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  • Tohat2.0.0.7 error when set bowtie2 to option (--b2-very-sensitive)

    I got the same errror when set --b2-very-sensitive option. No probelm when i use defualt.

    the errors were happen in the same step (apping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)) :

    [2012-08-01 18:35:56] Beginning TopHat run (v2.0.4)
    -----------------------------------------------
    [2012-08-01 18:35:56] Checking for Bowtie
    Bowtie version: 2.0.0.7
    [2012-08-01 18:35:56] Checking for Samtools
    Samtools version: 0.1.18.0
    [2012-08-01 18:35:56] Checking for Bowtie index files
    [2012-08-01 18:35:56] Checking for reference FASTA file
    [2012-08-01 18:35:56] Generating SAM header for /c3se/NOBACKUP/groups/c3-sysbio/GC/tools/bowtie-0.12.8/indexes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
    format: fastq
    quality scale: phred33 (default)
    [2012-08-01 18:36:30] Preparing reads
    left reads: min. length=25, max. length=101, 29317658 kept reads (17769 discarded)
    right reads: min. length=25, max. length=101, 29183210 kept reads (152217 discarded)
    [2012-08-01 19:00:12] Mapping left_kept_reads to genome genome with Bowtie2
    [2012-08-01 20:29:51] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
    [2012-08-01 20:49:59] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
    [2012-08-01 21:10:48] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
    [2012-08-01 21:26:41] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
    [2012-08-01 21:35:19] Mapping right_kept_reads to genome genome with Bowtie2
    [2012-08-01 23:04:48] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
    [2012-08-01 23:25:23] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
    [2012-08-01 23:48:05] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
    [2012-08-02 00:08:14] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
    [2012-08-02 00:20:07] Searching for junctions via segment mapping
    [2012-08-02 00:36:37] Retrieving sequences for splices
    [2012-08-02 00:39:02] Indexing splices
    [2012-08-02 00:39:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
    [2012-08-02 00:46:38] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
    [2012-08-02 00:52:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
    [2012-08-02 00:57:21] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
    [2012-08-02 01:00:24] Joining segment hits
    [2012-08-02 01:29:42] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
    Traceback (most recent call last):
    File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3948, in <module>
    sys.exit(main())
    File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3912, in main
    user_supplied_deletions)
    File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3572, in spliced_alignment
    _segs_vs_J)
    File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 2256, in bowtie
    stderr=open(bwt_logname, "w"))
    IOError: [Errno 1] Operation not permitted: '/c3se/NOBACKUP/groups/c3-sysbio/GC/RNAseq/Intawat_tophat/tophat_CA1_very_sen_1/logs/bowtie.right_kept_reads_seg1.log'

    The write read permittion is no problem. I dont know why ?

    Inrawar

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