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  • #1

    a tophat running problem

    I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

    ../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

    [Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
    [Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie
    Bowtie version: 0.12.4.0
    [Fri Apr 9 13:17:33 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
    [Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
    [Fri Apr 9 13:17:34 2010] Indexing splices
    Traceback (most recent call last):
    File "../bin/tophat", line 1635, in ?
    sys.exit(main())
    File "../bin/tophat", line 1595, in main
    user_supplied_juncs)
    File "../bin/tophat", line 1456, in spliced_alignment
    ref_fasta)
    File "../bin/tophat", line 981, in build_juncs_index
    external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
    File "../bin/tophat", line 943, in build_juncs_bwt_index
    exit(1)
    TypeError: 'str' object is not callable
    Tags: None
  • #2
    Please help me out. I am sure many people here has experience with tophat. Could you please point me to the right direction how I could fix it?


    Originally posted by clariet View Post
    I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

    ../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

    [Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
    [Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie
    Bowtie version: 0.12.4.0
    [Fri Apr 9 13:17:33 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
    [Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
    [Fri Apr 9 13:17:34 2010] Indexing splices
    Traceback (most recent call last):
    File "../bin/tophat", line 1635, in ?
    sys.exit(main())
    File "../bin/tophat", line 1595, in main
    user_supplied_juncs)
    File "../bin/tophat", line 1456, in spliced_alignment
    ref_fasta)
    File "../bin/tophat", line 981, in build_juncs_index
    external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
    File "../bin/tophat", line 943, in build_juncs_bwt_index
    exit(1)
    TypeError: 'str' object is not callable

    Comment

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