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  • MapSplice 1.15.1 error

    Hi everyone,

    I'm running MapSplice 1.15.1 and get an error:

    [Thu Sep 15 11:19:36 2011] Preparing output location /home/ipulyakhina/Programs/MapSplice_1.15.2/RESULTS//

    [Thu Sep 15 11:19:36 2011] Beginning Mapsplice run (v1.15.2)
    -----------------------------------------------
    bin directory: [/home/ipulyakhina/Programs/MapSplice_1.15.2/bin/]
    [Thu Sep 15 11:19:36 2011] Checking for chromosomes files or directory
    [Thu Sep 15 11:19:36 2011] Checking for chromosomes files or directory passed
    [Thu Sep 15 11:19:36 2011] Checking for Bowtie index files
    [Thu Sep 15 11:19:36 2011] Indexing chromosome sequences
    [Thu Sep 15 11:23:46 2011] check reads format
    [Thu Sep 15 11:23:46 2011] merge paired end reads remove short
    [Thu Sep 15 11:23:46 2011] Converting bowtie mapped to SAM format
    [Thu Sep 15 11:23:46 2011] divide reads
    [Thu Sep 15 11:23:46 2011] Mapping reads against with Bowtie
    [FAILED]
    Error: could not execute Bowtie

    Of course I have the latest version of bowtie, I've written the path to bowtie in the .bashrc and I can execute it from the command line.

    Does anyone know what is the problem?

    Thanks in advance,
    Irina

  • #2
    Can you check error message

    in
    ~/logs/unspliced_segments.log
    or
    ~/logs/unspliced_reads.log
    ?

    Comment


    • #3
      Thank you for your reply! I found out the problem and MapSplice is passing through this point no, but I do get the other error:

      =======================
      Warning: Empty input file
      Error: No unambiguous stretches of characters in the input. Aborting...
      =======================

      It's being thrown at the step of "Indexing chromosome sequences". Maybe you know what the problem is?

      I don't have any ~/logs/unspliced_reads.log file; the ~/logs/unspliced_segments.log is:
      =======================
      # reads processed: 807695920
      # reads with at least one reported alignment: 184993777 (22.90%)
      # reads that failed to align: 622702143 (77.10%)
      Reported 1875904633 alignments to 1 output stream(s)
      =======================

      Thanks in advance!

      Comment


      • #4
        Originally posted by Irina Pulyakhina View Post
        Thank you for your reply! I found out the problem and MapSplice is passing through this point no, but I do get the other error:

        =======================
        Warning: Empty input file
        Error: No unambiguous stretches of characters in the input. Aborting...
        =======================

        It's being thrown at the step of "Indexing chromosome sequences". Maybe you know what the problem is?

        I don't have any ~/logs/unspliced_reads.log file; the ~/logs/unspliced_segments.log is:
        =======================
        # reads processed: 807695920
        # reads with at least one reported alignment: 184993777 (22.90%)
        # reads that failed to align: 622702143 (77.10%)
        Reported 1875904633 alignments to 1 output stream(s)
        =======================

        Thanks in advance!

        This means no original junctions generated, can you send ~/logs/ directory to mapsplice (at) netlab.uky.edu?
        Last edited by greenshell; 09-27-2011, 06:22 AM.

        Comment


        • #5
          Yes, I've just sent it, the email "MapSplice logs directory" to [email protected] (just netlab.uky.edu didn't work). Thank again!

          Comment

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