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PengNi / ccsmethphase

Methylatino phasing using PacBio CCS reads
MIT License
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Unknown error when running demo data #4

Open zzbbf123 opened 4 months ago

zzbbf123 commented 4 months ago

Run command：nextflow run main.nf --dsname test -profile singularity,test

Error information：

[process] DSS_callDMR status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: ch_utils port 2: (cntrl) - ; channel: $

Mar-01 17:31:40.300 [main] DEBUG nextflow.Session - Session await > all processes finished Mar-01 17:31:40.301 [main] DEBUG nextflow.Session - Session await > all barriers passed Mar-01 17:31:40.332 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (3) Mar-01 17:31:40.382 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill CheckCMModel (CheckCMModel) -- command: kill -TERM 215509; exit: 1 bash: line 0: kill: (215509) - No such process

Mar-01 17:31:40.411 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: SAMTOOLS_index_bam (hg002.chr20_demo.hifi); status: COMPLETED; exit: 255; error: -; workDir: /mnt/Data_disk/zhoubiaofeng/opt/ccsmethphase/ccsmethphase/work/2b/7203a95eebc6f145e92847bfb52178] Mar-01 17:31:40.412 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=SAMTOOLS_index_bam (hg002.chr20_demo.hifi); work-dir=/mnt/Data_disk/zhoubiaofeng/opt/ccsmethphase/ccsmethphase/work/2b/7203a95eebc6f145e92847bfb52178 error [nextflow.exception.ProcessFailedException]: Process SAMTOOLS_index_bam (hg002.chr20_demo.hifi) terminated with an error exit status (255) Mar-01 17:31:40.415 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Mar-01 17:31:40.452 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=2; succeedDuration=0ms; failedDuration=1m 44s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=20; peakMemory=48 GB; ] Mar-01 17:31:40.452 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Mar-01 17:31:40.455 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Mar-01 17:31:42.313 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Mar-01 19:20:03.349 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Mar-01 19:20:03.386 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Any suggestions to fix this problem?

zzbbf123 commented 4 months ago

Please close this issue, I've found solution to it.