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Error while running gatk GenomicsDBImport

I am trying to create a panelofnormals file using this tutorial: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php

I have an interval file that looks like this:
chr1:1-248956422
chr2:1-242193529
chr3:1-198295559
chr4:1-190214555
chr5:1-181538259
chr6:1-170805979
chr7:1-159345973
chr8:1-145138636
chr9:1-138394717
chr10:1-133797422

I am getting an error like this:
htsjdk.tribble.TribbleException: Invalid interval record contains 1 fields: chr1:1-248956422, for input source: /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/my.interval_list

I tried changing my interval files to something like this (with tabs):
chr1 1 248956422
chr2 1 242193529
chr3 1 198295559
chr4 1 190214555
chr5 1 181538259
chr6 1 170805979
chr7 1 159345973
chr8 1 145138636
chr9 1 138394717
chr10 1 133797422
But i still get an error like this:
htsjdk.tribble.TribbleException: Invalid interval record contains 3 fields: chr1 1 248956422, for input source: /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/my_new.interval_list

What do I do now to solve this?

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @saimukund
    The tutorial shows -L using intervals.interval_list and I see your file is called "my_new.interval_list", which I believe should be formatted like point A described here (Picard-style .interval_list). The easier route may be to reformat your file like point B and rename it to be a .list or .intervals file. If you just want to specify chromosomes you can use <chr> or specify them directly at the command line instead of writing them in a file. Hope this helps!

  • saimukundsaimukund Member

    I converted the file to point B like you said. It looks like this now:
    chr1 1 248956422
    chr2 1 242193529
    chr3 1 198295559
    chr4 1 190214555
    chr5 1 181538259
    chr6 1 170805979
    chr7 1 159345973
    chr8 1 145138636
    chr9 1 138394717
    chr10 1 133797422
    ....
    ...
    ...
    HLA-DRB114:05:01 1 13933
    HLA-DRB1
    14:54:01 1 13936
    HLA-DRB115:01:01:01 1 11080
    HLA-DRB1
    15:01:01:02 1 11571
    HLA-DRB115:01:01:03 1 11056
    HLA-DRB1
    15:01:01:04 1 11056
    HLA-DRB115:02:01 1 10313
    HLA-DRB1
    15:03:01:01 1 11567
    HLA-DRB115:03:01:02 1 11569
    HLA-DRB1
    16:02:01 1 11005

    But now I get a new error:
    A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "chr1 1 248956422" is not valid for this input.

    This is kind of an error i got earlier while running mutect2 using this interval list. Then i changed the interval list to something like this:
    chr1:1-248956422
    chr2:1-242193529
    chr3:1-198295559
    chr4:1-190214555
    chr5:1-181538259
    chr6:1-170805979
    chr7:1-159345973
    chr8:1-145138636
    chr9:1-138394717

    Now its again coming!

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Did you rename the file to .list or .intervals with the new format?

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin
    edited September 6

    Hi @saimukund , there are a lot of suggestions in this thread on what to do when you see an error similar to this: https://gatkforums.broadinstitute.org/gatk/discussion/2224/badly-formed-genome-loc

    Can you provide your exact command, version of GATK, and attach your interval file here (leave the file name the same as when you ran it)? If it is too large, you can upload it to our ftp server following these instructions.

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