No version in header ERROR...

willpitcherswillpitchers Michigan State UMember

Dear GATK-ers,

I have a script that runs an array of BQSR jobs – each job being handed a different input file from an array. My problem is that just one of the 648 files causes this error message:

INFO  14:56:44,389 HelpFormatter - ----------------------------------------------------------------------------------
INFO  14:56:44,390 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO  14:56:44,391 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO  14:56:44,391 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO  14:56:44,391 HelpFormatter - [Wed Nov 01 14:56:44 EDT 2017] Executing on Linux 2.6.32-642.11.1.el6.x86_64 amd64
INFO  14:56:44,391 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13
INFO  14:56:44,394 HelpFormatter - Program Args: -T BaseRecalibrator -R /mnt/ls15/scratch/groups/efish/P_kings_genome/supercontigs.fasta -I /mnt/ls15/scratch/groups/efish/WILL/Pipeline7//BAM_6865_S25_L007_R1_se.aligned.dedup.bam -BQSR BAM_6865_S25_L007_R1_se.aligned.dedup.recal_data.table -o BAM_6865_S25_L007_R1_se.aligned.dedup.post_recal_data.table --run_without_dbsnp_potentially_ruining_quality -nct 10 -rf BadCigar
INFO  14:56:44,428 HelpFormatter - Executing as [email protected] on Linux 2.6.32-642.11.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13.
INFO  14:56:44,428 HelpFormatter - Date/Time: 2017/11/01 14:56:44
INFO  14:56:44,429 HelpFormatter - ----------------------------------------------------------------------------------
INFO  14:56:44,429 HelpFormatter - ----------------------------------------------------------------------------------
INFO  14:56:44,435 GenomeAnalysisEngine - Strictness is SILENT
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
##### ERROR
##### 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
##### 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
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Bad input: The GATK report has no version specified in the header
##### ERROR ------------------------------------------------------------------------------------------

Does the "GATK report" refer to one of the pre/post data_table's?

If so how can it have NO version (as opposed to having the wrong version no.)?

I"m using GATK version 3.7.0

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited November 2017

    @willpitchers
    Hi,

    Yes, the GATKReport refers to the tables output by BaseRecalibrator. Have a look at this thread for a couple of tips.

    -Sheila

    EDIT: I am hoping either giving more memory or finding that the tool actually errored somewhere in your script will help.

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