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