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  • abyss error

    Hi,
    I am doing an ABySS assembly recently. Here is the problem i met:

    Mapped 419743499 of 454426594 reads (92.4%)
    Mapped 419741912 of 454426594 reads uniquely (92.4%)
    Read 454426594 alignments
    Mateless 454426594 100%
    Unaligned 0
    Singleton 0
    FR 0
    RF 0
    FF 0
    Different 0
    Total 454426594
    error: the histogram `scale-3.hist' is empty
    sort: write failed: standard output: Broken pipe
    sort: write error
    make: *** [scale-3.dist] Error 1
    make: *** Deleting file `scale-3.dist'

    Could anyone help me figure this out?

  • #2
    That seems very odd. What was the command line that got you this far and the rest of the output?

    Also, the ABySS user group is usually pretty helpful. So you might try there too.

    Comment


    • #3
      Hi,
      Here is the script i used.

      for k in {56..60}; do mkdir k$k; cd k$k; abyss-pe k=$k name=scale in='/scratch/zjr/scale/data/trimedpaired.fasta' OVERLAP_OPTIONS=--no-scaffold SIMPLEGRAPH_OPTIONS=--no-scaffold E=1 n=10 v=-v; cd ..; done

      Comment


      • #4
        By the way, the other output seems fine. No error report else was found.

        Comment


        • #5
          Do your reads have /1 and /2 after them? Otherwise, I don't think ABySS can understand the paired information.

          Comment


          • #6
            For example, the first two paired reads in fasta file were displayed with head:
            >HWI-ST1280:130:C1GYVACXX:8:1101:1161:2106_1:N:0:GGCTAGA
            >HWI-ST1280:130:C1GYVACXX:8:1101:1161:2106_2:N:0:GGCTAGA
            which were transformed from fastq file.

            Is this the problem?

            Comment


            • #7
              I think so. From the documentation, either the names have to be the same, which they aren't, or you need a /1 and /2 to end them.

              You could use sed to fix them something like:

              The following should fix it sed 's/:N/ /' INFILE | awk '{print $1}' | sed -e 's|_1|/1|' -e 's|_2|/2|' > OUTFILE

              Comment


              • #8
                Thanks, I will try

                Comment


                • #9
                  Actually, you might be a little more careful and change the first sed command to:

                  sed 's/:N:/ /'

                  Comment

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