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ERROR MESSAGE of VariantsToTable

LeanStreamLeanStream guangzhou, ChinaMember

I encountered an issue when I use VariantsToTable. Thanks.

command:

Ref: hg19

    java -Djava.io.tmpdir=$tmp \
    -jar $GATK \
            -T VariantsToTable \
            -R $Ref \
            -V $InputDir/BQSR_AutosomeFilteredSNVs.vcf \
            -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F AC -F AN -F AF -F MQ \
            -GF FT -GF GT -GF AD -GF DP -GF GQ -GF PL -GF PGT -GF PID \
            -o $OutputDir/BQSR_AutosomeFilteredSNVs.table \
            2> $stderr/BQSR_filteredSNVs_toTable.stderr
ERROR --
ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.prettyPrintObject(VariantsToTable.java:370)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.addFieldValue(VariantsToTable.java:350)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.extractFields(VariantsToTable.java:334)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.map(VariantsToTable.java:213)
at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToTable.map(VariantsToTable.java:108)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
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.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

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