omic/digital-trial
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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
Download Patch File Download Diff File Expand all files Collapse all files

94
nf_metabol_screen_adaptive/.nextflow.log Normal file
View File

@@ -0,0 +1,94 @@
Jul-21 03:07:10.282 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf
Jul-21 03:07:10.349 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.2
Jul-21 03:07:10.366 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.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@1.11.2,nf-wave@1.12.1
Jul-21 03:07:10.387 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-21 03:07:10.388 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-21 03:07:10.390 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-21 03:07:10.399 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-21 03:07:10.415 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-21 03:07:10.417 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/nextflow.config
Jul-21 03:07:10.442 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Jul-21 03:07:10.445 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@759d81f3] - activable => nextflow.secret.LocalSecretsProvider@759d81f3
Jul-21 03:07:10.450 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jul-21 03:07:10.819 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-21 03:07:10.830 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [confident_euler] DSL2 - revision: b00b655f5b
Jul-21 03:07:10.831 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-21 03:07:10.831 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Session UUID: 5e2c3d52-6405-43b3-a203-f96c06488e9b
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Run name: confident_euler
Jul-21 03:07:10.871 [main] DEBUG nextflow.Session - Executor pool size: 20
Jul-21 03:07:10.878 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-21 03:07:10.883 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-21 03:07:10.901 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.2 build 5947
Created: 13-05-2025 21:58 UTC (14:58 PDT)
System: Linux 6.8.0-52-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 17.0.15+6-Ubuntu-0ubuntu122.04
Encoding: UTF-8 (UTF-8)
Process: 3902257@alien [127.0.1.1]
CPUs: 20 - Mem: 62.6 GB (836.3 MB) - Swap: 2 GB (96.4 MB)
Jul-21 03:07:10.924 [main] DEBUG nextflow.Session - Work-dir: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work [ext2/ext3]
Jul-21 03:07:10.925 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/bin
Jul-21 03:07:10.935 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-21 03:07:10.946 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-21 03:07:10.967 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-21 03:07:10.993 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-21 03:07:11.002 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000
Jul-21 03:07:11.051 [main] DEBUG nextflow.Session - Session start
Jul-21 03:07:11.055 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/execution_trace.txt
Jul-21 03:07:11.178 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-21 03:07:11.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-21 03:07:11.315 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-21 03:07:11.320 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-21 03:07:11.324 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=62.6 GB; capacity=20; pollInterval=100ms; dumpInterval=5m
Jul-21 03:07:11.327 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-21 03:07:11.348 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'METABOLITE_SCREEN': maxForks=0; fair=false; array=0
Jul-21 03:07:11.396 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-21 03:07:11.397 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-21 03:07:11.398 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-21 03:07:11.399 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_9d98cafae0c3b8e5: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/test.nf
Script_c8d2b32ed0aeeac9: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/main.nf
Jul-21 03:07:11.399 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-21 03:07:11.399 [main] DEBUG nextflow.Session - Session await
Jul-21 03:07:11.552 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-21 03:07:11.554 [Task submitter] INFO nextflow.Session - [f9/21c381] Submitted process > METABOLITE_SCREEN
Jul-21 03:07:11.590 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 127; error: -; workDir: /dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9]
Jul-21 03:07:11.591 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=60; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-21 03:07:11.600 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=METABOLITE_SCREEN; work-dir=/dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9
error [nextflow.exception.ProcessFailedException]: Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Jul-21 03:07:11.615 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'METABOLITE_SCREEN'
Caused by:
Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Command executed:
set -e
python /app/screen.py -i metabolites-rev.tsv -z protein_seq.zarr
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 3: python: command not found
Work dir:
/dbs/metabolite-screen-alt/nf_metabol_screen_adaptive/work/f9/21c381bcd7594501602fb392f344c9
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jul-21 03:07:11.621 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-21 03:07:11.628 [TaskFinalizer-1] DEBUG nextflow.Session - Session aborted -- Cause: Process `METABOLITE_SCREEN` terminated with an error exit status (127)
Jul-21 03:07:11.643 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-21 03:07:11.643 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-21 03:07:11.648 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=18ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-21 03:07:11.648 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-21 03:07:11.649 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-21 03:07:12.149 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-21 03:07:12.189 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-21 03:07:12.197 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye