NFCORE_QUANTMS:QUANTMS:LFQ:MSSTATS Missing output file(s) `*.csv`

[Ministreliya131]

Description of the bug

Greetings!

We want to use quantms on a computing cluster in a Docker virtual environment. We installed it according to the instructions in documentatiob. In the test example "test_lfq" (test_lfq.config), the workflow worked without errors, but when using test data "test_full_lfq" (test_full_lfq.config), an error occurred:

Missing output file(s) *.csv expected by process NFCORE_QUANTMS:QUANTMS:LFQ:MSSTATS (table.sdrf_openms_design_msstats_in.csv) (note: input files are not included in the default matching set)

What could this be related to?

Thank you!

Command used and terminal output

No response

Relevant files

Command error: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Attaching package: ‘MSstats’

The following object is masked from ‘package:grDevices’:

  savePlot

Work dir: /home/fox/quantms/work/48/0b7093c90d9b457996be9ca5cd9966

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run Jan-08 14:20:10.877 [TaskFinalizer-3] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Jan-08 14:20:10.884 [Actor Thread 41] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 14; slices: 1; internal sort time: 0.005 s; external sort time: 0.002 s; total time: 0.007 s Jan-08 14:20:10.884 [TaskFinalizer-3] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Jan-08 14:20:10.885 [main] DEBUG nextflow.Session - Session await > all processes finished Jan-08 14:20:10.888 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Jan-08 14:20:10.893 [main] DEBUG nextflow.Session - Session await > all barriers passed Jan-08 14:20:10.899 [Actor Thread 41] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/fox/quantms/work/collect-file/ab941bf65146d8f6c9b46658397d55e2 Jan-08 14:20:10.902 [Actor Thread 41] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-3751523623559604251 Jan-08 14:20:10.906 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Jan-08 14:20:10.906 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Jan-08 14:20:10.912 [main] INFO nextflow.Nextflow - -[nf-core/quantms] Pipeline completed with errors- Jan-08 14:20:10.916 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=72; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=15h 25m 13s; failedDuration=28s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=18; peakCpus=36; peakMemory=108 GB; ] Jan-08 14:20:10.916 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jan-08 14:20:10.917 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jan-08 14:20:11.815 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jan-08 14:20:12.113 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jan-08 14:20:12.128 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin '[email protected]' Jan-08 14:20:12.129 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation Jan-08 14:20:12.130 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jan-08 14:20:12.132 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye fox@proteomics:~/quantms$

System information

Nextflow version -- 24.04.4.5917 Hardware -- Cloud Container engine -- Docker OS -- Linux Ubuntu (Linux 5.4.0-128-generic) CPUs -- 48 - Mem: 94.4 GB (90.6 GB) - Swap: 0 (0) Runtime -- Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.16+8-post-Ubuntu-0ubuntu120.04 Version of nf-core/quantms -- 1.3.0

[emilsporre]

I also have this issue, did you ever solve it?

[jpfeuffer]

You need to check the logs in the workdir printed (/home/fox/quantms/work/48/0b7093c90d9b457996be9ca5cd9966 in the above case) to see what actually went wrong in the msstats step. The nextflow log is often not detailed enough.