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9e75f44f1acdf35c2b091b900a920ddc21bad0f0
digital-trial/nf_metabol_screen_adaptive/.nextflow.log.2
Olamide Isreal 9e75f44f1a Digital Trials pipeline configured for WES 
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.
2026-07-27 21:59:52 +01:00

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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
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