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