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Digital Trials pipeline configured for WES

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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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nf_metabol_screen_adaptive/.nextflow.log.4 Normal file
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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