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  • error in Cufflinks v2.0.2 when using Cuffmerge

    When I run Cuffmerge, I receive the following error:
    You are using Cufflinks v2.0.2, which is the most recent release.
    Error creating output file tmp_meta_asm.stats!
    [FAILED]
    Error: could not execute cuffcompare

    No merged.gtf file is being produced, but genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf and transcritps.gtf are all being produced.

    I am running on SUSE Linxux, Linux version 2.6.32.59-0.3-default.

  • #2
    I had the same problem when I used the option -o to specify a path to the output folder.. If I changed to the wished directory before running cuffmerge it worked (i.e. I omitted the -o option)

    Soren

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    • #3
      Thanks. I had the same problem again, and I just re-ran the cuffmerge command in the cuffmerge output folder it had created in the first try.

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