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  • Tophat2: Error running bowtie:

    I am trying to map illumina paired-end datasets using tophat2. Everything seems to work fine but I suddenly get an errormessage concerning bowtie:

    [2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
    -----------------------------------------------
    [2013-02-15 16:16:36] Checking for Bowtie
    Bowtie version: 2.0.6.0
    [2013-02-15 16:16:36] Checking for Samtools
    Samtools version: 0.1.18.0
    [2013-02-15 16:16:36] Checking for Bowtie index files
    [2013-02-15 16:16:36] Checking for reference FASTA file
    [2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
    format: fastq
    quality scale: phred33 (default)
    [2013-02-15 16:16:42] Preparing reads
    left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
    [2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
    [FAILED]
    Error running bowtie:

  • #2
    Please look at the tophat.log file. Does it give you an error?

    Comment


    • #3
      Thanks,
      but I solved it. Ran out of memory...

      Comment


      • #4
        Tophat2 error at the end

        Hi dfhdfh:

        I am newer in NGS analysis. I recently used tophat2 to align illumina PE RNA-seq. At the end of running, there is an error, I really don't know how to solve this problem. Please help, thanks.
        I am using Oracle VM VirtualBox linux system.

        calgary@ChanLab:~/BT2_HOME$ tophat2 -o 81MAGABXX_5PE ./indexes/hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq

        [2013-04-26 15:28:53] Beginning TopHat run (v2.0.8)
        -----------------------------------------------
        [2013-04-26 15:28:53] Checking for Bowtie
        Bowtie version: 2.1.0.0
        [2013-04-26 15:28:53] Checking for Samtools
        Samtools version: 0.1.18.0
        [2013-04-26 15:28:53] Checking for Bowtie index files
        [2013-04-26 15:28:53] Checking for reference FASTA file
        [2013-04-26 15:28:53] Generating SAM header for ./indexes/hg19
        format: fastq
        quality scale: phred33 (default)
        [2013-04-26 15:29:26] Preparing reads
        left reads: min. length=100, max. length=100, 87918264 kept reads (261507 discarded)
        right reads: min. length=100, max. length=100, 87900059 kept reads (279712 discarded)
        [2013-04-26 16:17:30] Mapping left_kept_reads to genome hg19 with Bowtie2
        [2013-04-27 07:09:46] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
        [2013-04-27 08:22:55] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
        [2013-04-27 09:35:45] Mapping left_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
        [2013-04-27 10:57:53] Mapping left_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
        [2013-04-27 12:17:29] Mapping right_kept_reads to genome hg19 with Bowtie2
        [2013-04-28 07:23:39] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
        [2013-04-28 08:35:06] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
        [2013-04-28 09:44:22] Mapping right_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
        [2013-04-28 11:43:32] Mapping right_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
        [2013-04-28 13:01:44] Searching for junctions via segment mapping
        [2013-04-28 15:05:19] Retrieving sequences for splices
        [2013-04-28 15:07:08] Indexing splices
        [2013-04-28 15:09:25] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
        [2013-04-28 15:33:00] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
        [2013-04-28 15:56:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
        [2013-04-28 16:21:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
        [2013-04-28 16:43:47] Joining segment hits
        [2013-04-28 17:22:01] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
        [2013-04-28 17:44:55] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
        [2013-04-28 18:06:19] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
        [2013-04-28 18:33:27] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
        [2013-04-28 18:53:58] Joining segment hits
        [2013-04-28 19:39:27] Reporting output tracks
        [FAILED]
        Error: [Errno 2] No such file or directory
        Found 313015 junctions from happy spliced reads





        Originally posted by JonB View Post
        I am trying to map illumina paired-end datasets using tophat2. Everything seems to work fine but I suddenly get an errormessage concerning bowtie:

        [2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
        -----------------------------------------------
        [2013-02-15 16:16:36] Checking for Bowtie
        Bowtie version: 2.0.6.0
        [2013-02-15 16:16:36] Checking for Samtools
        Samtools version: 0.1.18.0
        [2013-02-15 16:16:36] Checking for Bowtie index files
        [2013-02-15 16:16:36] Checking for reference FASTA file
        [2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
        format: fastq
        quality scale: phred33 (default)
        [2013-02-15 16:16:42] Preparing reads
        left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
        [2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
        [FAILED]
        Error running bowtie:

        Comment


        • #5
          Originally posted by chanwu View Post
          Hi dfhdfh:

          I am newer in NGS analysis. I recently used tophat2 to align illumina PE RNA-seq. At the end of running, there is an error, I really don't know how to solve this problem. Please help, thanks.
          I am using Oracle VM VirtualBox linux system.

          calgary@ChanLab:~/BT2_HOME$ tophat2 -o 81MAGABXX_5PE ./indexes/hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq

          [2013-04-26 15:28:53] Beginning TopHat run (v2.0.8)

          [2013-04-28 19:39:27] Reporting output tracks
          [FAILED]
          Error: [Errno 2] No such file or directory
          Found 313015 junctions from happy spliced reads
          Ouch. It is painful to get that error after running the analysis for 2 days!

          So it did not make the "81MAGABXX_5PE" directory?

          Comment


          • #6
            Originally posted by JonB View Post
            Thanks,
            but I solved it. Ran out of memory...
            can you please tell what is your system configuration and which genome are you using

            Comment

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