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  • Tophat-fusion-post error

    Hi all,

    I know my question is a very naive and basic and I know, something is just wrong with the directories creation.

    I am working with Tophat v2.0.6. I already ran tophat2 with bowtie1 and got the fusions.out file.

    While using ./tophat-fusion-post, the error is arising at the first step.

    The folder tree is as below:

    TopHat Linux (Main directory)
    • hg19 bowtie1 index
      ensGene.txt
      refGene.txt
      fusions.out
      blastall
      blastn
      ./blast_human/human_genomic*, nt*, other_genomic*


    The error message is:
    [Mon Jan 21 13:09:33 2013] Beginning TopHat-Fusion post-processing run (v2.0.6)
    -----------------------------------------------
    [Mon Jan 21 13:09:33 2013] Extracting 23-mer around fusions and mapping them using Bowtie
    Traceback (most recent call last):
    File "./tophat-fusion-post", line 2091, in ?
    sys.exit(main())
    File "./tophat-fusion-post", line 2059, in main
    map_fusion_kmer(bwt_idx_prefix, params, sample_updated)
    File "./tophat-fusion-post", line 315, in map_fusion_kmer
    subprocess.call(cmd, stdout=open(output_dir + 'fusion_seq.bwtout', 'w'), stderr=open('/dev/null', 'w'))
    File "/usr/lib64/python2.4/subprocess.py", line 412, in call
    return Popen(*args, **kwargs).wait()
    File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
    errread, errwrite)
    File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
    raise child_exception
    OSError: [Errno 2] No such file or directory

    On the TopHat page, it is mentioned as:
    Install BLAST binaries (blastall and blastn).
    Make (top_dir)/blast directory, download human_genomic*, other_genomic*, and nt* from blast database, and extract them under (top_dir)/blast_human.

    blastall and blastn should be in the blast folder? To be very honest, I am unable to understand the folders creation.

    Thanking in advance.
    Aso
    Last edited by AsoBioInfo; 01-21-2013, 03:03 AM. Reason: Completing it

  • #2
    It's solved......

    Comment


    • #3
      Originally posted by AsoBioInfo View Post
      It's solved......
      May I ask how to solve the problem. I got the same problem

      Comment


      • #4
        Originally posted by AsoBioInfo View Post
        It's solved......
        Can you please post solution.. I have same error
        thank you

        Comment


        • #5
          File "/apps/tophat2//tophat-fusion-post", line 937, in alignments_region
          popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=open('/dev/null'))


          Problem is related to subprocess module in python. Go to line 937 and add shell=True at the end.

          subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=open('/dev/null'),shell=True)


          This solved mine.

          Comment

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