Trying to run the website example

sm87
2012-06-06
2013-06-05
  • sm87

    sm87 - 2012-06-06

    Hi,

    I am a very new tophat user and am trying to run the tophat example shown on the website – http://tophat.cbcb.umd.edu/tutorial.html. I have downloaded test_data.tar.gz and am running the following command:
    tophat2 -bowtie1 -r 20 test_ref reads_1.fq reads_2.fq

    I get the following output. Could someone please tell me why this test run is failing when I am following instructions as listed on the website? Thank you for your help!

    Beginning TopHat run (v2.0.2)

    Checking for Bowtie
                      Bowtie version:        0.12.8.0
    Checking for Samtools
                    Samtools version:        0.1.18.0
    Checking for Bowtie index files
    Checking for reference FASTA file
    Generating SAM header for test_ref
            format:          fastq
            quality scale:   phred33 (default)
    Preparing reads
             left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
            right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    Mapping left_kept_reads to genome test_ref with Bowtie
    Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    Mapping right_kept_reads to genome test_ref with Bowtie
    Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    Searching for junctions via segment mapping
           
    Error: segment-based junction search failed with err =127

     

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