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  • Error with Tophat2 no output

    I just ran tophat2 on some data that I previously have alligned. It goes until the last step and I get an error and no output:

    [2012-05-03 19:05:31] Beginning TopHat run (v2.0.0)
    -----------------------------------------------
    [2012-05-03 19:05:31] Checking for Bowtie
    Bowtie version: 2.0.0.5
    [2012-05-03 19:05:31] Checking for Samtools
    Samtools version: 0.1.16.0
    [2012-05-03 19:05:31] Checking for Bowtie index files
    [2012-05-03 19:05:32] Checking for reference FASTA file
    [2012-05-03 19:05:32] Generating SAM header for /scratch0/ref/hg19/bowtie/hg19
    format: fastq
    quality scale: phred33 (default)
    [2012-05-03 19:06:04] Reading known junctions from GTF file
    [2012-05-03 19:06:23] Preparing reads
    left reads: min. length=100, count=28502086
    right reads: min. length=100, count=28482455
    [2012-05-03 19:33:03] Creating transcriptome data files..
    [2012-05-03 19:34:30] Building Bowtie index from edited_igenome_Homo_Sapiens_GRCh37_genes.fa
    [2012-05-03 20:16:30] Mapping left_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
    [2012-05-03 21:23:04] Mapping right_kept_reads against transcriptome edited_igenome_Homo_Sapiens_GRCh37_genes with Bowtie2
    [2012-05-03 22:29:54] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
    [2012-05-03 22:53:32] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
    [2012-05-03 23:17:06] Resuming TopHat pipeline with unmapped reads
    [2012-05-03 23:17:58] Mapping left_kept_reads.m2g_um against hg19 with Bowtie2
    [2012-05-03 23:44:12] Mapping left_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
    [2012-05-03 23:49:55] Mapping left_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
    [2012-05-03 23:55:08] Mapping left_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
    [2012-05-04 00:01:12] Mapping left_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
    [2012-05-04 00:07:12] Mapping right_kept_reads.m2g_um against hg19 with Bowtie2
    [2012-05-04 00:33:45] Mapping right_kept_reads.m2g_um_seg1 against hg19 with Bowtie2 (1/4)
    [2012-05-04 00:39:45] Mapping right_kept_reads.m2g_um_seg2 against hg19 with Bowtie2 (2/4)
    [2012-05-04 00:46:05] Mapping right_kept_reads.m2g_um_seg3 against hg19 with Bowtie2 (3/4)
    [2012-05-04 00:52:44] Mapping right_kept_reads.m2g_um_seg4 against hg19 with Bowtie2 (4/4)
    [2012-05-04 00:58:14] Retrieving sequences for splices
    [2012-05-04 01:01:41] Indexing splices
    [2012-05-04 01:04:08] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
    [2012-05-04 01:06:15] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
    [2012-05-04 01:08:52] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
    [2012-05-04 01:11:06] Mapping left_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
    [2012-05-04 01:13:16] Joining segment hits
    [2012-05-04 01:37:45] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/4)
    [2012-05-04 01:40:01] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie2 (2/4)
    [2012-05-04 01:42:15] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie2 (3/4)
    [2012-05-04 01:44:31] Mapping right_kept_reads.m2g_um_seg4 against segment_juncs with Bowtie2 (4/4)
    [2012-05-04 01:46:38] Joining segment hits
    [2012-05-04 02:09:51] Reporting output tracks
    Traceback (most recent call last):
    File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3774, in ?
    sys.exit(main())
    File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3746, in main
    params.gff_annotation)
    File "/share/apps/tophat-2.0.0.Linux_x86_64/tophat", line 2522, in compile_reports
    os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
    IndexError: list index out of range

    I ran on another dataset and the same thing happens.
    This is the command I used:
    tophat -G $GTF --no-novel-juncs --num-threads 8 -o $DSTDIR/output/tophat200/${BARCODE}_newGTF $REFERENCE $DSTDIR/reads/s_${LANE}_${BARCODE}_1.fastq $DSTDIR/reads/s_${LANE}_${BARCODE}_3.fastq

    The only errors I see in the logs are:
    reports.log
    /share/apps/tophat-2.0.0.Linux_x86_64/tophat_reports: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory
    long_spanning_reads.segs.log
    /share/apps/tophat-2.0.0.Linux_x86_64/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.47.0: cannot open shared object file: No such file or directory

    These files do in fact exist.

    Does any one else have this problem?

  • #2
    It looks like my problem is that I need a higher version of Boost C++ libraries.

    Comment


    • #3
      I redownloaded tophat2.0.0 today and reran it with no errors. Previously the tophat_reports program at the end (generating final output) would give me the above error. An update fixed it, and it now works.

      Comment


      • #4
        tophat 2.0.9.

        Dear all,

        I keep getting the following error message when using tophat:

        Error running 'long_spanning_reads':/util/opt/tophat/2.0.9/gcc/4.4.7/bin/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

        /util/opt/cufflinks/2.1.1/gcc/4.4.7/bin/cufflinks: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

        What does this mean?
        How do I find out which version of boost that tophat uses?
        Also, how can I find out which version of boost long_spanning_reads uses?

        Thanks, csmatyi
        Last edited by csmatyi; 08-05-2013, 08:09 AM. Reason: addition

        Comment


        • #5
          csmatyi,

          Have you tried using a precompiled version of tophat rather than building from source? That might be easier than sorting out your boost issue.

          Comment


          • #6
            Originally posted by csmatyi View Post
            Dear all,

            I keep getting the following error message when using tophat:

            Error running 'long_spanning_reads':/util/opt/tophat/2.0.9/gcc/4.4.7/bin/long_spanning_reads: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

            /util/opt/cufflinks/2.1.1/gcc/4.4.7/bin/cufflinks: error while loading shared libraries: libboost_thread.so.1.51.0: cannot open shared object file: No such file or directory

            What does this mean?
            How do I find out which version of boost that tophat uses?
            Also, how can I find out which version of boost long_spanning_reads uses?

            Thanks, csmatyi
            I second NKAkers suggestion of using pre-compiled binaries for linux for TopHat, if feasible. It will save you additional headaches with boost install.

            But if you are up for the challenge here is a thread that goes over how to fix some boost library installation problems (look on the last couple of pages, it is a long thread): http://seqanswers.com/forums/showthread.php?t=4058

            Post any errors you run into and we can tackle them.

            Comment

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