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While running GenomeSTRIP preprocessing step the pipeline crushes: java.lang.RuntimeException

SVPreprocess-11.out and SVPreprocess-13.out are showing this error. Cannot build RC cache for empty readGroup list.

ERROR stack trace

java.lang.RuntimeException: Cannot build RC cache for empty readGroup list
at org.broadinstitute.sv.metadata.depth.ReadCountFileWriter.computeReadGroupIndexMap(ReadCountFileWriter.j
ava:303)
at org.broadinstitute.sv.metadata.depth.ReadCountFileWriter.writeHeaderInternal(ReadCountFileWriter.java:1
82)
at org.broadinstitute.sv.metadata.depth.ReadCountFileWriter.writeHeader(ReadCountFileWriter.java:98)
at org.broadinstitute.sv.metadata.depth.ComputeReadCountsWalker.initialize(ComputeReadCountsWalker.java:10
1)
at org.broadinstitute.sv.metadata.ComputeMetadataWalker.initialize(ComputeMetadataWalker.java:195)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:59)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Cannot build RC cache for empty readGroup list
ERROR ------------------------------------------------------------------------------------------

Best Answers

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    Please post the software version and the command line for SVPreprocess-11 or SVPreprocess-13.

    What do the @RG headers look like in your input bam files?

  • arwalkerarwalker WVUMember

    Hi and thanks for the super fast reply.

    I'm not sure how to check the version, but this program was installed last week on this machine, so I would say is the most recent version.

    For now, since I'm just getting into this pipeline, I'm running the preprocessing step as follows:

    java -cp ${classpath} -Xmx4g \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/SVPreprocess.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -cp ${classpath} \
    -configFile /difazio/populus/arwalker/metadata/popv3/popv3/genstrip_parameters.txt \
    -tempDir ${SV_TMPDIR} \
    -R /difazio/populus/arwalker/metadata/popv3/popv3/work/popv3.fa \
    -genomeMaskFile /difazio/populus/arwalker/metadata/popv3/popv3/work/svmask.fasta \
    -genderMapFile /difazio/populus/arwalker/metadata/popv3/popv3/work/gender.map \
    -ploidyMapFile /difazio/populus/arwalker/metadata/popv3/popv3/work/ploidy.map \
    -runDirectory ${runDir} \
    -md /difazio/populus/arwalker/metadata/popv3/popv3/work \
    -I /difazio/populus/arwalker/Alignments/koreana/trichocarpa_koreana_local.bam \
    -I /difazio/populus/arwalker/Alignments/maximowiczii/trichocarpa_maximowiczii_local.bam \
    -l DEBUG \
    -run \
    || exit 1

    All the required system variables are previously created as needed!!!

    This is the header of one of the sam files:
    @HD VN:1.0 SO:unsorted
    @SQ SN:Chr01 LN:50495391
    @SQ SN:Chr02 LN:25263035
    @SQ SN:Chr03 LN:21816808
    @SQ SN:Chr04 LN:24267051
    @SQ SN:Chr05 LN:25890704

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    java -jar path-to-SVToolkit.jar will give you the version.

    It would be helpful if you look in the output file from Queue (QCommandLine) to see what was run as SVPreprocess-11.

    samtools view -H input-file.bam | grep ^@RG to get the read group headers.
    You files will need to have properly defined read groups with the reads linked to the read groups.

  • arwalkerarwalker WVUMember

    Regarding version, this is what I got:

    java -jar path-to-SVToolkit.jar
    SVToolkit version 2.00 (build 1602)
    Build date: 2015/07/21 09:43:14

    Regarding the second tip the grep command did not find any @RC string on the bam file.

  • arwalkerarwalker WVUMember

    Interesting!!! Thanks Bob. Probably I'll be coming back to this discussion. Cheers!!!

  • arwalkerarwalker WVUMember
    edited October 2015

    Hi Bob,
    I'm still facing a crush on the preprocessing. I'm trying now a new set of BAM files. They look fine since they have the @RG. By now I cant find a error output that can give me more about the crush.
    Additionally we have documentation about Genome STRIP running on this machine with sudo access. Is that really necessary? Is the program writing on directories with restricted access to regular access users?

    Apparently the program stopped after the merging and I restarted it and now looks like it's running. Should it have stopped? Is that normal?

    Thanks

  • arwalkerarwalker WVUMember

    Well it crushed with this error message.

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.utils.commandline.InvalidArgumentValueException:
    Argument '--baminputs' requires a value but none was provided
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:334)
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:279)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:216)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version ):
    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 http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Argument '--baminputs' requires a value but none was provided
    ERROR ------------------------------------------------------------------------------------------

    INFO 13:59:07,383 QCommandLine - Shutting down jobs. Please wait...

    Any suggestion?

  • arwalkerarwalker WVUMember
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