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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
25 stars 12 forks source link

Use docker profile run test data error #14

Open flowhub-team opened 1 year ago

flowhub-team commented 1 year ago

Description of the bug

When I run the Docker profile using virtoprofiler, I run test data with the command/ Nextflow run deng lab/viroprofiler - r main - profile docker, test, but an error was reported.

Command used and terminal output

./nextflow run deng-lab/viroprofiler -r main -profile docker,test

-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
  Process `VIROPROFILER:CHECKV` terminated with an error exit status (1)

Command executed:

  run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /root/viroprofiler/checkv
  mv viruses.fna checkv_qc.fasta
  while [ -s proviruses_nextInput.fna ] ; do
      dir_new=run_$(date +"%Y%m%d%h%s")
      run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /root/viroprofiler/checkv
      cat $dir_new/viruses.fna >> checkv_qc.fasta
      csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
      cp quality_summary.tsv quality_summary_viruses.tsv
      sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
      cat $dir_new/proviruses_short.fna >> proviruses_short.fna
      cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
      cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
      cp $dir_new/proviruses_nextInput.fna .
      sleep 1
  done
  seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:CHECKV":
      CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:

  CheckV v1.0.1: contamination
  [1/8] Reading database info...
  [2/8] Reading genome info...
  [3/8] Calling genes with Prodigal...
  [4/8] Reading gene info...
  [5/8] Running hmmsearch...
  [6/8] Annotating genes...
  [7/8] Identifying host regions...
  [8/8] Writing results...
  Run time: 73.23 seconds
  Peak mem: 0.24 GB

  CheckV v1.0.1: completeness
  [1/8] Skipping gene calling...
  [2/8] Initializing queries and database...
  [3/8] Running DIAMOND blastp search...
  [4/8] Computing AAI...
  [5/8] Running AAI based completeness estimation...
  [6/8] Running HMM based completeness estimation...
  [7/8] Determining genome copy number...
  [8/8] Writing results...
  Run time: 23.19 seconds
  Peak mem: 1.92 GB

  CheckV v1.0.1: complete_genomes
  [1/7] Reading input sequences...
  [2/7] Finding complete proviruses...
  [3/7] Finding direct/inverted terminal repeats...
  [4/7] Filtering terminal repeats...
  [5/7] Checking genome for completeness...
  [6/7] Checking genome for large duplications...
  [7/7] Writing results...
  Run time: 0.02 seconds
  Peak mem: 1.92 GB

  CheckV v1.0.1: quality_summary
  [1/6] Reading input sequences...
  [2/6] Reading results from contamination module...
  [3/6] Reading results from completeness module...
  [4/6] Reading results from complete genomes module...
  [5/6] Classifying contigs into quality tiers...
  [6/6] Writing results...
  Run time: 0.01 seconds
  Peak mem: 1.92 GB
  Traceback (most recent call last):
    File "/root/.nextflow/assets/deng-lab/viroprofiler/bin/correct_spades_contig_length.py", line 5, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /root/work/ec/257e6e3b81260568daf2a6d5051fb4

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`

 -- Check '.nextflow.log' file for details

Relevant files

Aug-04 09:56:56.412 [main] DEBUG nextflow.cli.Launcher - $> nextflow run deng-lab/viroprofiler -r main -profile docker,test Aug-04 09:56:56.476 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2 Aug-04 09:56:56.492 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3 Aug-04 09:56:56.499 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Aug-04 09:56:56.500 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Aug-04 09:56:56.503 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Aug-04 09:56:56.510 [main] INFO org.pf4j.AbstractPluginManager - No plugins Aug-04 09:56:56.521 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /root/.nextflow/scm Aug-04 09:56:57.689 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git Aug-04 09:56:57.707 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Aug-04 09:56:57.714 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git Aug-04 09:56:58.739 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config Aug-04 09:56:58.740 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config Aug-04 09:56:58.746 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker,test Aug-04 09:56:59.441 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, debug, test, apptainer, docker, shifter, charliecloud, test_denglab, conda, singularity, charliecloud_denglab, podman, slurm_denglab2] Aug-04 09:56:59.466 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Aug-04 09:56:59.466 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/deng-lab/viroprofiler [big_wozniak] DSL2 - revision: c2a1f1871b [main] Aug-04 09:56:59.467 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Aug-04 09:56:59.467 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Aug-04 09:56:59.469 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json Aug-04 09:56:59.471 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@240a2619] - activable => nextflow.secret.LocalSecretsProvider@240a2619 Aug-04 09:56:59.512 [main] DEBUG nextflow.Session - Session UUID: 8366e9d9-2a58-4580-9412-d6b9ec23aa9c Aug-04 09:56:59.512 [main] DEBUG nextflow.Session - Run name: big_wozniak Aug-04 09:56:59.513 [main] DEBUG nextflow.Session - Executor pool size: 8 Aug-04 09:56:59.521 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Aug-04 09:56:59.535 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.2 build 5870 Created: 08-06-2023 08:29 UTC (16:29 CDT) System: Linux 5.15.0-73-generic Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.8+7-Ubuntu-122.04 Encoding: UTF-8 (UTF-8) Process: 43715@iZj6c6klemvicp1e0upziuZ [172.24.234.30] CPUs: 8 - Mem: 14.7 GB (8.4 GB) - Swap: 0 (0) Aug-04 09:56:59.545 [main] DEBUG nextflow.Session - Work-dir: /root/work [ext2/ext3] Aug-04 09:56:59.557 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Aug-04 09:56:59.563 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Aug-04 09:56:59.661 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Aug-04 09:56:59.668 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Aug-04 09:56:59.717 [main] DEBUG nextflow.Session - Session start Aug-04 09:56:59.721 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /root/output/pipeline_info/execution_trace_2023-08-04_09-56-59.txt Aug-04 09:56:59.727 [main] DEBUG nextflow.Session - Using default localLib path: /root/.nextflow/assets/deng-lab/viroprofiler/lib Aug-04 09:56:59.729 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/deng-lab/viroprofiler/lib Aug-04 09:56:59.729 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/deng-lab/viroprofiler/lib/nfcore_external_java_deps.jar Aug-04 09:57:00.498 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Aug-04 09:57:00.628 [main] INFO nextflow.Nextflow -

----------------------------------------------------------------------------------------------------------------    oooooo oooo o8o 88 88 .o88o. o8o oooo   888. .8'"' 88 ss 88 888 ""' 888  888. .8' oooo oooo d8b .ooooo. 8888 oooo d8b .ooooo. o888oo oooo 888 .ooooo. oooo d8b   888. .8'888 888""8P d88'88b || 888""8P d88'88b 888 888 888 d88'88b 888""8P  888.8' 888 888 888 888 || 888 888 888 888 888 888 888ooo888 888   888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888  8' o888o d888b Y8bod8P' // \\ d888bY8bod8P' o888o o888o o888o `Y8bod8P' d888b   ViroProfiler v0.2.4 ---------------------------------------------------------------------------------------------------------------- Core Nextflow options revision : main runName : big_wozniak containerEngine : docker launchDir : /root workDir : /root/work projectDir : /root/.nextflow/assets/deng-lab/viroprofiler userName : root profile : docker,test configFiles : /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options mode : all input : https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv db : /root/viroprofiler outdir : output

QC contamref_idx : /root/viroprofiler/contamination_refs/hg19/ref

Contig library parameters assemblies : scaffolds

Others use_iphop : true use_dram : true

Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function

Max job request options max_cpus : 2 max_memory : 6.GB max_time : 24.h

!! Only displaying parameters that differ from the pipeline defaults !! ---------------------------------------------------------------------------------------------------------------- If you use ViroProfiler for your analysis please cite:

Caused by: Process VIROPROFILER:CHECKV terminated with an error exit status (1)

Command executed:

run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /root/viroprofiler/checkv mv viruses.fna checkv_qc.fasta while [ -s proviruses_nextInput.fna ] ; do dirnew=run$(date +"%Y%m%d%h%s") run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /root/viroprofiler/checkv cat $dir_new/viruses.fna >> checkv_qc.fasta csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv cp quality_summary.tsv quality_summary_viruses.tsv sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv cat $dir_new/proviruses_short.fna >> proviruses_short.fna cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list cp $dir_new/proviruses_nextInput.fna . sleep 1 done seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

cat <<-END_VERSIONS > versions.yml "VIROPROFILER:CHECKV": CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//')) END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error:

CheckV v1.0.1: contamination [1/8] Reading database info... [2/8] Reading genome info... [3/8] Calling genes with Prodigal... [4/8] Reading gene info... [5/8] Running hmmsearch... [6/8] Annotating genes... [7/8] Identifying host regions... [8/8] Writing results... Run time: 73.23 seconds Peak mem: 0.24 GB

CheckV v1.0.1: completeness [1/8] Skipping gene calling... [2/8] Initializing queries and database... [3/8] Running DIAMOND blastp search... [4/8] Computing AAI... [5/8] Running AAI based completeness estimation... [6/8] Running HMM based completeness estimation... [7/8] Determining genome copy number... [8/8] Writing results... Run time: 23.19 seconds Peak mem: 1.92 GB

CheckV v1.0.1: complete_genomes [1/7] Reading input sequences... [2/7] Finding complete proviruses... [3/7] Finding direct/inverted terminal repeats... [4/7] Filtering terminal repeats... [5/7] Checking genome for completeness... [6/7] Checking genome for large duplications... [7/7] Writing results... Run time: 0.02 seconds Peak mem: 1.92 GB

CheckV v1.0.1: quality_summary [1/6] Reading input sequences... [2/6] Reading results from contamination module... [3/6] Reading results from completeness module... [4/6] Reading results from complete genomes module... [5/6] Classifying contigs into quality tiers... [6/6] Writing results... Run time: 0.01 seconds Peak mem: 1.92 GB Traceback (most recent call last): File "/root/.nextflow/assets/deng-lab/viroprofiler/bin/correct_spades_contig_length.py", line 5, in from Bio import SeqIO ModuleNotFoundError: No module named 'Bio'

Work dir: /root/work/ec/257e6e3b81260568daf2a6d5051fb4

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 Aug-04 10:00:08.241 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Aug-04 10:00:08.246 [main] DEBUG nextflow.Session - Session await > all processes finished Aug-04 10:00:08.246 [main] DEBUG nextflow.Session - Session await > all barriers passed Aug-04 10:00:08.249 [Actor Thread 12] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 4; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s Aug-04 10:00:08.252 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /root/work/collect-file/7ccdbcda8a5a638859c958f166ae11db Aug-04 10:00:08.253 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5278134370414411846 Aug-04 10:00:08.256 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Aug-04 10:00:08.257 [main] INFO nextflow.Nextflow - -[ViroProfiler] Pipeline completed with errors- Aug-04 10:00:08.260 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=16; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3m 2s; failedDuration=1m 38s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=7; peakCpus=7; peakMemory=14 GB; ] Aug-04 10:00:08.260 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Aug-04 10:00:08.261 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Aug-04 10:00:08.290 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":129.3,"min":112.1,"q1":113.3,"q2":117.1,"q3":132.8,"max":171.2,"minLabel":"VIROPROFILER:FASTQC (UC21)","maxLabel":"VIROPROFILER:FASTQC (UC24)","q1Label":"VIROPROFILER:FASTQC (UC20)","q2Label":"VIROPROFILER:FASTQC (HT04)","q3Label":"VIROPROFILER:FASTQC (HT02)"},"process":"FASTQC","mem":{"mean":286574182.4,"min":239505408,"q1":261390336,"q2":291016704,"q3":308551680,"max":332406784,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"memUsage":{"mean":13.34,"min":11.15,"q1":12.17,"q2":13.55,"q3":14.37,"max":15.48,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.02,"max":0.02,"minLabel":"VIROPROFILER:FASTQC (UC24)","maxLabel":"VIROPROFILER:FASTQC (UC20)","q1Label":"VIROPROFILER:FASTQC (HT02)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (HT04)"},"vmem":{"mean":3303808204.8,"min":3283750912,"q1":3284742144,"q2":3307405312,"q3":3307405312,"max":3335737344,"minLabel":"VIROPROFILER:FASTQC (UC20)","maxLabel":"VIROPROFILER:FASTQC (UC21)","q1Label":"VIROPROFILER:FASTQC (HT04)","q2Label":"VIROPROFILER:FASTQC (HT02)","q3Label":"VIROPROFILER:FASTQC (UC24)"},"reads":{"mean":23803429.4,"min":22835380,"q1":23135026,"q2":23560292,"q3":24362904,"max":25123545,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC21)","q2Label":"VIROPROFILER:FASTQC (UC24)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"cpu":{"mean":129.3,"min":112.1,"q1":113.3,"q2":117.1,"q3":132.8,"max":171.2,"minLabel":"VIROPROFILER:FASTQC (UC21)","maxLabel":"VIROPROFILER:FASTQC (UC24)","q1Label":"VIROPROFILER:FASTQC (UC20)","q2Label":"VIROPROFILER:FASTQC (HT04)","q3Label":"VIROPROFILER:FASTQC (HT02)"},"time":{"mean":6200,"min":5000,"q1":6000,"q2":6000,"q3":7000,"max":7000,"minLabel":"VIROPROFILER:FASTQC (UC24)","maxLabel":"VIROPROFILER:FASTQC (UC20)","q1Label":"VIROPROFILER:FASTQC (HT02)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (HT04)"},"writes":{"mean":3906933.6,"min":3867657,"q1":3895060,"q2":3895592,"q3":3931918,"max":3944441,"minLabel":"VIROPROFILER:FASTQC (HT04)","maxLabel":"VIROPROFILER:FASTQC (HT02)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC20)","q3Label":"VIROPROFILER:FASTQC (UC21)"}},{"cpuUsage":{"mean":98.14,"min":91.8,"q1":98.1,"q2":99.4,"q3":100.4,"max":101,"minLabel":"VIROPROFILER:FASTP (HT02)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (UC20)","q2Label":"VIROPROFILER:FASTP (HT04)","q3Label":"VIROPROFILER:FASTP (UC21)"},"process":"FASTP","mem":{"mean":840258355.2,"min":222191616,"q1":250228736,"q2":1201082368,"q3":1229742080,"max":1298046976,"minLabel":"VIROPROFILER:FASTP (UC20)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (HT04)","q2Label":"VIROPROFILER:FASTP 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Aug-04 10:00:08.628 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Aug-04 10:00:08.849 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Aug-04 10:00:08.857 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Aug-04 10:00:08.858 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

nextflow version 23.04.2.5870 ubuntu 22.04

rujinlong commented 1 year ago

Hi @flowhub-team. This issue arises from the multi-env in micromamba (refer to https://github.com/nextflow-io/nextflow/issues/3206). It seems that your Docker didn't activate the correct conda environment. However, I can't reproduce this error. Could you please update Docker to the latest version and try again? If the problem persists, you have two other options:

  1. Use Singularity instead of Docker.
  2. In the next release (scheduled for the end of this month), I will separate the multi-env into different container images, so that each image contains only one base environment.