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Bowtie, Tophat and Python

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  • Bowtie, Tophat and Python

    Dear all,
    I installed bowtie 0.12.5, tophat 1.0.13 and I have Pyhton 2.4 on my Linux.
    When I launch tophat with the test files downloaded from their websites, I get this error message

    $ ./tophat -r 20 ../test_data/test_ref ../test_data/reads_1.fq ../test_data/reads_2.fq

    [Tue May 25 14:38:26 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Tue May 25 14:38:26 2010] Preparing output location ./tophat_out/
    [Tue May 25 14:38:26 2010] Checking for Bowtie index files
    [Tue May 25 14:38:26 2010] Checking for reference FASTA file
    [Tue May 25 14:38:26 2010] Checking for Bowtie
    Bowtie version: 0.12.5.0
    [Tue May 25 14:38:26 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Tue May 25 14:38:26 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:26 2010] Joining segment hits
    Splitting reads into 3 segments
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Joining segment hits
    Splitting reads into 3 segments
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against test_ref with Bowtie
    [Tue May 25 14:38:27 2010] Searching for junctions via segment mapping
    [Tue May 25 14:38:27 2010] Retrieving sequences for splices
    [Tue May 25 14:38:27 2010] Indexing splices
    [Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
    [Tue May 25 14:38:27 2010] Mapping reads against segment_juncs with Bowtie
    [Tue May 25 14:38:27 2010] Joining segment hits
    Traceback (most recent call last):
    File "./tophat", line 1635, in ?
    sys.exit(main())
    File "./tophat", line 1595, in main
    user_supplied_juncs)
    File "./tophat", line 1502, in spliced_alignment
    stdout=open(merged_map,"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

    Any idea of what's wrong?
    Thanks!

  • #2
    same problem

    Hi,

    did you find a reason for this error? I get the same error running

    tophat -p 8 --output-dir output/26_1 genome/Homo
    _sapiens.hg19/hg19 readfiles/s_100617_3_1.fastq

    ******************************************************
    Error log:
    [Mon Oct 25 10:44:10 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Mon Oct 25 10:44:10 2010] Preparing output location output/26_1/
    [Mon Oct 25 10:44:10 2010] Checking for Bowtie index files
    [Mon Oct 25 10:44:10 2010] Checking for reference FASTA file
    [Mon Oct 25 10:44:10 2010] Checking for Bowtie
    Bowtie version: 0.12.1.0
    [Mon Oct 25 10:44:10 2010] Checking reads
    seed length: 51bp
    format: fastq
    quality scale: phred33 (default)
    [Mon Oct 25 10:54:50 2010] Mapping reads against hg19 with Bowtie
    [Mon Oct 25 11:30:57 2010] Joining segment hits
    Splitting reads into 2 segments
    [Mon Oct 25 11:42:02 2010] Mapping reads against hg19 with Bowtie
    [Mon Oct 25 11:47:40 2010] Mapping reads against hg19 with Bowtie
    [Mon Oct 25 11:52:33 2010] Searching for junctions via segment mapping
    [Mon Oct 25 12:01:35 2010] Retrieving sequences for splices
    [Mon Oct 25 12:04:01 2010] Indexing splices
    [Mon Oct 25 12:23:04 2010] Mapping reads against segment_juncs with Bowtie
    [Mon Oct 25 12:26:55 2010] Mapping reads against segment_juncs with Bowtie
    [Mon Oct 25 12:30:42 2010] Joining segment hits
    Traceback (most recent call last):
    File "tophat", line 1635, in <module>
    sys.exit(main())
    File "tophat", line 1595, in main
    user_supplied_juncs)
    File "tophat", line 1502, in spliced_alignment
    stdout=open(merged_map,"w"))
    File "/usr/lib64/python2.6/subprocess.py", line 444, in call
    return Popen(*popenargs, **kwargs).wait()
    File "/usr/lib64/python2.6/subprocess.py", line 595, in __init__
    errread, errwrite)
    File "/usr/lib64/python2.6/subprocess.py", line 1106, in _execute_child
    raise child_exception
    OSError: [Errno 2] No such file or directory
    ******************************************************

    Last entry in run.log was:

    sort -k 1,1n --temporary-directory=output/26_1/tmp/ output/26_1/tmp/file
    vsmUly output/26_1/left_kept_reads.fq.candidate_hits.sam > output/26_1/tmp/file5jC6td

    file5jC6td have been created in tmp/ but it's empty.

    Any suggestions?

    Thanks

    Comment


    • #3
      This may be because the 'sort' command (and probably the rest of the default system-wide bin) cannot be found in your PATH. Check that your $PATH environment variable is properly set (be careful to append or prepend additional PATH locations rather than overwrite).

      Comment

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