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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
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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