Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

                  Latest Articles

                  Collapse

                  • seqadmin
                    Exploring the Dynamics of the Tumor Microenvironment
                    by seqadmin




                    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                    07-08-2024, 03:19 PM
                  • seqadmin
                    Exploring Human Diversity Through Large-Scale Omics
                    by seqadmin


                    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                    06-25-2024, 06:43 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 07-19-2024, 07:20 AM
                  0 responses
                  29 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-16-2024, 05:49 AM
                  0 responses
                  42 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-15-2024, 06:53 AM
                  0 responses
                  50 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 07-10-2024, 07:30 AM
                  0 responses
                  43 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X