CWL : file could not be created with exception File not found
0
1
Entering edit mode
8.4 years ago
skanwal ▴ 50

Hi,

We are trying to create GATK workflow using CWL-draft3. The tool "PrintReads" is throwing the following error:

##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: **Couldn't write file /var/spool/cwl/printReads-2016-25-07.bam because file could not be created with exception File not found: printReads-2016-25-07.bam**
##### ERROR ------------------------------------------------------------------------------------------
Error collecting output for parameter 'output_printReads'
Traceback (most recent call last):
  File "build/bdist.macosx-10.11-intel/egg/cwltool/draft2tool.py", line 330, in collect_output_ports
    ret[fragment] = self.collect_output(port, builder, outdir)
  File "build/bdist.macosx-10.11-intel/egg/cwltool/draft2tool.py", line 405, in collect_output
    raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
WorkflowException: Did not find output file with glob pattern: '['printReads-2016-25-07.bam']'

The command generated by the tool is:

 run \
    -i \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta:/var/lib/cwl/stg301d393b/hg19.fasta:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.amb:/var/lib/cwl/stg301d393b/hg19.fasta.amb:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.ann:/var/lib/cwl/stg301d393b/hg19.fasta.ann:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rbwt:/var/lib/cwl/stg301d393b/hg19.fasta.rbwt:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.pac:/var/lib/cwl/stg301d393b/hg19.fasta.pac:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.sa:/var/lib/cwl/stg301d393b/hg19.fasta.sa:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/indelRealigner-2016-03-07.bai:/var/lib/cwl/stg6208674/indelRealigner-2016-03-07.bai:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.fai:/var/lib/cwl/stg301d393b/hg19.fasta.fai:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/indelRealigner-2016-03-07.bam:/var/lib/cwl/stg6208674/indelRealigner-2016-03-07.bam:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rsa:/var/lib/cwl/stg301d393b/hg19.fasta.rsa:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.bwt:/var/lib/cwl/stg301d393b/hg19.fasta.bwt:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.dict:/var/lib/cwl/stg301d393b/hg19.dict:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rpac:/var/lib/cwl/stg301d393b/hg19.fasta.rpac:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/baseRecalibrator-2016-03-07.table:/var/lib/cwl/stg2d0f63bf/baseRecalibrator-2016-03-07.table:ro' \
    --volume=/var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpaTh8Zp:/var/spool/cwl:rw \
    --volume=/var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpbBNmiv:/tmp:rw \
    --workdir=/var/spool/cwl \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/var/spool/cwl \
    --env=PATH=/usr/local/bin/:/usr/bin:/bin \
    fzkhan/picard-1.136-gatk-2.8 \
    java \
    -Xmx4g \
    -Djava.io.tmpdir=/tmp \
    -jar \
    /home/biodocker/bin/GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar \
    -T \
    PrintReads \
    -R \
    /var/lib/cwl/stg301d393b/hg19.fasta \
    -I \
    /var/lib/cwl/stg6208674/indelRealigner-2016-03-07.bam \
    -BQSR \
    /var/lib/cwl/stg2d0f63bf/baseRecalibrator-2016-03-07.table \
    -o \
    printReads-2016-25-07.bam

Can someone please suggest a possible reason for this? Not sure why is this tool not able to create the final output file. Thanks.
cwl gatk • 3.5k views
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0
Entering edit mode

Can you share your CWL descriptions & how you ran cwltool? Thanks!

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Entering edit mode

The command we are running is: cwltool --debug --tmpdir-prefix=/Users/sehrish/Google\ Drive/Analysis\ using\ Galaxy\,\ Cpipe\ and\ CWL/GATK-worflow/draft3/ --tmp-outdir-prefix=/Users/sehrish/Google\ Drive/Analysis\ using\ Galaxy\,\ Cpipe\ and\ CWL/GATK-worflow/draft3/ ./GATK-PrintReads.cwl ./GATK-PrintReads.json

We have also tried using: cwltool --debug GATK-PrintReads.cwl GATK-PrintReads.json

Here is the link to the CWL descriptions: https://gist.github.com/skanwal/3cf091a377cc49597f3cc045be369122

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0
Entering edit mode

Does this work without Docker by running --no-container?

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0
Entering edit mode

We have changed the script to use jar file but now it's not able to find the jar file and throws the following error:

[job GATK-PrintReads.cwl] /var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpbVvTvC$ java \
    -Xmx4g \
    -Djava.io.tmpdir=/tmp \
    -jar \
    '/Users/sehrish/Google Drive/Analysis using Galaxy, Taverna, cpipe and CWL/GATK-workflow/tools/GATK-2.8/GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar' \
    -T \
    PrintReads \
    -R \
    /var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpmmXRLF/stg21864f8f/hg19.fasta \
    -I \
    /var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpmmXRLF/stg10d0cee8/indelRealigner-2016-03-07.bam \
    -BQSR \
    /var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpmmXRLF/stg21f0b0ef/baseRecalibrator-2016-03-07.table \
    -o \
    printReads-2016-25-07.bam
Error: **Unable to access jarfile /Users/sehrish/Google Drive/Analysis using Galaxy, Taverna, cpipe and CWL/GATK-workflow/tools/GATK-2.8/GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar**
Error collecting output for parameter 'output_printReads'
ADD REPLY •
0
Entering edit mode

So the jar is now an input to the tool?

Can you update your gist or post a new one?

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0
Entering edit mode

Yes. I have added an argument for jar file in the cwltool file I have updated the gist with the new file.

ADD REPLY •
0
Entering edit mode

One problem:

This needs to be a separate input of type File.

Alternatively you can follow the approach recommended in https://github.com/common-workflow-language/workflows/issues/78#issuecomment-217117284

  1. Remove explicit mention of the jar (Lines 195-197)

  2. Change the basecommand:

baseCommand: [ java, org.broadinstitute.sting.gatk.CommandLineGATK ]

  1. Set the CLASSPATH environment variable to the location of the installed jar file 
hints:
 - class: DockerRequirement
   dockerPull: fzkhan/picard-1.136-gatk-2.8
 - class: EnvVarRequirement
   CLASSPATH: /home/biodocker/bin/GenomeAnalysisTK-2.8-1-g932cd3a/
ADD REPLY •
0
Entering edit mode

I have incorporated these changes (updated the gist file with the changes I did) It's throwing the following error Tool definition failed validation: Validating hint EnvVarRequirement: missing required field envDef

The CLASSPATH is the path of the docker file or the locally installed jar file?

ADD REPLY •
0
Entering edit mode

Pardon me, that should have been 

hints:
 - class: DockerRequirement
   dockerPull: fzkhan/picard-1.136-gatk-2.8
 - class: EnvVarRequirement
   envDef: 
     - envName: CLASSPATH
       envValue: /home/biodocker/bin/GenomeAnalysisTK-2.8-1-g932cd3a/

I got that path from your Docker image. If running locally you would set the CLASSPATH in your job input document:

#GATK-PrintReads.yaml
"cwl:requirements":
 - class: EnvVarRequirement
   envDef: 
     - envName: CLASSPATH
       envValue: /local/path/to/GATK-jar/
inputBam_printReads:
  class: File
  path: "../tools/indelRealigner-2016-03-07.bam"
reference:
  class: File
  path: "../tools/outputFiles/hg19.fasta"
input_baseRecalibrator:
  class: File
  path: "../tools/baseRecalibrator-2016-03-07.table"
outputfile_printReads: printReads-2016-25-07.bam
ADD REPLY •
0
Entering edit mode

Hi.

I have tried with and without docker. It's complaining about the "envValue" field (the error below). Also I have updated the GIST repository with the new cwltool definition I am using.

/usr/local/bin/cwltool 1.0.20160701210210
Tool definition failed validation:
Validating hint `EnvVarRequirement`: could not validate field `envDef` because
  At position 0
    missing required field `envValue`
Traceback (most recent call last):
  File "build/bdist.macosx-10.11-intel/egg/cwltool/main.py", line 643, in main
    makeTool, {})
  File "build/bdist.macosx-10.11-intel/egg/cwltool/load_tool.py", line 163, in make_tool
    tool = makeTool(processobj, **kwargs)
  File "build/bdist.macosx-10.11-intel/egg/cwltool/workflow.py", line 32, in defaultMakeTool
    return draft2tool.CommandLineTool(toolpath_object, **kwargs)
  File "build/bdist.macosx-10.11-intel/egg/cwltool/draft2tool.py", line 117, in __init__
    super(CommandLineTool, self).__init__(toolpath_object, **kwargs)
  File "build/bdist.macosx-10.11-intel/egg/cwltool/process.py", line 337, in __init__
    self.validate_hints(kwargs["avsc_names"], self.tool.get("hints", []), strict=kwargs.get("strict"))
  File "build/bdist.macosx-10.11-intel/egg/cwltool/process.py", line 523, in validate_hints
    raise validate.ValidationException(u"Validating hint `%s`: %s" % (r["class"], str(v)))
ValidationException: Validating hint `EnvVarRequirement`: could not validate field `envDef` because
  At position 0
    missing required field `envValue`
ADD REPLY •
0
Entering edit mode

Okay, I fixed my code above (the - before envValue shouldn't have been there).

One should also be able to write that as:

hints:
 - class: DockerRequirement
   dockerPull: fzkhan/picard-1.136-gatk-2.8
 - class: EnvVarRequirement
   envDef: 
     CLASSPATH: /home/biodocker/bin/GenomeAnalysisTK-2.8-1-g932cd3a/

Using the new mapping shorthand in v1.0.

ADD REPLY •
0
Entering edit mode

Hi Michael,

Thanks for your time. The previous error has been solved and a new one has popped up:

Error: Could not find or load main class org.broadinstitute.sting.gatk.CommandLineGATK
Error collecting output for parameter 'output_printReads'
Traceback (most recent call last):
  File "build/bdist.macosx-10.11-intel/egg/cwltool/draft2tool.py", line 330, in collect_output_ports
    ret[fragment] = self.collect_output(port, builder, outdir)
  File "build/bdist.macosx-10.11-intel/egg/cwltool/draft2tool.py", line 405, in collect_output
    raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
WorkflowException: Did not find output file with glob pattern: '['printReads-2016-25-07.bam']'
Error while running job: Error collecting output for parameter 'output_printReads': Did not find output file with glob pattern: '['printReads-2016-25-07.bam']'
[job GATK-PrintReads-copy.cwl] completed permanentFail
[job GATK-PrintReads-copy.cwl] {}
Final process status is permanentFail

The command produced by the tool is:

docker \
    run \
    -i \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta:/var/lib/cwl/stg26cdaa03/hg19.fasta:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.amb:/var/lib/cwl/stg26cdaa03/hg19.fasta.amb:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.ann:/var/lib/cwl/stg26cdaa03/hg19.fasta.ann:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rbwt:/var/lib/cwl/stg26cdaa03/hg19.fasta.rbwt:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.pac:/var/lib/cwl/stg26cdaa03/hg19.fasta.pac:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.sa:/var/lib/cwl/stg26cdaa03/hg19.fasta.sa:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/indelRealigner-2016-03-07.bai:/var/lib/cwl/stg16e8042e/indelRealigner-2016-03-07.bai:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.fai:/var/lib/cwl/stg26cdaa03/hg19.fasta.fai:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/indelRealigner-2016-03-07.bam:/var/lib/cwl/stg16e8042e/indelRealigner-2016-03-07.bam:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rsa:/var/lib/cwl/stg26cdaa03/hg19.fasta.rsa:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.bwt:/var/lib/cwl/stg26cdaa03/hg19.fasta.bwt:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.dict:/var/lib/cwl/stg26cdaa03/hg19.dict:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/outputFiles/hg19.fasta.rpac:/var/lib/cwl/stg26cdaa03/hg19.fasta.rpac:ro' \
    '--volume=/Users/sehrish/Google Drive/Analysis using Galaxy, Cpipe and CWL/GATK-worflow/tools/baseRecalibrator-2016-03-07.table:/var/lib/cwl/stg8f0f4f0/baseRecalibrator-2016-03-07.table:ro' \
    --volume=/var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpQqNEqX:/var/spool/cwl:rw \
    --volume=/var/folders/q6/2hgf2qtj1k5gw2vkbfxjn6br0000gp/T/tmpeQgLQV:/tmp:rw \
    --workdir=/var/spool/cwl \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/var/spool/cwl \
    --env=PATH=/usr/local/bin/:/usr/bin:/bin \
    fzkhan/picard-1.136-gatk-2.8 \
    java \
    org.broadinstitute.sting.gatk.CommandLineGATK \
    -Xmx4g \
    -Djava.io.tmpdir=/tmp \
    -T \
    PrintReads \
    -R \
    /var/lib/cwl/stg26cdaa03/hg19.fasta \
    -I \
    /var/lib/cwl/stg16e8042e/indelRealigner-2016-03-07.bam \
    -BQSR \
    /var/lib/cwl/stg8f0f4f0/baseRecalibrator-2016-03-07.table \
    -o \
    printReads-2016-25-07.bam

I think the base command is causing a problem (not sure though). I have updated gist as well.

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Entering edit mode

I think the import of envar-global.yml is conflicting with the later hints, have you tried removing that?

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Entering edit mode

Yes, I have tried removing the import but the error is exactly the same. 

Error: Could not find or load main class org.broadinstitute.sting.gatk.CommandLineGATK
Error collecting output for parameter 'output_printReads'
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