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  • gnajm
    Junior Member
    • Jul 2020
    • 1
    #1

    htseq-count issue: ID attribute in GFF file

    In Galaxy, I've been attempting to run htseq-count on BAM files created in hisat2, and I keep getting this error:

    [bam_sort_core] merging from 36 files and 1 in-memory blocks...
    Error occured when processing GFF file (line 16 of file /galaxy-repl/main/files/042/181/dataset_42181741.dat):
    Failure parsing GFF attribute line
    [Exception type: ValueError, raised in __init__.py:175]

    I've attached a screenshot of my GFF file. I recognize that this issue is a result of the ID attribute, and in a GFF3 file, it would have ID=x. Is there a way to indicate an ID attribute in Galaxy with this file so it can run properly?
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