there aren't enough columns for line 96340 when GenotypeGVCFs

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Line 11786771: there aren't enough columns for line 96340 GT:DP:GQ:MIN_DP:PL 0/0:19:51:19:0,51,765 (we expected 9 tokens, and saw 3 ), for input source: /public/home/zll/zll_data/lyp/PY/PYreseq/DES00336_raw_variants.g.vcf
ERROR ------------------------------------------------------------------------------------------


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Can you please post the exact command you ran?


  • YangpingLiYangpingLi QingDaoMember


    The command I used is:

    java -jar ../../software/GenomeAnalysisTK.jar -T GenotypeGVCFs -V DES00295_raw_variants.g.vcf -V DES00296_raw_variants.g.vcf -V DES00297_raw_variants.g.vcf -V DES00298_raw_variants.g.vcf -V DES00299_raw_variants.g.vcf -V DES00300_raw_variants.g.vcf -V DES00301_raw_variants.g.vcf -V DES00302_raw_variants.g.vcf -V DES00303_raw_variants.g.vcf -V DES00304_raw_variants.g.vcf -V DES00305_raw_variants.g.vcf -V DES00306_raw_variants.g.vcf -V DES00307_raw_variants.g.vcf -V DES00308_raw_variants.g.vcf -V DES00334_raw_variants.g.vcf -V DES00335_raw_variants.g.vcf -V DES00336_raw_variants.g.vcf -V DES00337_raw_variants.g.vcf -V DES00338_raw_variants.g.vcf -V DES00339_raw_variants.g.vcf -o DES.variants

    Thanks for your help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, your command looks fine; you'll need to look into the file named in the error and check if it is malformed at line 96340. It's possible that there was a system glitch or your file got corrupted. If that is the case you'll need to regenerate it.

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