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  • MapSplice V1.15.2 error

    Hi all

    Im using Mapsplice with pair reads. I got the error message:


    error: open entended file error

    [FAILED]

    Error: check reads format failed


    Any idea to solve this error??

    Regards

  • #2
    It's probably "error: open extended file error", not "error: open entended file error"

    Any previous output? , there's usually a complete narrative which looks like this example ...

    [Thu Jun 21 11:17:06 2012] Checking for chromosomes files or directory
    [Thu Jun 21 11:17:07 2012] Checking for chromosomes files or directory passed
    [Thu Jun 21 11:17:07 2012] Checking for Bowtie index files
    [Thu Jun 21 11:17:07 2012] check reads format
    [Thu Jun 21 11:19:23 2012] merge paired end reads remove short
    [Thu Jun 21 11:27:15 2012] Mapping reads against bowtie_index_basename with Bowtie

    What is the name of the last output in the logs directory ???


    The program bin/mapsplice_segments.py contains the "check reads format failed" strings at line 4946 of 7830 ...
    Code:
        if DEBUG == 1:
            print >> sys.stderr, "[%s] check reads format" % dividereads_cmd
        #print >> sys.stderr, "[%s] divide reads" % dividereads_cmd
        try:
            retcode = subprocess.call(dividereads_cmd, stdout=mapsplice_log)
    
            if retcode > 0:
                print >> sys.stderr, fail_str, "Error: check reads format failed"
                exit(1)
    So it's dividereads_cmd is failing.

    It looks like there's a nice debug command in the "if DEBUG == 1" clause on line 4939.

    Try turning on DEBUG = 1 on line 120 of the python source file "bin/mapsplice_segments.py", then re-run it. That should give you a better hint.

    Remember to set the path to point to the mapsplice "bin" directory in addition to your regular path.

    Comment


    • #3
      Hi

      Problem solved. I forgot to put the path of the read_end2:

      I put "path/read_end1, read_end2" but the correct is "path/read_end1, path/read_end2".

      Many thanks,

      P

      Comment

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