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  • TopHat running error

    Hi,
    I found the same problem of boahua100 while running tophat. I moved the executable files bowtie, bowtie-inspect e bowtie-build in the same path where tophat, the reference file and the reads file are but:

    student@410083:~/Desktop/tophat-1.0.9/PROVA$ ./tophat -o GINO -m 2 -G pizzolo.gff Scaffold_bowtizzato Reads1

    [Thu Jul 23 18:09:15 2009] Beginning TopHat run (v1.0.9)
    -----------------------------------------------
    [Thu Jul 23 18:09:15 2009] Preparing output location GINO/
    [Thu Jul 23 18:09:15 2009] Checking for Bowtie index files
    [Thu Jul 23 18:09:15 2009] Checking for reference FASTA file
    [Thu Jul 23 18:09:15 2009] Checking for Bowtie
    Traceback (most recent call last):
    File "./tophat", line 1484, in <module>
    sys.exit(main())
    File "./tophat", line 1420, in main
    check_bowtie()
    File "./tophat", line 567, in check_bowtie
    bowtie_version = get_bowtie_version()
    File "./tophat", line 548, in get_bowtie_version
    proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
    File "/usr/lib/python2.6/subprocess.py", line 595, in __init__
    errread, errwrite)
    File "/usr/lib/python2.6/subprocess.py", line 1092, in _execute_child
    raise child_exception
    OSError: [Errno 2] No such file or directory
    student@410083:~/Desktop/tophat-1.0.9/PROVA$

    Any suggestions?

    Thanks!!

    P

  • #2
    Originally posted by pfranchini View Post
    Hi,
    I found the same problem of boahua100 while running tophat. I moved the executable files bowtie, bowtie-inspect e bowtie-build in the same path where tophat, the reference file and the reads file are but:

    student@410083:~/Desktop/tophat-1.0.9/PROVA$ ./tophat -o GINO -m 2 -G pizzolo.gff Scaffold_bowtizzato Reads1

    [Thu Jul 23 18:09:15 2009] Beginning TopHat run (v1.0.9)
    -----------------------------------------------
    [Thu Jul 23 18:09:15 2009] Preparing output location GINO/
    [Thu Jul 23 18:09:15 2009] Checking for Bowtie index files
    [Thu Jul 23 18:09:15 2009] Checking for reference FASTA file
    [Thu Jul 23 18:09:15 2009] Checking for Bowtie
    Traceback (most recent call last):
    File "./tophat", line 1484, in <module>
    sys.exit(main())
    File "./tophat", line 1420, in main
    check_bowtie()
    File "./tophat", line 567, in check_bowtie
    bowtie_version = get_bowtie_version()
    File "./tophat", line 548, in get_bowtie_version
    proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
    File "/usr/lib/python2.6/subprocess.py", line 595, in __init__
    errread, errwrite)
    File "/usr/lib/python2.6/subprocess.py", line 1092, in _execute_child
    raise child_exception
    OSError: [Errno 2] No such file or directory
    student@410083:~/Desktop/tophat-1.0.9/PROVA$

    Any suggestions?

    Thanks!!

    P


    Hi,
    I was ever met such errors.This happens when you don't put bowtie in your PATH.

    Geng

    Comment


    • #3
      Thanks,
      I checked again and bowtie was not in the PATH..Now I put it there and TopHat correctly works.

      Paolo

      Comment

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