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Error executing process > 'pipeline:porechop (1)' #7

Closed passelma42 closed 6 months ago

passelma42 commented 6 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.0.0

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-amplicon --fastq ./fastq --reference ./reference.fa -profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

When running the default command on the testdata provided on the git wf-amplicon:

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'pipeline:porechop (1)'

Relevant log output

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'pipeline:porechop (1)'

Caused by:
  Process `pipeline:porechop (1)` terminated with an error exit status (1)

Command executed:

  (
      # only run porechop if the FASTQ isn't empty
      if [[ -n $(zcat reads.fastq.gz | head -c1) ]]; then
          porechop -i reads.fastq.gz -t 2 --discard_middle
      else
          echo -n
      fi
  )     | fastcat /dev/stdin -s barcode02 -f porechopped-per-file-stats.tsv     | bgzip > porechopped.fastq.gz

Command exit status:
  1

Command output:
  (empty)

Command error:

  Loading reads
  reads.fastq.gz
  586 reads loaded

  Looking for known adapter sets

  0 / 586 (0.0%)Traceback (most recent call last):
    File "/home/epi2melabs/conda/bin/porechop", line 11, in 
      sys.exit(main())
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/porechop/porechop.py", line 38, in main
      matching_sets = find_matching_adapter_sets(check_reads, args.verbosity, args.end_size,
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/porechop/porechop.py", line 312, in find_matching_adapter_sets
      with ThreadPool(threads) as pool:
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/dummy/__init__.py", line 124, in Pool
      return ThreadPool(processes, initializer, initargs)
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/pool.py", line 925, in __init__
      Pool.__init__(self, processes, initializer, initargs)
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/pool.py", line 196, in __init__
      self._change_notifier = self._ctx.SimpleQueue()
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/context.py", line 113, in SimpleQueue
      return SimpleQueue(ctx=self.get_context())
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/queues.py", line 336, in __init__
      self._rlock = ctx.Lock()
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/context.py", line 68, in Lock
      return Lock(ctx=self.get_context())
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/synchronize.py", line 162, in __init__
      SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx)
    File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/synchronize.py", line 57, in __init__
      sl = self._semlock = _multiprocessing.SemLock(
  FileNotFoundError: [Errno 2] No such file or directory

Work dir:
  /home/pieter/test/wf-ampliconseq/wf-amplicon-demo/work/6f/ffbde00bdfad56cf4cc2b63f4a47e4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Application activity log entry

No response

julibeg commented 6 months ago

Hi @passelma42! This one indeed looks interesting! Could you please do the following:

Thanks!

passelma42 commented 6 months ago

I reran with same settings, same issue with porchop. Then I reran with --threads 1 and now I get an issue ' pipeline:variantCallingPipeline:medakaVariant (1)`. Here is the complete log:

Dec-14 16:41:26.878 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-amplicon --fastq wf-amplicon-demo/fastq --reference wf-amplicon-demo/reference.fa --threads 1 -profile singularity Dec-14 16:41:26.935 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.0 Dec-14 16:41:26.958 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/pieter/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.2,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.0 Dec-14 16:41:26.967 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Dec-14 16:41:26.968 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Dec-14 16:41:26.971 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Dec-14 16:41:26.982 [main] INFO org.pf4j.AbstractPluginManager - No plugins Dec-14 16:41:26.999 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/pieter/.nextflow/scm Dec-14 16:41:27.874 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-amplicon.git Dec-14 16:41:27.893 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Dec-14 16:41:27.902 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-amplicon.git Dec-14 16:41:28.869 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/nextflow.config Dec-14 16:41:28.870 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/nextflow.config Dec-14 16:41:28.881 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity Dec-14 16:41:29.042 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, conda, singularity, awsbatch, local] Dec-14 16:41:29.075 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Dec-14 16:41:29.075 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/epi2me-labs/wf-amplicon [cheeky_bell] DSL2 - revision: 20c598be87 [master] Dec-14 16:41:29.076 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Dec-14 16:41:29.076 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Dec-14 16:41:29.079 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/pieter/.nextflow/secrets/store.json Dec-14 16:41:29.083 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@c1e14f] - activable => nextflow.secret.LocalSecretsProvider@c1e14f Dec-14 16:41:29.148 [main] DEBUG nextflow.Session - Session UUID: c3073d1b-5d3c-4e11-b3e4-0cababa345ff Dec-14 16:41:29.148 [main] DEBUG nextflow.Session - Run name: cheeky_bell Dec-14 16:41:29.149 [main] DEBUG nextflow.Session - Executor pool size: 8 Dec-14 16:41:29.160 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Dec-14 16:41:29.164 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Dec-14 16:41:29.188 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.0 build 5889 Created: 15-10-2023 15:07 UTC (17:07 CEST) System: Linux 5.10.102.1-microsoft-standard-WSL2 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.21+9-post-Ubuntu-0ubuntu122.04 Encoding: UTF-8 (UTF-8) Process: 22347@UG-GWH89Y2 [127.0.1.1] CPUs: 8 - Mem: 24.9 GB (11.4 GB) - Swap: 7 GB (7 GB) Dec-14 16:41:29.210 [main] DEBUG nextflow.Session - Work-dir: /home/pieter/test/ampliconseq/work [ext2/ext3] Dec-14 16:41:29.226 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Dec-14 16:41:29.239 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Dec-14 16:41:29.297 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Dec-14 16:41:29.306 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Dec-14 16:41:29.397 [main] DEBUG nextflow.Session - Session start Dec-14 16:41:29.403 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/pieter/test/ampliconseq/output/execution/trace.txt Dec-14 16:41:29.412 [main] DEBUG nextflow.Session - Using default localLib path: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/lib Dec-14 16:41:29.415 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/lib Dec-14 16:41:29.416 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/lib/nfcore_external_javadeps.jar Dec-14 16:41:31.782 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Dec-14 16:41:33.416 [main] INFO nextflow.Nextflow - |||||||||| ____ _ __ _ |||||||||| | _| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-amplicon v1.0.0-g20c598b

Core Nextflow options revision : master runName : cheeky_bell containerEngine: singularity container : [withLabel:wf_common:ontresearch/wf-common:sha91452ece4f647f62b32dac3a614635a6f0d7f8b5, withLabel:wfamplicon:ontresearch/wf-amplicon:sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9, withLabel:medaka:ontresearch/medaka:sha61a9438d745a78030738352e084445a2db3daa2a] launchDir : /home/pieter/test/ampliconseq workDir : /home/pieter/test/ampliconseq/work projectDir : /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon userName : pieter profile : singularity configFiles : /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/nextflow.config

Input Options fastq : wf-amplicon-demo/fastq reference : wf-amplicon-demo/reference.fa

Miscellaneous Options threads : 1

!! Only displaying parameters that differ from the pipeline defaults !!

If you use epi2me-labs/wf-amplicon for your analysis please cite:

This is epi2me-labs/wf-amplicon v1.0.0-g20c598b.

Dec-14 16:41:33.700 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. Dec-14 16:41:33.875 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels ingress,wf_common for process with name fastcat Dec-14 16:41:33.881 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:33.881 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:33.888 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Dec-14 16:41:33.895 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=24.9 GB; capacity=8; pollInterval=100ms; dumpInterval=5m Dec-14 16:41:33.899 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Dec-14 16:41:33.980 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:getVersions Dec-14 16:41:33.981 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:33.981 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:33.984 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:medaka matches labels medaka for process with name pipeline:addMedakaToVersionsFile Dec-14 16:41:33.985 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:33.985 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:33.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:getParams Dec-14 16:41:33.988 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:33.988 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:subsetReads Dec-14 16:41:34.007 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.008 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.026 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:porechop Dec-14 16:41:34.027 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.028 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.086 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:lookupMedakaModel Dec-14 16:41:34.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.087 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.094 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:sanitizeRefFile Dec-14 16:41:34.095 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.095 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.156 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:subsetRefFile Dec-14 16:41:34.157 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.157 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.172 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:alignReads Dec-14 16:41:34.173 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.178 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:bamstats Dec-14 16:41:34.179 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.179 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.187 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:downsampleBAMforMedaka Dec-14 16:41:34.188 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.195 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:medaka matches labels medaka for process with name pipeline:variantCallingPipeline:medakaConsensus Dec-14 16:41:34.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:medaka matches labels medaka for process with name pipeline:variantCallingPipeline:medakaVariant Dec-14 16:41:34.206 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.206 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:mosdepth Dec-14 16:41:34.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.215 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.220 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:variantCallingPipeline:concatMosdepthResultFiles Dec-14 16:41:34.221 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.221 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:collectFilesInDir Dec-14 16:41:34.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.243 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name pipeline:makeReport Dec-14 16:41:34.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wfamplicon matches labels wfamplicon for process with name output Dec-14 16:41:34.257 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Dec-14 16:41:34.257 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Dec-14 16:41:34.260 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: move_or_compress_fq_file, pipeline:getParams, mosdepthWindows, racon, bamstatsPolished, pipeline:addMedakaToVersionsFile, mergeBAMs, checkBamHeaders, alignReads, mergeBams, output, medakaVariant, pipeline:variantCallingPipeline:medakaVariant, makeReport, getVersions, bamstats, pipeline:subsetReads, downsampleReads, downsampleBAMforMedaka, fastcat, miniasm, pipeline:variantCallingPipeline:sanitizeRefFile, lookupMedakaModel, pipeline:variantCallingPipeline:medakaConsensus, subsetReads, collectFilesInDir, mosdepthPerBase, getParams, pipeline:collectFilesInDir, medakaConsensus, sortBam, validate_sample_sheet, alignDraft, alignPolished, sanitizeRefFile, pipeline:variantCallingPipeline:bamstats, pipeline:makeReport, pipeline:variantCallingPipeline:lookupMedakaModel, trimAndQC, pipeline:variantCallingPipeline:subsetRefFile, spoa, pipeline:variantCallingPipeline:alignReads, subsetRefFile, pipeline:variantCallingPipeline:concatMosdepthResultFiles, concatTSVs, porechop, mergeVCFs, pipeline:variantCallingPipeline:downsampleBAMforMedaka, pipeline:getVersions, pipeline:variantCallingPipeline:mosdepth, concatMosdepthResultFiles, addMedakaToVersionsFile, mosdepth, pipeline:porechop, catSortBams, bamstatsDraft Dec-14 16:41:34.262 [main] DEBUG nextflow.Session - Igniting dataflow network (24) Dec-14 16:41:34.269 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat Dec-14 16:41:34.271 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions Dec-14 16:41:34.271 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:addMedakaToVersionsFile Dec-14 16:41:34.271 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams Dec-14 16:41:34.272 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:subsetReads Dec-14 16:41:34.273 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:porechop Dec-14 16:41:34.273 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:lookupMedakaModel Dec-14 16:41:34.273 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:sanitizeRefFile Dec-14 16:41:34.275 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:subsetRefFile Dec-14 16:41:34.276 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:alignReads Dec-14 16:41:34.277 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:bamstats Dec-14 16:41:34.278 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:downsampleBAMforMedaka Dec-14 16:41:34.278 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:medakaConsensus Dec-14 16:41:34.278 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:medakaVariant Dec-14 16:41:34.279 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:mosdepth Dec-14 16:41:34.279 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:variantCallingPipeline:concatMosdepthResultFiles Dec-14 16:41:34.280 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:collectFilesInDir Dec-14 16:41:34.280 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport Dec-14 16:41:34.281 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output Dec-14 16:41:34.286 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_2e4636f81299b22c: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/./modules/local/de-novo.nf Script_c1b12b2c3382efac: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/./modules/local/variant-calling.nf Script_041e7e8878c9f792: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/./modules/local/./common.nf Script_f885de694c629aa8: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/./lib/ingress.nf Script_75200e6a630f4384: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/main.nf Dec-14 16:41:34.287 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Dec-14 16:41:34.287 [main] DEBUG nextflow.Session - Session await Dec-14 16:41:34.405 [Actor Thread 22] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/pieter/test/ampliconseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Dec-14 16:41:34.408 [Actor Thread 10] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-common:sha91452ece4f647f62b32dac3a614635a6f0d7f8b5 [cache /home/pieter/test/ampliconseq/work/singularity/ontresearch-wf-common-sha91452ece4f647f62b32dac3a614635a6f0d7f8b5.img] Dec-14 16:41:34.408 [Actor Thread 22] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/wf-amplicon:sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9 [cache /home/pieter/test/ampliconseq/work/singularity/ontresearch-wf-amplicon-sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9.img] Dec-14 16:41:35.628 [Actor Thread 10] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://ontresearch/wf-common:sha91452ece4f647f62b32dac3a614635a6f0d7f8b5 path=/home/pieter/test/ampliconseq/work/singularity/ontresearch-wf-common-sha91452ece4f647f62b32dac3a614635a6f0d7f8b5.img Dec-14 16:41:35.650 [Actor Thread 22] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://ontresearch/wf-amplicon:sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9 path=/home/pieter/test/ampliconseq/work/singularity/ontresearch-wf-amplicon-sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9.img Dec-14 16:41:35.660 [Actor Thread 24] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/data/medaka_models.tsv Dec-14 16:41:35.664 [Actor Thread 24] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pieter/.nextflow/assets/epi2me-labs/wf-amplicon/bin/workflow-glue Dec-14 16:41:35.723 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:35.725 [Task submitter] INFO nextflow.Session - [c0/0e0b82] Submitted process > pipeline:getParams Dec-14 16:41:35.736 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:35.736 [Task submitter] INFO nextflow.Session - [a6/01b0f3] Submitted process > pipeline:variantCallingPipeline:sanitizeRefFile Dec-14 16:41:35.745 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:35.745 [Task submitter] INFO nextflow.Session - [29/d6dc20] Submitted process > pipeline:variantCallingPipeline:lookupMedakaModel Dec-14 16:41:35.753 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:35.753 [Task submitter] INFO nextflow.Session - [16/5ba808] Submitted process > pipeline:getVersions Dec-14 16:41:35.761 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:35.762 [Task submitter] INFO nextflow.Session - [02/5b191f] Submitted process > fastcat (1) Dec-14 16:41:36.024 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/c0/0e0b8269eef7fa72e499458ccdaa83] Dec-14 16:41:36.267 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: pipeline:variantCallingPipeline:sanitizeRefFile; status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/a6/01b0f37f1a4d543e7d437a6b84178f] Dec-14 16:41:36.274 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:36.297 [Task submitter] INFO nextflow.Session - [93/68045f] Submitted process > fastcat (2) Dec-14 16:41:36.826 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/02/5b191f4f79f1ea28302a6f9aa55548] Dec-14 16:41:36.852 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:36.852 [Task submitter] INFO nextflow.Session - [bf/eac796] Submitted process > pipeline:subsetReads (1) Dec-14 16:41:36.957 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: fastcat (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/93/68045f9ccfcd3e98a40139a0e885e9] Dec-14 16:41:36.974 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:36.975 [Task submitter] INFO nextflow.Session - [d2/b6d5dc] Submitted process > pipeline:subsetReads (2) Dec-14 16:41:55.118 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: pipeline:variantCallingPipeline:lookupMedakaModel; status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/29/d6dc2061d164ba596a87fc7bf696a7] Dec-14 16:41:55.827 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: pipeline:subsetReads (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/bf/eac796bee24aa07d0af0442c08c93c] Dec-14 16:41:55.839 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:55.840 [Task submitter] INFO nextflow.Session - [70/aff73f] Submitted process > pipeline:porechop (1) Dec-14 16:41:56.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: pipeline:subsetReads (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/d2/b6d5dc6393578db41bb641edb304c4] Dec-14 16:41:56.015 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:41:56.015 [Task submitter] INFO nextflow.Session - [8d/c833f5] Submitted process > pipeline:porechop (2) Dec-14 16:41:58.046 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/16/5ba80860bea18a921b7fc10a608bec] Dec-14 16:41:58.050 [Actor Thread 6] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://ontresearch/medaka:sha61a9438d745a78030738352e084445a2db3daa2a [cache /home/pieter/test/ampliconseq/work/singularity/ontresearch-medaka-sha61a9438d745a78030738352e084445a2db3daa2a.img] Dec-14 16:42:08.447 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: pipeline:porechop (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/70/aff73f9021918f6b8b1a8b68f92b19] Dec-14 16:42:11.517 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: pipeline:porechop (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/8d/c833f5886443a60e2b9de833727fb3] Dec-14 16:42:11.539 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:11.540 [Task submitter] INFO nextflow.Session - [70/b4f005] Submitted process > pipeline:variantCallingPipeline:alignReads (2) Dec-14 16:42:11.546 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:11.546 [Task submitter] INFO nextflow.Session - [b6/41fe5a] Submitted process > pipeline:variantCallingPipeline:alignReads (1) Dec-14 16:42:12.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: pipeline:variantCallingPipeline:alignReads (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/70/b4f005a49474ae3b14c9ee1acc1dd3] Dec-14 16:42:12.351 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.352 [Task submitter] INFO nextflow.Session - [0f/e5f6d6] Submitted process > pipeline:variantCallingPipeline:mosdepth (3) Dec-14 16:42:12.358 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.358 [Task submitter] INFO nextflow.Session - [b1/f02547] Submitted process > pipeline:variantCallingPipeline:bamstats (1) Dec-14 16:42:12.367 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.367 [Task submitter] INFO nextflow.Session - [51/dfc658] Submitted process > pipeline:variantCallingPipeline:mosdepth (5) Dec-14 16:42:12.380 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: pipeline:variantCallingPipeline:alignReads (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/b6/41fe5a3f9814864f52f1c8a2fc03ef] Dec-14 16:42:12.381 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.381 [Task submitter] INFO nextflow.Session - [82/f45fb8] Submitted process > pipeline:variantCallingPipeline:mosdepth (1) Dec-14 16:42:12.408 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.408 [Task submitter] INFO nextflow.Session - [5b/a523ce] Submitted process > pipeline:variantCallingPipeline:mosdepth (2) Dec-14 16:42:12.428 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.428 [Task submitter] INFO nextflow.Session - [9e/7ddf59] Submitted process > pipeline:variantCallingPipeline:mosdepth (4) Dec-14 16:42:12.444 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:12.444 [Task submitter] INFO nextflow.Session - [c6/13cc3c] Submitted process > pipeline:variantCallingPipeline:bamstats (2) Dec-14 16:42:13.109 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: pipeline:variantCallingPipeline:mosdepth (5); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/51/dfc6583d10d8f23224732670c3826a] Dec-14 16:42:13.114 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:13.115 [Task submitter] INFO nextflow.Session - [7c/3bdf68] Submitted process > pipeline:variantCallingPipeline:mosdepth (7) Dec-14 16:42:13.319 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: pipeline:variantCallingPipeline:mosdepth (3); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/0f/e5f6d6a1f7427aeb9f3da9bc05b8ef] Dec-14 16:42:13.386 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:13.395 [Task submitter] INFO nextflow.Session - [53/2ae134] Submitted process > pipeline:variantCallingPipeline:mosdepth (6) Dec-14 16:42:13.591 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: pipeline:variantCallingPipeline:mosdepth (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/82/f45fb8c0a41cfe1aacbc843efd85ec] Dec-14 16:42:13.604 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:13.605 [Task submitter] INFO nextflow.Session - [bf/b2679e] Submitted process > pipeline:variantCallingPipeline:mosdepth (10) Dec-14 16:42:13.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: pipeline:variantCallingPipeline:bamstats (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/b1/f02547fa6199210bf871687606a5aa] Dec-14 16:42:13.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: pipeline:variantCallingPipeline:mosdepth (4); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/9e/7ddf59e287fd19ac0532b3724428ae] Dec-14 16:42:13.858 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:13.859 [Task submitter] INFO nextflow.Session - [0a/d7ff6c] Submitted process > pipeline:variantCallingPipeline:mosdepth (9) Dec-14 16:42:13.917 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: pipeline:variantCallingPipeline:mosdepth (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/5b/a523ceeb9011a7fc711834e217d666] Dec-14 16:42:13.931 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:13.931 [Task submitter] INFO nextflow.Session - [10/2c1ab9] Submitted process > pipeline:variantCallingPipeline:mosdepth (8) Dec-14 16:42:13.933 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: pipeline:variantCallingPipeline:bamstats (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/c6/13cc3ccd561e776d562a2c2e5108a0] Dec-14 16:42:14.203 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: pipeline:variantCallingPipeline:mosdepth (7); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/7c/3bdf68a33986b1523da79478ecbddd] Dec-14 16:42:14.212 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:14.212 [Task submitter] INFO nextflow.Session - [7d/b2662c] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (1) Dec-14 16:42:14.685 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: pipeline:variantCallingPipeline:mosdepth (6); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/53/2ae1344cda5f81a7402def49245ad7] Dec-14 16:42:14.760 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: pipeline:variantCallingPipeline:mosdepth (10); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/bf/b2679ea09a2852a15f3f74a69f7176] Dec-14 16:42:14.765 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:14.765 [Task submitter] INFO nextflow.Session - [f2/137519] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (2) Dec-14 16:42:14.875 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: pipeline:variantCallingPipeline:mosdepth (9); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/0a/d7ff6c3ce28126145b8441131bc41b] Dec-14 16:42:14.987 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: pipeline:variantCallingPipeline:mosdepth (8); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/10/2c1ab9f30dc45d5bacdcca8da0d1de] Dec-14 16:42:15.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:15.009 [Task submitter] INFO nextflow.Session - [ec/172681] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (1) Dec-14 16:42:15.019 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:42:15.019 [Task submitter] INFO nextflow.Session - [86/3e766f] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (2) Dec-14 16:42:15.518 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: pipeline:variantCallingPipeline:concatMosdepthResultFiles (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/86/3e766f90ab28d0249c2ff4765ebc0e] Dec-14 16:42:15.567 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: pipeline:variantCallingPipeline:concatMosdepthResultFiles (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/ec/172681d1ad0c1ace78984f78724d6b] Dec-14 16:42:39.867 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: pipeline:variantCallingPipeline:downsampleBAMforMedaka (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/7d/b2662c34e0da6dab402a872731729a] Dec-14 16:42:39.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: pipeline:variantCallingPipeline:downsampleBAMforMedaka (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/f2/137519ae908cc83b3d7919cd7aca87] Dec-14 16:46:34.094 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > No more task to compute -- The following nodes are still active: [process] pipeline:addMedakaToVersionsFile status=ACTIVE port 0: (value) bound ; channel: old_versions.txt port 1: (cntrl) - ; channel: $

[process] pipeline:variantCallingPipeline:medakaConsensus status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: medaka_model port 2: (cntrl) - ; channel: $

[process] pipeline:variantCallingPipeline:medakaVariant status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: min_coverage port 2: (cntrl) - ; channel: $

[process] pipeline:collectFilesInDir status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] pipeline:makeReport status=ACTIVE port 0: (value) OPEN ; channel: data/* port 1: (value) bound ; channel: ref port 2: (value) bound ; channel: sample_sheet port 3: (value) OPEN ; channel: versions.txt port 4: (value) bound ; channel: params.json port 5: (cntrl) - ; channel: $

[process] output status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

Dec-14 16:47:17.202 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://ontresearch/medaka:sha61a9438d745a78030738352e084445a2db3daa2a path=/home/pieter/test/ampliconseq/work/singularity/ontresearch-medaka-sha61a9438d745a78030738352e084445a2db3daa2a.img Dec-14 16:47:17.216 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:17.217 [Task submitter] INFO nextflow.Session - [06/bedc69] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (1) Dec-14 16:47:17.223 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:17.223 [Task submitter] INFO nextflow.Session - [dd/f8f899] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (2) Dec-14 16:47:17.229 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:17.229 [Task submitter] INFO nextflow.Session - [f1/3046a5] Submitted process > pipeline:addMedakaToVersionsFile Dec-14 16:47:17.231 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 8 -- tasks to be submitted are shown below ~> TaskHandler[id: 37; name: pipeline:variantCallingPipeline:medakaConsensus (8); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/b6/b764ab6cc766020da3979c395b3082] ~> TaskHandler[id: 34; name: pipeline:variantCallingPipeline:medakaConsensus (5); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/3a/c440e2def6d0d9a04214a829d90d80] ~> TaskHandler[id: 36; name: pipeline:variantCallingPipeline:medakaConsensus (7); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/22/6c396d9d2962ffdf4e83ad0c4a56a1] ~> TaskHandler[id: 33; name: pipeline:variantCallingPipeline:medakaConsensus (4); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/63/574983f4c85b7d9f01f8b66a9d23e3] ~> TaskHandler[id: 32; name: pipeline:variantCallingPipeline:medakaConsensus (3); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/0d/a4872f14759eb5323aef539efc15bd] ~> TaskHandler[id: 35; name: pipeline:variantCallingPipeline:medakaConsensus (6); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/37/d8da423707a282ad7eb540e0bc92c8] ~> TaskHandler[id: 39; name: pipeline:variantCallingPipeline:medakaConsensus (10); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/82/26bd005921d0c7a227cc1cab54d5a7] ~> TaskHandler[id: 38; name: pipeline:variantCallingPipeline:medakaConsensus (9); status: NEW; exit: -; error: -; workDir: /home/pieter/test/ampliconseq/work/1a/52393eff3ae2a92fd1d8936dfe17b1] Dec-14 16:47:22.649 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: pipeline:addMedakaToVersionsFile; status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/f1/3046a57bc4abeb957cbca8d07f5d35] Dec-14 16:47:22.654 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:22.654 [Task submitter] INFO nextflow.Session - [b6/b764ab] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (8) Dec-14 16:47:38.537 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: pipeline:variantCallingPipeline:medakaConsensus (2); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/dd/f8f899aaa6b541837f5a77d1be75b5] Dec-14 16:47:38.542 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:38.542 [Task submitter] INFO nextflow.Session - [3a/c440e2] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (5) Dec-14 16:47:40.870 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: pipeline:variantCallingPipeline:medakaConsensus (8); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/b6/b764ab6cc766020da3979c395b3082] Dec-14 16:47:40.875 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:40.875 [Task submitter] INFO nextflow.Session - [22/6c396d] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (7) Dec-14 16:47:47.307 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: pipeline:variantCallingPipeline:medakaConsensus (1); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/06/bedc696ec4a3246cab72209bfb92e9] Dec-14 16:47:47.313 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:47:47.313 [Task submitter] INFO nextflow.Session - [63/574983] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (4) Dec-14 16:48:02.331 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: pipeline:variantCallingPipeline:medakaConsensus (4); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/63/574983f4c85b7d9f01f8b66a9d23e3] Dec-14 16:48:02.342 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:02.342 [Task submitter] INFO nextflow.Session - [0d/a4872f] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (3) Dec-14 16:48:14.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: pipeline:variantCallingPipeline:medakaConsensus (5); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/3a/c440e2def6d0d9a04214a829d90d80] Dec-14 16:48:14.091 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:14.092 [Task submitter] INFO nextflow.Session - [37/d8da42] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (6) Dec-14 16:48:16.191 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: pipeline:variantCallingPipeline:medakaConsensus (7); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/22/6c396d9d2962ffdf4e83ad0c4a56a1] Dec-14 16:48:16.196 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:16.197 [Task submitter] INFO nextflow.Session - [82/26bd00] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (10) Dec-14 16:48:29.638 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: pipeline:variantCallingPipeline:medakaConsensus (6); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/37/d8da423707a282ad7eb540e0bc92c8] Dec-14 16:48:29.642 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:29.643 [Task submitter] INFO nextflow.Session - [1a/52393e] Submitted process > pipeline:variantCallingPipeline:medakaConsensus (9) Dec-14 16:48:32.486 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: pipeline:variantCallingPipeline:medakaConsensus (10); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/82/26bd005921d0c7a227cc1cab54d5a7] Dec-14 16:48:33.287 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: pipeline:variantCallingPipeline:medakaConsensus (3); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/0d/a4872f14759eb5323aef539efc15bd] Dec-14 16:48:52.347 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: pipeline:variantCallingPipeline:medakaConsensus (9); status: COMPLETED; exit: 0; error: -; workDir: /home/pieter/test/ampliconseq/work/1a/52393eff3ae2a92fd1d8936dfe17b1] Dec-14 16:48:52.360 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:52.360 [Task submitter] INFO nextflow.Session - [80/d3b8b6] Submitted process > pipeline:variantCallingPipeline:medakaVariant (2) Dec-14 16:48:52.371 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Dec-14 16:48:52.372 [Task submitter] INFO nextflow.Session - [44/01d831] Submitted process > pipeline:variantCallingPipeline:medakaVariant (1) Dec-14 16:48:54.413 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: pipeline:variantCallingPipeline:medakaVariant (2); status: COMPLETED; exit: 1; error: -; workDir: /home/pieter/test/ampliconseq/work/80/d3b8b6145a0857dfddf1550f647ff5] Dec-14 16:48:54.417 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=pipeline:variantCallingPipeline:medakaVariant (2); work-dir=/home/pieter/test/ampliconseq/work/80/d3b8b6145a0857dfddf1550f647ff5 error [nextflow.exception.ProcessFailedException]: Process pipeline:variantCallingPipeline:medakaVariant (2) terminated with an error exit status (1) Dec-14 16:48:54.428 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:variantCallingPipeline:medakaVariant (2)'

Caused by: Process pipeline:variantCallingPipeline:medakaVariant (2) terminated with an error exit status (1)

Command executed:

medaka variant reference.fasta consensus_probs*.hdf medaka.vcf medaka tools annotate --dpsp medaka.vcf reference.fasta input.bam medaka.annotated.unfiltered.vcf

use the sample alias as sample name in the VCF and filter variants

bcftools reheader medaka.annotated.unfiltered.vcf -s <(echo 'barcode01') | bcftools filter -e 'INFO/DP < 20' -s LOW_DEPTH -Oz -o medaka.annotated.vcf.gz

make consensus seqs

bcftools index medaka.annotated.vcf.gz bcftools consensus -f reference.fasta medaka.annotated.vcf.gz -i 'FILTER="PASS"' -o medaka.consensus.fasta

Command exit status: 1

Command output: (empty)

Command error: Cannot import pyabpoa, some features may not be available. Traceback (most recent call last): File "/home/epi2melabs/conda/bin/medaka", line 8, in sys.exit(main()) File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 814, in main args.func(args) File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/variant.py", line 190, in variants_from_hdf index = medaka.datastore.DataIndex(args.inputs) File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/datastore.py", line 422, in init self._extract_sample_registries() File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/datastore.py", line 433, in _extract_sample_registries with ProcessPoolExecutor(self.threads) as executor: File "/home/epi2melabs/conda/lib/python3.8/concurrent/futures/process.py", line 555, in init self._call_queue = _SafeQueue( File "/home/epi2melabs/conda/lib/python3.8/concurrent/futures/process.py", line 165, in init super().init(max_size, ctx=ctx) File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/queues.py", line 42, in init self._rlock = ctx.Lock() File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/context.py", line 68, in Lock return Lock(ctx=self.get_context()) File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/synchronize.py", line 162, in init SemLock.init(self, SEMAPHORE, 1, 1, ctx=ctx) File "/home/epi2melabs/conda/lib/python3.8/multiprocessing/synchronize.py", line 57, in init sl = self._semlock = _multiprocessing.SemLock( FileNotFoundError: [Errno 2] No such file or directory

Work dir: /home/pieter/test/ampliconseq/work/80/d3b8b6145a0857dfddf1550f647ff5

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line Dec-14 16:48:54.436 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process pipeline:variantCallingPipeline:medakaVariant (2) terminated with an error exit status (1) Dec-14 16:48:54.442 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] pipeline:collectFilesInDir status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

[process] pipeline:makeReport status=ACTIVE port 0: (value) OPEN ; channel: data/* port 1: (value) bound ; channel: ref port 2: (value) bound ; channel: sample_sheet port 3: (value) bound ; channel: versions.txt port 4: (value) bound ; channel: params.json port 5: (cntrl) - ; channel: $

[process] output status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $

Dec-14 16:48:54.754 [main] DEBUG nextflow.Session - Session await > all processes finished Dec-14 16:48:54.755 [main] DEBUG nextflow.Session - Session await > all barriers passed Dec-14 16:48:54.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: pipeline:variantCallingPipeline:medakaVariant (1); status: COMPLETED; exit: 1; error: -; workDir: /home/pieter/test/ampliconseq/work/44/01d831770c2c8f92afe579e5535821] Dec-14 16:48:54.769 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=pipeline:variantCallingPipeline:medakaVariant (1); work-dir=/home/pieter/test/ampliconseq/work/44/01d831770c2c8f92afe579e5535821 error [nextflow.exception.ProcessFailedException]: Process pipeline:variantCallingPipeline:medakaVariant (1) terminated with an error exit status (1) Dec-14 16:48:54.775 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Dec-14 16:48:54.837 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=39; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=6m 39s; failedDuration=4.3s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=7; peakCpus=8; peakMemory=24 GB; ] Dec-14 16:48:54.838 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Dec-14 16:48:54.840 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Dec-14 16:48:55.741 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Dec-14 16:48:55.993 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Dec-14 16:48:56.062 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

julibeg commented 6 months ago

My best guess is that this is related to Singularity and permissions on your /dev/shm and / or /run/shm (https://github.com/apptainer/singularity/issues/875).

Could you please try the following:

passelma42 commented 6 months ago

hi Julibeg,

Thanks for the suggestion! Adding the -B part to the .command.run did the trick, I'm working in WSL and the permissions for this directory are: $ ll /run/shm/ total 0 drwxrwxrwt 2 root root 40 Dec 15 11:32 ./ drwxr-xr-x 8 root root 160 Dec 15 11:20 ../

For this wf in particular (I already successfully ran other ONT wf with singularity) what would be the best/safest approach? Change the permission of /run/shm to 777?

julibeg commented 6 months ago

hmm, I'm also on WSL and the permissions or /run/shm are the same for me.

Could you paste the perms for /dev/shm and also the output of singularity --version please?

passelma42 commented 6 months ago

$ ll /dev/shm lrwxrwxrwx 1 root root 8 Dec 15 11:20 /dev/shm -> /run/shm/

$ ll /run/shm total 0 drwxrwxrwt 2 root root 40 Dec 15 11:32 ./ drwxr-xr-x 9 root root 180 Dec 15 11:48 ../ (base)

$ singularity --version singularity-ce version 4.0.0-rc.1+254-g8c1e06338

julibeg commented 6 months ago

Ok, looks like this is not the issue then. Do you know if the Singularity setup / config is customised on your machine in any way (e.g. by setting some singularity env vars in your ~/.bashrc)? Another thing you could try is nuking and re-installing Singularity (or Apptainer). Once done that, you don't need to run the wf to see if the problem was fixed. Simply trying to create a Python multiprocessing.Pool within the container should be enough (as shown in the issue I linked above).

Alternatively, you could put the singularity run options into your global nextflow config (at ~/.nextflow/config like below):

profiles {
    singularity {
        singularity.runOptions = "-B /run/shm:/run/shm"
    }
}

Or you could put the above into a separate config file and add it to the nextflow run command with -c my-local-config.

passelma42 commented 6 months ago

I went with the "~.nextflow/config file". This option worked for me. Thanks a lot for the help!