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  • BRAKER1 fails: inappropriate ioctl for device

    Hi all, I'm having a problem which is more linux related than biology related. I'm running the BRAKER1 pipeline (which involves Augustus and Gene-mark ET) for a gene prediction, and I'm getting back a weird error which I wasn't able to solve using StackOverflow or other troubleshooting websites.
    This is the STDERR:

    Code:
    NEXT STEP: check files and settings
    NEXT STEP: check options
    ... options check complete.
    NEXT STEP: check fasta headers
    fasta headers check complete.
    NEXT STEP: create SAM header file [...].
    SAM file [...] complete.
    NEXT STEP: check BAM headers
    headers check for BAM file [...] complete.
    NEXT STEP: make hints from BAM file [...]
    failed to execute: Inappropriate ioctl for device
    Inappropriate ioctl for device is something I never had the pleasure to solve. Can anybody help me?

    Thank you very much,
    Matteo

  • #2
    I solved it trying the solutions suggested here.
    GeneMark/Braker issue. GitHub Gist: instantly share code, notes, and snippets.

    Comment


    • #3
      I fix this compiling augustus with gcc/5.3.0

      Comment


      • #4
        Yep, exactly how I did.
        I have other problems with BRAKER1, fancy take a look? Maybe you know:
        Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

        Comment

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