Running Genome STRiP SVPreprocess, but I got error message: "Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker"

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Norio Tanaka

• June 15, 2021 14:22

Dear GATK developers, 

I tried to run Genome STRiP (latest version at 2021/6/14 Release 2.00.1982) SVPreprocess following the website http://software.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html 

export SV_DIR=/home/ntanaka/Project_Tech/WGS/GenomeStrip/svtoolkit/
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
/usr/local/package/java/1.8.0_181/bin/java -Xmx4g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -jobNative "-S /bin/bash -l s_vmem=12G,mem_req=12G -cwd -e log -o log" \
     -S ${SV_DIR}/qscript/SVPreprocess.q \
     -S ${SV_DIR}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
     -R /home/ntanaka/Project_Tech/WGS/Sanger/reference/reference_files/genome.fa \
     -I test/bam_preprocess/input_bam_files.list \
     -md test/bam_preprocess/ \
     -bamFilesAreDisjoint true \
     -jobLogDir test/bam_preprocess/logDir \
     -run

But I got error message bellow.

##### ERROR --
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$MalformedWalkerArgumentsException: Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker
at org.broadinstitute.gatk.engine.WalkerManager.createMalformedArgumentException(WalkerManager.java:165)
at org.broadinstitute.gatk.utils.classloader.PluginManager.createByName(PluginManager.java:280)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getWalkerByName(GenomeAnalysisEngine.java:332)
at org.broadinstitute.gatk.engine.CommandLineExecutable.getArgumentSources(CommandLineExecutable.java:163)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:214)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:95)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:66)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1941-0-gb493839):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker
##### ERROR ------------------------------------------------------------------------------------------

 

I will really appreciate that you could tell me how to fix this problem.

Thanks in advance,

Sincerely yours,

Norio Tanaka

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• 

  Genevieve Brandt (she/her)

  • June 15, 2021 15:43

  Bob Handsaker could you take a look at this?

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  Mat Nightingale

  • June 22, 2021 13:14

  I have a similar same error when trying to run the same pipeline I've been using successfully for the last several years but with the RealignerTargetCreator tool.

  I've tried the same command with GATK 3.0-0, 3.8-0 and 3.8-1 all give the same error.

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  Genevieve Brandt (she/her)

  • June 22, 2021 20:49

  Hi Mat Nightingale, the above question is for GenomeSTRiP, while it looks like your question involves GATK3. Our support team no longer supports GATK3, so for GATK3 questions we recommend asking other community members or looking for help on our legacy forum. We recommend upgrading to GATK4, we offer support and it is a great update!

  Please let me know if you have any questions.

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  Bob Handsaker

  • June 28, 2021 15:16

  It is hard to say for sure what the problem is, but I would guess it has something to do with the classpath and not finding the all of the jar files. Some things you can try to get more information:

  Try to run the problematic command outside of Queue (e.g. with a script directly on the cluster) based on what Queue is running.

  Did any of the other preprocessing steps have problems? There are several other steps that should run before this, but this is the first step using reflection to find the walker to run.

   

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