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SVCNVDiscivery Error: "Caused by: java.lang.NullPointerException"

Dear Genome STRiP users,

I completed SVCNVDiscovery to certain cohort based on the interval list: 1-500000. However, when I changed the interval list to 151000-198000, the error below poped up:

ERROR 18:54:30,495 FunctionEdge - Contents of /proj/yunligrp/users/minzhi/gs/PAGE_chr16/svcnv_PAGE_chr16_standard_full_single_151000-198000over1-500000_serial/cnv_stage7/seq_chr16/logs/CNVDiscoveryStage7-2.out:
INFO  18:54:05,386 HelpFormatter - --------------------------------------------------------------- 
INFO  18:54:05,389 HelpFormatter - Program Name: org.broadinstitute.sv.discovery.MergeBrigVcfFiles 
INFO  18:54:05,394 HelpFormatter - Program Args: -R /proj/yunligrp/users/minzhi/gs/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta -vcfFile /proj/yunligrp/users/minzhi/gs/PAGE_chr16/svcnv_PAGE_chr16_standard_full_single_151000-198000over1-500000_serial/cnv_stage7/seq_chr16/brig.vcf.file.list -mergedVcfFile /proj/yunligrp/users/minzhi/gs/PAGE_chr16/svcnv_PAGE_chr16_standard_full_single_151000-198000over1-500000_serial/cnv_stage7/seq_chr16/seq_chr16.brig.sites.vcf.gz 
INFO  18:54:05,400 HelpFormatter - Executing as [email protected] on Linux 3.10.0-957.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_191-b12. 
INFO  18:54:05,400 HelpFormatter - Date/Time: 2018/12/22 18:54:05 
INFO  18:54:05,401 HelpFormatter - --------------------------------------------------------------- 
INFO  18:54:05,401 HelpFormatter - --------------------------------------------------------------- 
Exception in thread "main" java.lang.RuntimeException
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
    at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.main(MergeBrigVcfFiles.java:52)
Caused by: java.lang.NullPointerException
    at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.updateVCFHeader(MergeBrigVcfFiles.java:118)
    at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.mergeVCFFiles(MergeBrigVcfFiles.java:90)
    at org.broadinstitute.sv.discovery.MergeBrigVcfFiles.run(MergeBrigVcfFiles.java:57)
    at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
    ... 5 more 
INFO  18:54:30,497 QGraph - Writing incremental jobs reports... 
INFO  18:54:30,498 QGraph - 3 Pend, 0 Run, 1 Fail, 1 Done 
INFO  18:54:30,500 QCommandLine - Writing final jobs report... 
INFO  18:54:30,501 QCommandLine - Done with errors 
INFO  18:54:30,510 QGraph - ------- 
INFO  18:54:30,512 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/proj/yunligrp/users/minzhi/gs/gs_tempdir/svcnv_tmp'  '-cp' '/proj/yunligrp/users/minzhi/svtoolkit/lib/SVToolkit.jar:/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/proj/yunligrp/users/minzhi/svtoolkit/lib/SVToolkit.jar:/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/yunligrp/users/minzhi/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.discovery.MergeBrigVcfFiles'  '-R' '/proj/yunligrp/users/minzhi/gs/

The script I used for SVCNVDiscovery is here

classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
gs_dir="/proj/yunligrp/users/minzhi/gs"
svpreprocess_dir="${gs_dir}/PAGE_chr16/svpre_PAGE_chr16_standard_full_single_1-500000over1-500000_serial_success"
rundir="${gs_dir}/PAGE_chr16/svcnv_PAGE_chr16_standard_full_single_151000-198000over1-500000_serial"

java -Xmx4g -cp ${classpath} \
    org.broadinstitute.gatk.queue.QCommandLine \
    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
    -S ${SV_DIR}/qscript/SVQScript.q \
    -cp ${classpath} \
    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
    -R ${gs_dir}/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta \
    -I ${gs_dir}/PAGE_chr16/supporting_PAGE_chr16/PAGE_chr16_full_sample.list \
    -genderMapFile ${gs_dir}/PAGE_chr16/supporting_PAGE_chr16/PAGE_chr16_full_all-male_gender.map \
    -ploidyMapFile ${gs_dir}/PAGE_chr16/supporting_PAGE_chr16/PAGE_chr16_standard_ploidy.map \
    -md ${svpreprocess_dir}/md_tempdir \
    -tempDir ${gs_dir}/gs_tempdir/svcnv_tmp \
    -runDirectory ${rundir} \
    -jobLogDir ${rundir}/logs \
    -intervalList ${gs_dir}/PAGE_chr16/supporting_PAGE_chr16/PAGE_chr16_151000-198000_interval.list \
    -tilingWindowSize 1000 \
    -tilingWindowOverlap 500 \
    -maximumReferenceGapLength 1000 \
    -boundaryPrecision 100 \
    -minimumRefinedLength 500 \
    -jobRunner Shell \
    -gatkJobRunner Shell \
    -run \
    || exit 1

Is this related to the narrow interval list? May I have your suggestion about this error? Thank you very much.

Best regards,
Wusheng

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Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    I think you are probably right that the small interval is triggering this bug.

    I would be curious to know the contents of /proj/yunligrp/users/minzhi/gs/PAGE_chr16/svcnv_PAGE_chr16_standard_full_single_151000-198000over1-500000_serial/cnv_stage7/seq_chr16/brig.vcf.file.list.
    Perhaps this file is empty because no candidate variants were found in this interval.

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