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  • Tophat...Mapping reads against Reference with Bowtie [FAILED]

    Hi,

    I am trying to run tophat with the sample data reads_1.fq and reads_2.fq.

    I built the bowtie index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command

    tophat -r 20 test_ref reads_1.fq reads_2.fq

    and the output i got is an error showing on console

    [Wed Jun 2 13:46:29 2010] Beginning TopHat run (v1.0.7)
    -----------------------------------------------
    [Wed Jun 2 13:46:29 2010] Preparing output location ./tophat_out/
    [Wed Jun 2 13:46:29 2010] Checking for Bowtie index files
    [Wed Jun 2 13:46:29 2010] Checking for reference FASTA file
    [Wed Jun 2 13:46:29 2010] Checking for Bowtie
    Bowtie version: 0.12.3.0
    [Wed Jun 2 13:46:29 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred
    Splitting reads into 3 segments
    [Wed Jun 2 13:46:29 2010] Mapping reads against test_ref with Bowtie
    Error: could not execute Bowtie
    Traceback (most recent call last):
    File "/usr/bin/tophat", line 1476, in ?
    sys.exit(main())
    File "/usr/bin/tophat", line 1450, in main
    user_supplied_juncs)
    File "/usr/bin/tophat", line 1297, in spliced_alignment
    unmapped_seg)
    File "/usr/bin/tophat", line 612, in bowtie
    exit(1)
    TypeError: 'str' object is not callable
    [FAILED]


    Could you please help me to sort out this issue.

    Thanks,
    Brajendra

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