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  • cuffmerge error

    Hi, I am confronted with some errors when doing cuffmerge analysis.

    /home/bin/cuffmerge -g Ptrichocarpa_156_gene.gff3 -s Ptrichocarpa_156_hardmasked.fa -p 10 assemblies.txt

    [Wed May 30 09:48:20 2012] Converting GTF files to SAM
    [FAILED]
    Error: gtf_to_sam not found on this system. Did you forget to include it in your PATH?

    I checked very carefully with my directory /home/bin and found that gtf_to_sam is actually in this directory. I cannot understand why the software cannot find it.

    Sorry for my naive questions.

    Any comments are very appreciated.

  • #2
    I have the same problem! Did you ever find a fix?

    Comment


    • #3
      Hi, gtf_to_sam should be specified in your PATH.
      You need to type the following command in your terminal:
      PATH=$PATH:/PATH/TO/gtf_to_sam

      Comment


      • #4
        Thanks wangli, but that doesn't appear to be the problem. Any other ideas?

        Comment


        • #5
          you can look into the following thread:
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

          Comment


          • #6
            I was running cuffmerge and got the following message. it seem it stopped for some reason. Does anybody have ideas on what is going on?

            [Thu Jul 19 11:38:15 2012] Beginning transcriptome assembly merge
            -------------------------------------------

            [Thu Jul 19 11:38:15 2012] Preparing output location Documents/RNA_Seq/LSD1_analysis_072012/cuffmerge_07172012//
            [Thu Jul 19 11:38:17 2012] Converting GTF files to SAM
            buszczak-macpro:~ zwang$

            Comment

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