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  • cuffdiff crashes on loading reference annotation

    Hi, has anybody experienced cuffdiff crashing with no error message upon loading the reference annotation? I've checked with a subset of my gff file (10 lines or so) to see if the problem was caused by the reference annotation file being massive but this made no difference. Any pointers appreciated, thank you.

  • #2
    Have you used this cuffdiff with other datasets successfully before?

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    • #3
      This is an old post, but it was the only thing that came up when I searched for this problem.

      For me at least, the problem was caused by something quite simple: when executing cuffdiff, I had included the path to the directory where the reference was stored but had neglected to include the reference gtf itself.

      A rather silly mistake, but I suspect others must make it so I wanted to post the solution. It is rather strange cuffdiff throws no error and simply exits.

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      • #4
        Yes, I know this is an old post, but I reproduced the same problem.
        I created a GFF file in Excel, transferred the file to the server and ran cuffdiff using the GFF file.
        For me, the problem was the GFF file was misformatted. I put the locus Id in the 9th column, where I should have prefixed the locus id with "ID=". Apparently Cufflinks needs that "ID=" tag.
        In any event, Cuffdiff should display the proper error message.

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