:08:35.777 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-03 12:08:35.914 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Jul-03 12:08:35.944 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Jul-03 12:08:35.978 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-03 12:08:35.979 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-03 12:08:35.983 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-03 12:08:35.996 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-03 12:08:36.024 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:36.028 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:36.073 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Jul-03 12:08:36.078 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@29314cc9] - activable => nextflow.secret.LocalSecretsProvider@29314cc9
Jul-03 12:08:36.086 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-03 12:08:36.792 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-03 12:08:36.833 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-03 12:08:36.850 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [insane_woese] DSL2 - revision: 063b5cd9a9
Jul-03 12:08:36.852 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-03 12:08:36.852 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-03 12:08:36.922 [main] DEBUG nextflow.Session - Session UUID: a62b6efd-60bb-4b97-a6e1-a68592f7d53f
Jul-03 12:08:36.923 [main] DEBUG nextflow.Session - Run name: insane_woese
Jul-03 12:08:36.923 [main] DEBUG nextflow.Session - Executor pool size: 80
Jul-03 12:08:36.935 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-03 12:08:36.943 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:36.975 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3786813@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (220.6 GB) - Swap: 0 (0)
Jul-03 12:08:37.006 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/metabolite-screen/nf_metabol_screen/work [btrfs]
Jul-03 12:08:37.007 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/metabolite-screen/nf_metabol_screen/bin
Jul-03 12:08:37.022 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-03 12:08:37.034 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-03 12:08:37.060 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-03 12:08:37.087 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-03 12:08:37.098 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Jul-03 12:08:37.228 [main] DEBUG nextflow.Session - Session start
Jul-03 12:08:37.233 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugra/metabolite-screen/nf_metabol_screen/execution_trace.txt
Jul-03 12:08:37.394 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-03 12:08:37.590 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-03 12:08:37.591 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-03 12:08:37.598 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-03 12:08:37.609 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Jul-03 12:08:37.612 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-03 12:08:37.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'METABOLITE_SCREEN': maxForks=0; fair=false; array=0
Jul-03 12:08:37.724 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-03 12:08:37.726 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-03 12:08:37.727 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-03 12:08:37.728 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_181c5ac3efe09ab5: /data/bugra/metabolite-screen/nf_metabol_screen/main.nf
Script_3b80613f4955047b: /data/bugra/metabolite-screen/nf_metabol_screen/test.nf
Jul-03 12:08:37.728 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-03 12:08:37.728 [main] DEBUG nextflow.Session - Session await
Jul-03 12:08:38.010 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-03 12:08:38.016 [Task submitter] INFO nextflow.Session - [3d/10f68f] Submitted process > METABOLITE_SCREEN
Jul-03 12:08:44.784 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/metabolite-screen/nf_metabol_screen/work/3d/10f68ffcfb09a7b35f3b90f43efbd9]
Jul-03 12:08:44.786 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:45.543 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-03 12:08:45.581 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-03 12:08:45.582 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-03 12:08:45.586 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-03 12:08:45.596 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3.7s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-03 12:08:45.596 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-03 12:08:45.598 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-03 12:08:46.431 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-03 12:08:46.525 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-03 12:08:46.538 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-03 12:08:46.538 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

78
nf_metabol_screen_adaptive/.nextflow.log.6 Normal file
View File

@@ -0,0 +1,78 @@
Jul-03 12:08:15.992 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-03 12:08:16.116 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Jul-03 12:08:16.165 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Jul-03 12:08:16.218 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-03 12:08:16.219 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-03 12:08:16.223 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-03 12:08:16.239 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-03 12:08:16.269 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:16.274 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:16.319 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Jul-03 12:08:16.323 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1ddd3478] - activable => nextflow.secret.LocalSecretsProvider@1ddd3478
Jul-03 12:08:16.339 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-03 12:08:17.003 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-03 12:08:17.044 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-03 12:08:17.064 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [insane_snyder] DSL2 - revision: 49b8a74e0c
Jul-03 12:08:17.066 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-03 12:08:17.066 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-03 12:08:17.150 [main] DEBUG nextflow.Session - Session UUID: 8cc53326-d69c-4269-9519-4eb256ccbbd2
Jul-03 12:08:17.151 [main] DEBUG nextflow.Session - Run name: insane_snyder
Jul-03 12:08:17.152 [main] DEBUG nextflow.Session - Executor pool size: 80
Jul-03 12:08:17.163 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-03 12:08:17.180 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:17.322 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3786432@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (220.7 GB) - Swap: 0 (0)
Jul-03 12:08:17.386 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/metabolite-screen/nf_metabol_screen/work [btrfs]
Jul-03 12:08:17.386 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/metabolite-screen/nf_metabol_screen/bin
Jul-03 12:08:17.401 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-03 12:08:17.413 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-03 12:08:17.440 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-03 12:08:17.469 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-03 12:08:17.483 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Jul-03 12:08:17.707 [main] DEBUG nextflow.Session - Session start
Jul-03 12:08:17.717 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugra/metabolite-screen/nf_metabol_screen/execution_trace.txt
Jul-03 12:08:17.950 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-03 12:08:18.079 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e80a6c5924994093: /data/bugra/metabolite-screen/nf_metabol_screen/test.nf
Script_181c5ac3efe09ab5: /data/bugra/metabolite-screen/nf_metabol_screen/main.nf
Jul-03 12:08:18.081 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: chunks for class: nextflow.script.WorkflowBinding
Jul-03 12:08:18.096 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: chunks for class: nextflow.script.WorkflowBinding
at groovy.lang.Binding.getVariable(Binding.java:61)
at nextflow.script.WorkflowBinding.getVariable(WorkflowBinding.groovy:143)
at groovy.lang.Binding.getProperty(Binding.java:117)
at nextflow.script.WorkflowBinding.getProperty(WorkflowBinding.groovy:132)
at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:167)
at groovy.lang.Closure.getPropertyTryThese(Closure.java:325)
at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:315)
at groovy.lang.Closure.getProperty(Closure.java:301)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at Script_e80a6c5924994093$_runScript_closure1$_closure2.doCall(Script_e80a6c5924994093:13)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at groovy.lang.Closure.call(Closure.java:433)
at groovy.lang.Closure.call(Closure.java:412)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.script.BaseScript.run0(BaseScript.groovy:182)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.script.BaseScript.run(BaseScript.groovy:193)
at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246)
at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:246)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
at nextflow.cli.CmdRun.run(CmdRun.groovy:379)
at nextflow.cli.Launcher.run(Launcher.groovy:513)
at nextflow.cli.Launcher.main(Launcher.groovy:673)

1
nf_metabol_screen_adaptive/.nextflow.pid Normal file
View File

@@ -0,0 +1 @@
2298940

20
nf_metabol_screen_adaptive/Dockerfile Normal file
View File

@@ -0,0 +1,20 @@
FROM mambaorg/micromamba:2.1.1
USER root
COPY ./app /app
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN micromamba install -n base -y -c conda-forge --channel-priority flexible \
python=3.12 \
numpy \
"pandas<3" \
scikit-learn \
parallelbar \
zarr=3.0.7 \
onnxruntime \
procps-ng && \
pip install \
/app/bitexpand-0.1.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl \
/app/mol_fingerprint-0.1.0-cp312-cp312-manylinux_2_34_x86_64.whl

BIN
nf_metabol_screen_adaptive/app/bitexpand-0.1.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Normal file
View File

Binary file not shown.

134
nf_metabol_screen_adaptive/app/convert.py Normal file
View File

@@ -0,0 +1,134 @@
#!/usr/bin/env python3
import argparse
import pandas as pd
import sys
from pathlib import Path
def create_smiles_file(drug_csv_path, metabolite_file_path, output_path="smiles.smi"):
"""
Create smiles.smi file by combining drug CSV and metabolite file.
Args:
drug_csv_path: Path to CSV file with 'SMILES' header
metabolite_file_path: Path to tab-separated file with SMILES and metabolite IDs
output_path: Output file path (default: smiles.smi)
"""
# Convert to Path objects for better handling
drug_csv_path = Path(drug_csv_path)
metabolite_file_path = Path(metabolite_file_path)
output_path = Path(output_path)
# Check if input files exist
if not drug_csv_path.exists():
raise FileNotFoundError(f"Drug CSV file not found: {drug_csv_path}")
if not metabolite_file_path.exists():
raise FileNotFoundError(f"Metabolite file not found: {metabolite_file_path}")
# Read drug CSV
try:
drug_df = pd.read_csv(drug_csv_path)
except Exception as e:
raise Exception(f"Error reading drug CSV file: {e}")
# Validate drug CSV has SMILES column
if 'SMILES' not in drug_df.columns:
raise ValueError("Drug CSV file must have 'SMILES' column")
# Check if metabolite file contains "NO_METABOLITES"
try:
with open(metabolite_file_path, 'r') as f:
first_line = f.readline().strip()
except Exception as e:
raise Exception(f"Error reading metabolite file: {e}")
# Handle no metabolites case
if first_line == "NO_METABOLITES":
print("No metabolites found, creating output file with drugs only")
# Create drug dataframe with drug_N format
drug_output = drug_df.copy()
drug_output['ID'] = [f'drug_{i}' for i in range(len(drug_df))]
drug_output = drug_output[['SMILES', 'ID']]
# Write only drugs to output file
try:
drug_output.to_csv(output_path, sep='\t', header=False, index=False)
except Exception as e:
raise Exception(f"Error writing output file: {e}")
print(f"Successfully created {output_path}")
print(f" - {len(drug_df)} drugs")
print(f" - 0 metabolites")
return
# Read metabolite file normally (tab-separated, no header)
try:
metabolite_df = pd.read_csv(metabolite_file_path, sep='\t', header=None, names=['SMILES', 'ID'])
except Exception as e:
raise Exception(f"Error reading metabolite file: {e}")
# Validate metabolite file has at least 2 columns
if metabolite_df.shape[1] < 2:
raise ValueError("Metabolite file must have at least 2 columns (SMILES and ID)")
# Create drug dataframe with drug_N format
drug_output = drug_df.copy()
drug_output['ID'] = [f'drug_{i}' for i in range(len(drug_df))]
drug_output = drug_output[['SMILES', 'ID']]
# Use metabolite dataframe as-is (already has SMILES and ID columns)
metabolite_output = metabolite_df[['SMILES', 'ID']]
# Combine drug and metabolite dataframes
combined_df = pd.concat([drug_output, metabolite_output], ignore_index=True)
# Write to output file (tab-separated, no header)
try:
combined_df.to_csv(output_path, sep='\t', header=False, index=False)
except Exception as e:
raise Exception(f"Error writing output file: {e}")
print(f"Successfully created {output_path}")
print(f" - {len(drug_df)} drugs")
print(f" - {len(metabolite_df)} metabolites")
def main():
parser = argparse.ArgumentParser(
description="Create smiles.smi file by combining drug CSV and metabolite file",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Examples:
python3 create_smiles.py drug.csv metabolites.txt
python3 create_smiles.py drug.csv metabolites.txt -o compounds.smi
"""
)
parser.add_argument(
'drug_csv',
help='Path to CSV file with SMILES column containing drug compounds'
)
parser.add_argument(
'metabolite_file',
help='Path to tab-separated file with SMILES and metabolite IDs'
)
parser.add_argument(
'-o', '--output',
default='smiles.smi',
help='Output file path (default: smiles.smi)'
)
args = parser.parse_args()
try:
create_smiles_file(args.drug_csv, args.metabolite_file, args.output)
except Exception as e:
print(f"Error: {e}", file=sys.stderr)
sys.exit(1)
if __name__ == "__main__":
main()

225
nf_metabol_screen_adaptive/app/get_round_2.py Executable file
View File

@@ -0,0 +1,225 @@
import argparse
import pandas as pd
import numpy as np
from collections import defaultdict
from itertools import chain
from pathlib import Path
import zarr
from zarr.storage import LocalStore
# Load reference data
seq_exist = pd.read_csv('/app/MANE_all_transcipts.csv')
def get_round_2(threshold, workdir, round, drug_csv: Path):
workdir = Path(workdir)
fasta_name = "patient_0"
drug_name = drug_csv.stem
name_out = f"{drug_name}_{fasta_name}"
# Load all zarr score stores produced by screen.py.
results_zarr = list(workdir.glob('*_results.zarr'))
if not results_zarr:
raise FileNotFoundError("No results Zarr stores found")
print("Loading Zarr results...")
# Lazy zarr handles per file; we read the (proteins, compounds) score matrix
# in protein chunks rather than loading it fully — keeps peak memory bounded
# regardless of compound count.
zarr_groups = []
compound_ids_per = []
protein_ids_per = []
for z_path in results_zarr:
store = LocalStore(z_path, read_only=True)
group = zarr.open(store, mode="r")
zarr_groups.append(group)
# numpy 2.4+ returns StringDType for these arrays; convert via tolist()
# because direct .astype(str) raises "cannot cast StringDType to StrDType".
compound_ids_per.append(np.array(group["compound_ids"][:].tolist(), dtype=str))
protein_ids_per.append(np.array(group["protein_ids"][:].tolist(), dtype=str))
# All zarrs share the same compound axis (drug + same metabolites).
all_compound_ids = compound_ids_per[0]
for cids in compound_ids_per[1:]:
if cids.shape != all_compound_ids.shape or not np.array_equal(cids, all_compound_ids):
raise ValueError("All *_results.zarr stores must share the same compound_ids axis")
all_protein_ids = np.concatenate(protein_ids_per) if len(protein_ids_per) > 1 else protein_ids_per[0]
n_proteins = sum(g["scores"].shape[0] for g in zarr_groups)
n_compounds = all_compound_ids.shape[0]
# ---- Compound-axis indices (tiny) ----
drug_mask_cmpd = np.array([s.startswith("drug") for s in all_compound_ids], dtype=bool)
if not drug_mask_cmpd.any():
raise ValueError("No 'drug_*' compounds present in compound_ids")
drug_cols_idx = np.where(drug_mask_cmpd)[0]
drug0_search = np.where(all_compound_ids == 'drug_0')[0]
if drug0_search.size == 0:
raise ValueError("'drug_0' not found in compound_ids")
drug0_idx = int(drug0_search[0])
# ---- Stream the score matrix in protein chunks, writing significant_interactions
# incrementally and accumulating per-protein summary stats. Avoids both the
# full score matrix load and the giant in-memory above-threshold DataFrame. ----
# Per chunk peak ≈ CHUNK_PROTEINS * n_compounds * 4 bytes; for 1000×38k ≈ 150 MB.
CHUNK_PROTEINS = 1000
drug_position = np.zeros(n_proteins, dtype=np.int64)
drug_0_col_full = np.empty(n_proteins, dtype=np.float32)
prot_count = defaultdict(int) # protein_id -> count of above-threshold compounds
prot_sum = defaultdict(float) # protein_id -> sum of above-threshold scores
# Open significant_interactions.tsv before the loop (round 2 only); write rows per chunk.
sig_path = workdir / f'{name_out}_significant_interactions.tsv'
sig_writer = None
smile_dict = None
if round == 2:
test_smiles = pd.read_csv(workdir / 'smiles.smi', sep='\t', header=None)
smile_dict = dict(zip(test_smiles[1], test_smiles[0]))
sig_writer = open(sig_path, 'w')
sig_writer.write("drug/metabolite\tsmile\ttranscipt\tconplex_score\n")
cursor = 0
for group in zarr_groups:
scores_arr = group["scores"]
n_this = scores_arr.shape[0]
for start in range(0, n_this, CHUNK_PROTEINS):
end = min(start + CHUNK_PROTEINS, n_this)
chunk = np.asarray(scores_arr[start:end]) # (chunk_size, n_compounds)
global_start = cursor + start
global_end = cursor + end
chunk_size = end - start
# drug score columns + max-per-protein for this chunk
chunk_max_drug = chunk[:, drug_cols_idx].max(axis=1)
# drug_position[i] = # compounds with score strictly > max_drug_score_i.
# Matches production's stable-sort + first-drug-position convention.
drug_position[global_start:global_end] = (chunk > chunk_max_drug[:, None]).sum(axis=1)
# drug_0 column
drug_0_col_full[global_start:global_end] = chunk[:, drug0_idx].astype(np.float32, copy=False)
# Above-threshold rows for this chunk
pi_local, ci = np.where(chunk > threshold)
if pi_local.size:
scores_vec = chunk[pi_local, ci].astype(np.float32, copy=False)
# Per-protein aggregates accumulated via bincount on local indices.
counts_local = np.bincount(pi_local, minlength=chunk_size)
sums_local = np.bincount(pi_local, weights=scores_vec.astype(np.float64), minlength=chunk_size)
for pi in np.flatnonzero(counts_local):
pid = all_protein_ids[global_start + pi]
prot_count[pid] += int(counts_local[pi])
prot_sum[pid] += float(sums_local[pi])
# Write significant_interactions rows for this chunk directly to the file.
if sig_writer is not None:
compound_ids_vec = all_compound_ids[ci]
protein_ids_vec = all_protein_ids[global_start + pi_local]
smiles_vec = np.array(
[smile_dict.get(c, "UNKNOWN") for c in compound_ids_vec]
)
pd.DataFrame({
"drug/metabolite": compound_ids_vec,
"smile": smiles_vec,
"transcipt": protein_ids_vec,
"conplex_score": scores_vec,
}).to_csv(sig_writer, sep='\t', index=False, header=False)
cursor += n_this
if sig_writer is not None:
sig_writer.close()
drug_0_score = pd.DataFrame({
"Drug": "drug_0",
"Transcript": all_protein_ids,
"Score": drug_0_col_full,
})
if round == 2:
drug_0_score.to_csv(workdir / f'{name_out}_drug_scores.tsv', sep='\t', index=False)
# ---- Per-protein summary (only proteins with any above-threshold compound) ----
drug_pos_map = dict(zip(all_protein_ids, drug_position))
if round == 1 and not prot_count:
# Equivalent to old "transcipts_summary.empty" early-out for round 1.
pd.DataFrame().to_csv(workdir / 'round_1.csv', index=False)
with open(workdir / 'round_1.fasta', 'w') as f:
f.write("all_data_is_filtered_out\n")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
if prot_count:
proteins_with_above = list(prot_count.keys())
# mean dtype kept as float32 to match the precision of the previous
# groupby-on-float32 path (CSV output is bit-identical that way).
means = np.array(
[prot_sum[p] / prot_count[p] for p in proteins_with_above],
dtype=np.float32,
)
summary = pd.DataFrame({
'transcipt_name': proteins_with_above,
'number_of_iteracting_compounds': [prot_count[p] for p in proteins_with_above],
'mean_binding_above_threshold': means,
})
else:
summary = pd.DataFrame(columns=[
'transcipt_name', 'number_of_iteracting_compounds', 'mean_binding_above_threshold'
])
summary['drug_position'] = summary['transcipt_name'].map(drug_pos_map)
path_out = workdir / f'round_{round}.csv'
if len(summary) == 0:
with path_out.open("w") as f:
f.write("NO TRANSCIPTS ABOVE THRESHOLD")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
summary['if_drug_above_threshold'] = (
summary['number_of_iteracting_compounds'] > summary['drug_position']
)
# MANE symbol lookup; strip mutated-protein "_2" suffix.
clean_transcript_names = [str(t).split('_')[0] for t in summary['transcipt_name']]
seq_lookup = seq_exist.set_index('transcipt')['symbol']
summary['protein_name'] = [
seq_lookup.get(t, "") for t in clean_transcript_names
]
summary.to_csv(path_out, index=False)
# ---- Round 1 also writes the round-2 FASTA ----
if round == 1:
name_2_filtered = list(summary['protein_name'])
transcipts_2 = list(chain.from_iterable(
list(seq_exist[seq_exist['symbol'] == sym]['transcipt'])
for sym in name_2_filtered
))
transcipts_2 = list(np.unique(transcipts_2))
existing = set(summary['transcipt_name'])
transcipts_2 = [t for t in transcipts_2 if t not in existing]
fasta_new = []
for t in transcipts_2:
row = seq_exist[seq_exist['transcipt'] == t]
if not row.empty:
fasta_new.append(f">{t}")
fasta_new.append(row['seq'].iloc[0])
with open(workdir / 'round_2.fasta', 'w') as f:
for line in fasta_new:
f.write(f"{line}\n")
print(f"Round {round} processing complete.")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--threshold", required=True, type=float,
help="Threshold for 1. round of conplex scores")
parser.add_argument("--workdir", required=True, type=Path, help="workdir")
parser.add_argument("--round", required=True, type=int, help="Round 1 or 2")
parser.add_argument("--drug-csv", required=True, type=Path,
help="csv file with drug smiles")
args = parser.parse_args()
get_round_2(args.threshold, args.workdir, args.round, args.drug_csv)

143
nf_metabol_screen_adaptive/app/old_get_round_20.py Normal file
View File

@@ -0,0 +1,143 @@
import argparse
import pandas as pd
import numpy as np
from itertools import chain
from pathlib import PosixPath as Path
seq_exist = pd.read_csv('/app/MANE_all_transcipts.csv')
def get_round_2(threshold, workdir, round, drug_csv : Path):
workdir = Path(workdir)
# Get output names
# Get patient fasta name
# fasta_files = list(workdir.glob('*_variants_transcript_id_mutations.fasta'))
# if not fasta_files:
# raise FileNotFoundError("No variants transcript mutations fasta file found")
# fasta_name = fasta_files[0].stem.replace('_variants_transcript_id_mutations', '')
fasta_name = "patient_0"
# Get test drug
drug_name = drug_csv.stem
name_out = f"{drug_name}_{fasta_name}"
# Get all work dir complex files
results_files = list(workdir.glob('*_results.tsv'))
if not results_files:
raise FileNotFoundError("No results TSV files found")
round_1_score_list = [str(f) for f in results_files]
# Read 1st round
transcipts_1 = [
pd.read_csv(i, sep='\t', header=None).sort_values([2], ascending=False)
for i in round_1_score_list
]
# Get position of drug interaction vs all metabolites
drug_pos = [
[
n
for n, j in enumerate(list(i[0]))
if j[:4] == 'drug'
]
for i in transcipts_1
]
# Drug score
drug_0_score = pd.concat([i[i[0] =='drug_0'] for i in transcipts_1]).rename({0:'Drug', 1:'Transcript', 2:'Score'}, axis=1)
# Filter all below threshold
transcipts_1 = [i[i[2] > threshold] for i in transcipts_1]
# Save transcript_complex above threshold to one file
if round == 2:
inter_import = pd.concat(transcipts_1, ignore_index=True).rename({0:'drug/metabolite',1:'transcipt',2:'conplex_score'},axis=1)
# Add drug
test_smiles = pd.read_csv(workdir / 'smiles.smi', sep='\t', header=None)
smi_ = [test_smiles[test_smiles[1] == i].iloc[0][0] for i in list(inter_import['drug/metabolite'])]
inter_import['smile'] = smi_
inter_import[['drug/metabolite','smile','transcipt','conplex_score']].to_csv(
workdir / f'{name_out}_significant_interactions.tsv', sep='\t', index=False
)
drug_0_score.to_csv(workdir / f'{name_out}_drug_scores.tsv', sep='\t', index=False)
transcipts_1 = pd.DataFrame([
(Path(j).stem.replace('_results', ''), i.shape[0], i[2].mean(), k[0])
for i, j, k in zip(transcipts_1, round_1_score_list, drug_pos)
if i.shape[0] != 0
])
# Check if any interaction is above threshold for first round
if round == 1:
if transcipts_1.shape == (0,0):
transcipts_1.to_csv(workdir / 'round_1.csv', index=False)
with open(workdir / 'round_1.fasta', 'w') as f:
f.write("all_data_is_filtered_out\n")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
transcipts_1 = transcipts_1.rename({
0:'transcipt_name',
1:'number_of_iteracting_compounds',
2:'mean_binding_above_threshold',
3:'drug_position'
}, axis='columns')
path_out = workdir / f'round_{round}.csv'
if len(transcipts_1) == 0:
with path_out.open("w") as f:
f.write("NO TRANSCIPTS ABOVE THRESHOLD")
return 'STOP NO TRANSCIPTS ABOVE THRESHOLD'
transcipts_1['if_drug_above_threshold'] = transcipts_1.iloc[:,1] > transcipts_1.iloc[:,3]
# If protein is mutated it has _2 in name, removes it
transcipt_names = [i.split('_')[0] for i in list(transcipts_1['transcipt_name'])]
temp = [
seq_exist[seq_exist['transcipt'] == i]
for i in transcipt_names
]
transcipts_1['protein_name'] =[
i.iloc[0]['symbol'] if len(i) > 0 else ""
for i in temp
]
# Save data on first round
transcipts_1.to_csv(path_out, index=False)
# Get fasta for second round
if round == 1:
# Get all transcripts of proteins above threshold
name_2_filttered = list(transcipts_1['protein_name'])
transcipts_2 = [list(seq_exist[seq_exist['symbol'] == i]['transcipt']) for i in name_2_filttered]
transcipts_2 = list(chain(*transcipts_2))
transcipts_2 = list(np.unique((transcipts_2)))
# Filter out transcripts already ran through complex
transcipts_2 = list(np.array(transcipts_2)[
[i not in list(transcipts_1['transcipt_name']) for i in transcipts_2]
])
fasta_new = [
['>'+i, seq_exist[seq_exist['transcipt'] == i]['seq'].iloc[0]]
for i in transcipts_2
]
fasta_new = list(chain(*fasta_new))
# Write fasta to run
with open(workdir / 'round_2.fasta', 'w') as f:
for line in fasta_new:
f.write(f"{line}\n")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Process and screen fragments.")
parser.add_argument("--threshold", required=True, type=float, help="Threshold for 1. round.of conplex scores")
parser.add_argument("--workdir", required=True, type=Path, help="workdir")
parser.add_argument("--round", required=True, type=int, help="Round 1 or 2")
parser.add_argument("--drug-csv", required=True, type=Path, help="csv file with drug smiles")
args = parser.parse_args()
get_round_2(args.threshold, args.workdir, args.round, args.drug_csv)

127
nf_metabol_screen_adaptive/app/old_screen.py Normal file
View File

@@ -0,0 +1,127 @@
# Custom Rust modules
import mol_fingerprint as mf
import bitexpand
import pandas as pd
import numpy as np
from pathlib import Path
from argparse import ArgumentParser
import zarr
from zarr.storage import LocalStore
from sklearn.preprocessing import normalize
from parallelbar import progress_map
import onnxruntime as ort
print('CUDA available:', 'CUDAExecutionProvider' in ort.get_available_providers())
def parse_args():
parser = ArgumentParser()
parser.add_argument("-i","--input-tsv", type=Path, required=True, help="Input TSV file with molecules to screen. It must not have any labels and has only two columns, 1st molecule_label, 2nd molecule_smiles")
parser.add_argument("-z","--zarr-protein", type=Path, required=True, help="Input Zarr DB that holds the protein ids and their normalized projection vectors")
return parser
parser = parse_args()
args = parser.parse_args()
# path_fp_basedir : Path = args.input_dir
# my_id :int = args.chunk_id
path_metabolites : Path = args.input_tsv
if not path_metabolites.is_file():
raise ValueError(f"{path_metabolites} IS MISSING OR NOT A FILE")
df_metabolite = pd.read_csv(
path_metabolites,
sep="\t",
header=None,
names=["smiles" ,"compound_id"]
)
path_zarr = args.zarr_protein
store_zarr = LocalStore(path_zarr , read_only=True)
group_zarr = zarr.open(store_zarr, mode="r")
protein_vecs = (group_zarr["normalized"][:])
path_onnx = Path("/app/drug_projector.onnx")
def load_model(model_path):
"""Load ONNX model with GPU support"""
model_path = Path(model_path)
# Set up providers for GPU execution
# providers = ['CUDAExecutionProvider', 'CPUExecutionProvider']
providers = ['CPUExecutionProvider']
# Create inference session
session = ort.InferenceSession(str(model_path), providers=providers)
# Verify GPU is being used
print(f"Available providers: {session.get_providers()}")
return session
session = load_model(path_onnx)
def run_inference(input_vector):
"""Run inference on the model"""
# Get input/output names
input_name = session.get_inputs()[0].name
output_name = session.get_outputs()[0].name
# Ensure input is the correct shape and type
# if input_vector.shape != (2048,):
# raise ValueError(f"Input shape should be (2048,), got {input_vector.shape}")
# Add batch dimension if needed
input_data = input_vector
# Run inference
outputs = session.run([output_name], {input_name: input_data})
# Return the output vector (remove batch dimension)
return outputs[0]
def normalize_vectors_sklearn(vectors):
"""Normalize using sklearn - often fastest for large arrays"""
return normalize(vectors, norm='l2', axis=1)
def project_drugs(smiles : list[str]) -> np.ndarray :
fps = bitexpand.expand_bits(np.array([
np.frombuffer(fp,dtype=np.uint8)
for fp in mf.generate_fingerprints(smiles)
]))
return normalize_vectors_sklearn(run_inference(fps))
pvecs = project_drugs(df_metabolite["smiles"].values.tolist())
my_results = np.dot(protein_vecs,pvecs.T)
pids = group_zarr["ids"][:]
path_outdir = Path("./")
def write_protein(i : int):
df_out = df_metabolite[["compound_id"]].copy()
df_out["protein_id"] = pids[i]
df_out["score"] = my_results[i]
# df_out["protein_sequence"] = group_zarr["sequences"][i]
path_out = path_outdir / f"{pids[i]}_results.tsv"
df_out.to_csv(
path_out,
sep="\t",
index=False,
header=False
)
tasks = list(range(my_results.shape[0]))
progress_map(
write_protein, tasks
)
print("PROCESS COMPLETED SUCCESSFULLY")

144
nf_metabol_screen_adaptive/app/screen.py Normal file
View File

@@ -0,0 +1,144 @@
# Custom Rust modules
import mol_fingerprint as mf
import bitexpand
import pandas as pd
import numpy as np
from pathlib import Path
from argparse import ArgumentParser
import zarr
from zarr.storage import LocalStore
from zarr.codecs import ZstdCodec
from sklearn.preprocessing import normalize
from parallelbar import progress_map
import onnxruntime as ort
print('CUDA available:', 'CUDAExecutionProvider' in ort.get_available_providers())
def parse_args():
parser = ArgumentParser()
parser.add_argument("-i","--input-tsv", type=Path, required=True, help="Input TSV file with molecules to screen. It must not have any labels and has only two columns, 1st molecule_label, 2nd molecule_smiles")
parser.add_argument("-z","--zarr-protein", type=Path, required=True, help="Input Zarr DB that holds the protein ids and their normalized projection vectors")
return parser
parser = parse_args()
args = parser.parse_args()
path_metabolites : Path = args.input_tsv
if not path_metabolites.is_file():
raise ValueError(f"{path_metabolites} IS MISSING OR NOT A FILE")
df_metabolite = pd.read_csv(
path_metabolites,
sep="\t",
header=None,
names=["smiles" ,"compound_id"]
)
path_zarr = args.zarr_protein
store_zarr = LocalStore(path_zarr, read_only=True)
group_zarr = zarr.open(store_zarr, mode="r")
protein_vecs = (group_zarr["normalized"][:])
path_onnx = Path("/app/drug_projector.onnx")
def load_model(model_path):
"""Load ONNX model with GPU support"""
model_path = Path(model_path)
# Set up providers for GPU execution
# providers = ['CUDAExecutionProvider', 'CPUExecutionProvider']
providers = ['CPUExecutionProvider']
# Create inference session
session = ort.InferenceSession(str(model_path), providers=providers)
# Verify GPU is being used
print(f"Available providers: {session.get_providers()}")
return session
session = load_model(path_onnx)
def run_inference(input_vector):
"""Run inference on the model"""
# Get input/output names
input_name = session.get_inputs()[0].name
output_name = session.get_outputs()[0].name
# Run inference
outputs = session.run([output_name], {input_name: input_vector})
return outputs[0]
def normalize_vectors_sklearn(vectors):
"""Normalize using sklearn - often fastest for large arrays"""
return normalize(vectors, norm='l2', axis=1)
def project_drugs(smiles : list[str]) -> np.ndarray :
fps = bitexpand.expand_bits(np.array([
np.frombuffer(fp,dtype=np.uint8)
for fp in mf.generate_fingerprints(smiles)
]))
return normalize_vectors_sklearn(run_inference(fps))
pvecs = project_drugs(df_metabolite["smiles"].values.tolist())
my_results = np.dot(protein_vecs, pvecs.T)
pids = group_zarr["ids"][:]
# Create output zarr store
path_outdir = Path("./")
zarr_name = path_zarr.stem + "_results.zarr"
path_output_zarr = path_outdir / zarr_name
# Create zarr store
store_output = LocalStore(path_output_zarr, read_only=False)
group_output = zarr.open(store_output, mode="w")
out_compress =[
ZstdCodec( level=13 )
]
# Store the data
# Similarity matrix: (n_proteins, n_compounds)
z1 = group_output.create_array(
"scores",
dtype="float32",
shape=my_results.shape,
chunks=(min(1000, my_results.shape[0]), my_results.shape[1]),
compressors=out_compress
)
z1[:] = my_results
# Compound IDs
z2 = group_output.create_array(
"compound_ids",
dtype="str",
shape=(len(df_metabolite),),
compressors=out_compress
)
z2[:] = df_metabolite["compound_id"].values
# Protein IDs
z3 = group_output.create_array(
"protein_ids",
dtype="str",
shape=(len(pids),),
compressors=out_compress
)
z3[:] = pids
# Store metadata
group_output.attrs['n_proteins'] = my_results.shape[0]
group_output.attrs['n_compounds'] = my_results.shape[1]
group_output.attrs['source_zarr'] = str(path_zarr)
print(f"Results saved to {path_output_zarr}")
print(f"Shape: {my_results.shape[0]} proteins x {my_results.shape[1]} compounds")
print("PROCESS COMPLETED SUCCESSFULLY")

14
nf_metabol_screen_adaptive/docker-compose.yml Normal file
View File

@@ -0,0 +1,14 @@
version: '3.8'
services:
metabolite-screen:
build:
context: .
dockerfile: Dockerfile
image: harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1
command: bash
stdin_open: true
tty: true
volumes:
- /mnt/dreamdock-data/digital_trials/workdir/52/6cdef3797446aec540843481dae1ca:/workdir
- /mnt/dreamdock-data/digital_trials:/mnt/dreamdock-data/digital_trials

223
nf_metabol_screen_adaptive/execution_timeline.html Normal file
View File

File diff suppressed because one or more lines are too long

2
nf_metabol_screen_adaptive/execution_trace.txt Normal file
View File

@@ -0,0 +1,2 @@
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
1 f9/21c381 3902375 METABOLITE_SCREEN FAILED 127 2025-07-21 03:07:11.554 35ms 18ms - - - - -

24
nf_metabol_screen_adaptive/main.nf Normal file
View File

@@ -0,0 +1,24 @@
#!/usr/bin/env nextflow
process METABOLITE_SCREEN {
memory '10 GB'
container "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive"
// containerOptions "--rm --gpus all"
// errorStrategy 'ignore'
input:
path input_tsv // TSV file with the smiles
path input_zarr // ZARR DB holding all the protein vectors and their names
output:
path "*_result.tsv"
script:
"""
set -e
python /app/screen.py -i ${input_tsv} -z ${input_zarr}
"""
}

113
nf_metabol_screen_adaptive/nextflow.config Normal file
View File

@@ -0,0 +1,113 @@
// Nextflow configuration file
// Execution report
report {
enabled = true
file = "execution_report.html"
overwrite = true}
// Resource usage tracking
trace {
enabled = true
file = "execution_trace.txt"
overwrite = true
}
// Error reporting
timeline {
enabled = true
file = "execution_timeline.html"
overwrite = true
}
// // Max resources
// executor {
// $local {
// memory = '80 GB'
// cpus = 2
// }
// }
// Default parameters (overridden by test.nf)
params {
// Set defaults here
// input = '/mnt/ZINC-22/conplex/total.zarr'
nshards = 12
outdir = "$launchDir"
}
profiles {
k8s {
process.executor = 'k8s'
process.namespace = 'bioinformatics'
process.debug = true
workDir = "/workdir/work"
k8s {
serviceAccount = 'nextflow-sa'
namespace = 'bioinformatics'
storageClaimName = 'conplex-data'
storageMountPath = '/workdir'
pullPolicy = 'IfNotPresent'
cleanup = true // delete pods after Ctrl+C or finished?
// RUN AS DIFFERENT USERS
// securityContext = [fsGroup: 1000]
// securityContext = [
// runAsUser: 1000,
// fsGroup: 1000,
// runAsNonRoot: true
// ]
}
// Use container image
// process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
// Pod-level customization
process.pod = [
[env: 'NXF_DEBUG', value: '0'],
[label: 'omic-app', value: 'conplex'],
[imagePullSecret: 'gitlab-registry-secret'],
[volumeClaim: 'fingerprint-data', mountPath: '/fingerprint-data']
//[nodeSelector: [gpu: 'yes', 'kubernetes.io/hostname': 'k8s-node25']],
// [privileged: true],
]
// process {
// withName: 'trainIndex' {
// container = 'harbor.cluster.omic.ai/omic/conplex-faiss-train:latest'
// accelerator = 1
// memory = '75 GB'
// cpus = 1
// // GPU-specific pod settings
// pod = [
// [nodeSelector: [gpu: 'yes']]
// ]
// }
// // Specific settings for addToIndex process (CPU only)
// withName: 'addToIndex' {
// container = 'harbor.cluster.omic.ai/omic/conplex-faiss-add:latest'
// memory = '75 GB'
// cpus = 1
// // Explicitly ensure no GPU requirements
// // No accelerator property set, and no GPU nodeSelector
// }
// }
}
docker {
// Docker/Singularity configuration
docker {
enabled = true
runOptions = '--rm'
}
}
}

17
nf_metabol_screen_adaptive/test.nf Normal file
View File

@@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
// params.input_tsv = '../sample/in-molecule/test_known_drugs.tsv' //metabolites.tsv'
params.input_tsv = '../sample/in-molecule/metabolites-rev.tsv' //metabolites.tsv'
params.input_zarr = '../data/protein_seq.zarr' //mane_all.zarr'
// Include the buildFaissIndex workflow from main.nf
include { METABOLITE_SCREEN } from './main.nf'
workflow {
input_tsv = file(params.input_tsv)
input_zarr = file(params.input_zarr)
// Call the combined workflow with both inputs
protein_scores = METABOLITE_SCREEN(input_tsv, input_zarr)
}

192
params.json Normal file
View File

@@ -0,0 +1,192 @@
{
"params": {
"// GENERAL PARAMETERS": {},
"outdir": {
"type": "folder",
"description": "Output directory for results",
"default": "/mnt/OmicNAS/private/old/gabe/digital_trials",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": [
"/mnt/OmicNAS/private/old/gabe/digital_trials",
"/path/to/custom/output"
],
"pattern": ".*",
"validation": {},
"notes": "Directory where all pipeline results will be stored"
},
"project_name": {
"type": "string",
"description": "Project identifier",
"default": "test",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.project_name",
"examples": [
"test",
"production",
"drug_metabolism_study"
],
"pattern": ".*",
"validation": {},
"notes": "Identifier for the digital trials project"
},
"containerOptions": {
"type": "string",
"description": "Container runtime options",
"default": "--gpus all --rm -v /mnt:/mnt",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions",
"examples": [
"--gpus all --rm -v /mnt:/mnt",
"--rm -v /data:/data"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container runtime options for GPU usage and volume mounts"
},
"// BIOTRANSFORMER PARAMETERS": {},
"container_biotransformer": {
"type": "string",
"description": "BioTransformer container image",
"default": "biotransformer:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_biotransformer",
"examples": [
"biotransformer:latest",
"biotransformer:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for BioTransformer module"
},
"ligands": {
"type": "folder",
"description": "Path to input ligands directory",
"default": "/Workspace/next/registry/pipelines/digital_trials/input",
"required": true,
"pipeline_io": "input",
"var_name": "params.ligands",
"examples": [
"/Workspace/next/registry/pipelines/digital_trials/input",
"/path/to/ligands"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing CSV files with ligand data for metabolic transformation"
},
"mode": {
"type": "string",
"description": "BioTransformer operation mode",
"default": "HUMAN",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.mode",
"examples": [
"HUMAN",
"SUPER",
"MASS",
"ORDERED"
],
"pattern": "^(HUMAN|SUPER|MASS|ORDERED)$",
"enum": [
"HUMAN",
"SUPER",
"MASS",
"ORDERED"
],
"validation": {},
"notes": "IMPORTANT: Use HUMAN mode as it's the only fully implemented option that returns expected metabolism to the last step"
},
"// CONPLEX PARAMETERS": {},
"container_conplex": {
"type": "string",
"description": "CONPLEX container image",
"default": "conplex_dig_pat:latest",
"required": true,
"pipeline_io": "parameter",
"var_name": "params.container_conplex",
"examples": [
"conplex_dig_pat:latest",
"conplex_dig_pat:v1.0"
],
"pattern": ".*",
"validation": {},
"notes": "Docker container image for CONPLEX module"
},
"mutated_protein_fasta": {
"type": "folder",
"description": "Path to mutated protein FASTA files directory",
"default": "/Workspace/next/registry/pipelines/digital_trials/input",
"required": true,
"pipeline_io": "input",
"var_name": "params.mutated_protein_fasta",
"examples": [
"/Workspace/next/registry/pipelines/digital_trials/input",
"/path/to/protein/fasta/files"
],
"pattern": ".*",
"validation": {},
"notes": "Directory containing FASTA files with mutated protein sequences"
},
"threshold": {
"type": "number",
"description": "Binding affinity threshold for interactions",
"default": 0.7,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.threshold",
"examples": [
0.5,
0.7,
0.9
],
"pattern": "^\\d+(\\.\\d+)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"notes": "Threshold value for determining significant binding interactions"
},
"screening_batch_size": {
"type": "integer",
"description": "Batch size for virtual screening",
"default": 100000,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.screening_batch_size",
"examples": [
10000,
100000,
1000000
],
"pattern": "^\\d+$",
"validation": {
"min": 1
},
"notes": "Batch size for virtual screening (100k is ideal to optimize performance)"
},
"protein_network_threshold": {
"type": "number",
"description": "Threshold for protein network analysis",
"default": 0.95,
"required": false,
"pipeline_io": "parameter",
"var_name": "params.protein_network_threshold",
"examples": [
0.9,
0.95,
0.99
],
"pattern": "^\\d+(\\.\\d+)?$",
"validation": {
"min": 0.0,
"max": 1.0
},
"notes": "Threshold value for protein-protein interaction network construction"
}
}
}

19
params/input_knowen_target.json Normal file
View File

@@ -0,0 +1,19 @@
{
"container_biotransformer": "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5",
"container_conplex": "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3",
"container_tissue": "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.2",
"container_preprocess": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17",
"container_mass_screen": "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1",
"container_chembl": "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0",
"containerOptions": "--rm",
"project_name": "test2",
"mode": "HUMAN",
"keep_enst": false,
"threshold": 0.65,
"protein_network_threshold": 0.65,
"outdir": "/mnt/dreamdock-data/digital_trials/output/test2",
"ligands": "/mnt/dreamdock-data/digital_trials/input/input_knowen_target",
"mutated_protein_fasta": "/mnt/dreamdock-data/digital_trials/input/blank",
"protein_zarr": "/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr",
"chembl_db": "/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db"
}

19
params/input_to_run.json Normal file
View File

@@ -0,0 +1,19 @@
{
"container_biotransformer": "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5",
"container_conplex": "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3",
"container_tissue": "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.2",
"container_preprocess": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17",
"container_mass_screen": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:89fe2221ff6c1e67d20294944f97418f2665d95b9fb873eba9e1fcf3dc6d1ea7",
"container_chembl": "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0",
"containerOptions": "--rm",
"mode": "HUMAN",
"keep_enst": false,
"threshold": 0.65,
"protein_network_threshold": 0.65,
"project_name": "input_to_run",
"outdir": "/mnt/dreamdock-data/digital_trials/output",
"ligands": "/mnt/dreamdock-data/digital_trials/input/input_to_run",
"mutated_protein_fasta": "/mnt/dreamdock-data/digital_trials/input/blank",
"protein_zarr": "/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr",
"chembl_db": "/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db"
}

61
test.nf.bk Executable file
View File

@@ -0,0 +1,61 @@
nextflow.enable.dsl=2
//BIOTRANSFORMER
params.container_biotransformer = 'biotransformer:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
params.project_name = 'test'
params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
//CONPLEX
params.container_conplex = 'conplex_dig_pat:latest'
params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input'
params.threshold = 0.8 //0.5 //0.7
params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
params.protein_network_threshold = 0.95
//TISSUE DISTRIBUTION
params.container_tissue = 'tissue:latest'
//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX } from './main_conplex.nf'
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
//TISSUE_DISTRIBUTION
include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
workflow {
//BIOTRANSFORMER
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
switch (params.mode) {
case 'SUPER':
SUPER_TRANSFORMER(lig_ch)
break
case 'HUMAN':
HUMAN_TRANSFORMER(lig_ch)
break
case 'MASS':
METABOLITES_BY_MASS(lig_ch)
break
case 'ORDERED':
ORDERED_SEQUENCE(lig_ch)
break
default:
println("Invalid mode specified: ${params.mode}")
}
GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
//CONPLEX
pat_fasta = Channel.fromPath("${params.mutated_protein_fasta}/*.fasta")
CONPLEX(lig_ch, GET_FINAL_METABOLITES.out, pat_fasta)
NETWORK_ENRICHMENT(CONPLEX.out.interactions)
//TISSUE DISTRIBUTION
TISSUE_DISTRIBUTION(CONPLEX.out.interactions)
}

49
test.nf.save Executable file
View File

@@ -0,0 +1,49 @@
nextflow.enable.dsl=2
//BIOTRANSFORMER
params.container_biotransformer = 'biotransformer:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
params.project_name = 'test'
params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
//CONPLEX
params.container_conplex= 'conplex_dig_pat'
params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input/*.fasta'
params.threshold = 0.2 //0.75
params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX } from './main_conplex.nf'
workflow {
//BIOTRANSFORMER
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
switch (params.mode) {
case 'SUPER':
SUPER_TRANSFORMER(lig_ch)
break
case 'HUMAN':
HUMAN_TRANSFORMER(lig_ch)
break
case 'MASS':
METABOLITES_BY_MASS(lig_ch)
break
case 'ORDERED':
ORDERED_SEQUENCE(lig_ch)
break
default:
println("Invalid mode specified: ${params.mode}")
}
GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
//CONPLEX
}

33
test_bio_metrics_only.nf Normal file
View File

@@ -0,0 +1,33 @@
nextflow.enable.dsl=2
// Default parameters (override via -params-file). Listed here to document every
// parameter this workflow needs. Values copied from a representative job
// (R06-ivan-gabe-bioprops-rerun/J17-bioprops/params.json).
params.container_biotransformer = "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5"
params.container_conplex = "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3"
params.container_tissue = "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.1.0"
params.container_preprocess = "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17"
params.container_mass_screen = "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1"
params.container_chembl = "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0"
params.containerOptions = "--rm"
params.project_name = "bioprops-gabe-run-drug-target"
params.outdir = "/mnt/dreamdock-data/digital_trials/runs/R06-ivan-gabe-bioprops-rerun/J17-bioprops/output"
params.ligands = "/mnt/dreamdock-data/digital_trials/input/gabe-run/input/ligand-drug-target"
params.metabolites = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/screening"
params.conplex_dir = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/conplex"
include { BIO_METRICS } from './main_tissue.nf'
workflow {
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
.map { [it.simpleName, it] }
met_ch = Channel.fromPath("${params.metabolites}/*_out.txt")
.map { f -> [f.simpleName.replaceAll(/_out$/, ''), f] }
drug_ch = Channel.fromPath("${params.conplex_dir}/*_patient_0_drug_scores.tsv")
.map { f -> [f.simpleName.replaceAll(/_patient_0_drug_scores$/, ''), f] }
int_ch = Channel.fromPath("${params.conplex_dir}/*_patient_0_significant_interactions.tsv")
.map { f -> [f.simpleName.replaceAll(/_patient_0_significant_interactions$/, ''), f] }
biometric_ch = lig_ch.join(met_ch).join(drug_ch).join(int_ch)
BIO_METRICS(biometric_ch)
}

93
test_no_bt.nf Normal file
View File

@@ -0,0 +1,93 @@
nextflow.enable.dsl=2
// Digital-trials pipeline WITHOUT biotransformer.
// Metabolites are supplied externally (e.g. the consolidated final-metabolites
// dir from prior gabe runs). Otherwise identical to test.nf.
//
// New required param vs test.nf:
// params.metabolites - dir of `<stem>_out.txt` files matching ligand `<stem>.csv`
// Dropped (no biotransformer/chembl):
// container_biotransformer, container_chembl, bt_* knobs, chembl_db, mode
params.container_conplex = 'harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3'
params.container_tissue = 'harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.6'
params.container_preprocess = 'harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17'
params.container_mass_screen = 'harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1'
params.containerOptions = '--rm'
params.project_name = 'test_no_bt'
//CONPLEX
params.keep_enst = 'false'
params.conplex_initial_memory = 5
params.conplex_growth_memory = 15
params.conplex_max_retries = 1
params.conplex_fail_action = 'ignore'
params.threshold = 0.65
params.protein_network_threshold = 0.65
// NETWORK_ENRICHMENT (string-db)
params.string_max_forks = 5
params.string_max_retries = 1
params.string_fail_action = 'ignore'
params.string_initial_memory = 1
params.string_growth_memory = 2
// TISSUE_DISTRIBUTION + BIO_METRICS
params.tissue_initial_memory = 5
params.tissue_growth_memory = 5
params.tissue_max_retries = 2
params.tissue_fail_action = 'ignore'
params.bio_initial_memory = 5
params.bio_growth_memory = 5
params.bio_max_retries = 2
params.bio_fail_action = 'ignore'
// ========================================= FILEPATHS ===================================================
params.outdir = '/mnt/omic-next-apis/wes/digital_trials/'
params.ligands = '/mnt/dreamdock-data/digital_trials/input/test_multitaget'
params.metabolites = '/mnt/dreamdock-data/digital_trials/input/test_metabolites'
params.mutated_protein_fasta = '/mnt/dreamdock-data/digital_trials/input/blank'
params.protein_zarr = '/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr'
// =====================================================================================================================================
include { CONPLEX as CONPLEX_ALL } from './main_conplex.nf'
include { PREPROCESS_PROTEIN } from './main_conplex.nf'
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
include { BIO_METRICS } from './main_tissue.nf'
workflow {
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
metabolite_ch = Channel.fromPath("${params.metabolites}/*_out.txt")
protein_fasta = Channel
.fromPath("${params.mutated_protein_fasta}/*.fasta")
.collect()
protein_zarr = PREPROCESS_PROTEIN(protein_fasta).collect().map { it[0] }
pre_protein_zarr = Channel.fromPath(params.protein_zarr)
merged_zarr = protein_zarr.concat(pre_protein_zarr).collect()
lig_with_id = lig_ch.map { csv ->
[csv.simpleName, csv]
}
metabolite_with_id = metabolite_ch.map { txt ->
def name = txt.simpleName.replaceAll(/_out$/, '')
[name, txt]
}
matched_ch = lig_with_id.join(metabolite_with_id)
CONPLEX_ALL(matched_ch, merged_zarr)
conplex_interactions_ch = CONPLEX_ALL.out.map { id, drug, interactions -> interactions }
NETWORK_ENRICHMENT(conplex_interactions_ch)
TISSUE_DISTRIBUTION(conplex_interactions_ch)
biometric_ch = matched_ch.join(CONPLEX_ALL.out)
BIO_METRICS(biometric_ch)
}

27
test_string_only.nf Normal file
View File

@@ -0,0 +1,27 @@
nextflow.enable.dsl=2
// STRING-only re-run workflow
// Feeds existing ConPLex significant_interactions files into NETWORK_ENRICHMENT
//
// Required params:
// interactions - directory containing *_significant_interactions.tsv files
// interaction_ids - comma-separated InChIKey prefixes to select (e.g. "PWKSKIMOESPYIA_SCSAIBSYSA_N,ZETLRLRYANUSAI_SCSAIBSYSA_N")
// if empty/not set, all files in the directory are used
params.protein_network_threshold = 0.65
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
workflow {
if (params.interaction_ids) {
// Build a channel from the explicit list of IDs
ids = params.interaction_ids.tokenize(',')
interactions_ch = Channel
.fromList(ids)
.map { id -> file("${params.interactions}/${id}_patient_0_significant_interactions.tsv") }
} else {
interactions_ch = Channel.fromPath("${params.interactions}/*_significant_interactions.tsv")
}
NETWORK_ENRICHMENT(interactions_ch)
}