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  • tophat: Indexing splices

    Hi

    I received the error below when running tophat with some old reads (35nt).

    the file, bowtie-build is references as a symlink in .../bin (bowtie2-build -> /seu/cs/home/user/c/charlesh/binf/src/bowtie2-2.2.3/bowtie2-build)



    tophat2 -o ./tophat_out --segment-length 17 -g 1 --b2-very-sensitive --min-intron-length 30 --max-intron-length 28000 $BOWTIE_INDEX/bowtie2/cre5.3 s1.fastqsanger.gz

    [2014-07-04 12:50:45] Beginning TopHat run (v2.0.10)
    -----------------------------------------------
    [2014-07-04 12:50:45] Checking for Bowtie
    Bowtie version: 2.1.0.0
    [2014-07-04 12:50:45] Checking for Samtools
    Samtools version: 0.1.18.0
    [2014-07-04 12:50:45] Checking for Bowtie index files (genome)..
    [2014-07-04 12:50:45] Checking for reference FASTA file
    [2014-07-04 12:50:45] Generating SAM header for /seu/cs/home/user/c/charlesh/binf/sto1/seq/bowtie_index/bowtie2/cre5.3
    [2014-07-04 12:50:45] Preparing reads
    left reads: min. length=35, max. length=35, 7157301 kept reads (5402 discarded)
    [2014-07-04 12:52:21] Mapping left_kept_reads to genome cre5.3 with Bowtie2
    [2014-07-04 13:00:19] Mapping left_kept_reads_seg1 to genome cre5.3 with Bowtie2 (1/2)
    [2014-07-04 13:03:38] Mapping left_kept_reads_seg2 to genome cre5.3 with Bowtie2 (2/2)
    [2014-07-04 13:06:50] Searching for junctions via segment mapping
    Coverage-search algorithm is turned on, making this step very slow
    Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
    [2014-07-04 13:26:10] Retrieving sequences for splices
    [2014-07-04 13:26:20] Indexing splices
    Traceback (most recent call last):
    File "/seu/cs/home/user/c/charlesh/binf/bin/bowtie2-build", line 95, in <module>
    main()
    File "/seu/cs/home/user/c/charlesh/binf/bin/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
    OSError: [Errno 2] No such file or directory
    [FAILED]
    Error: Splice sequence indexing failed with err =1


    Charles

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