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  • nunu_ping
    Junior Member
    • Apr 2010
    • 4

    #1

    tophat error

    Does anyone know what is wrong here? I used tophat for my RNA seq data, but error occurs...

    [Mon Jan 10 22:20:48 2011] Beginning TopHat run (v1.1.4)
    -----------------------------------------------
    [Mon Jan 10 22:20:48 2011] Preparing output location output_dir//
    [Mon Jan 10 22:20:48 2011] Checking for Bowtie index files
    [Mon Jan 10 22:20:48 2011] Checking for reference FASTA file
    [Mon Jan 10 22:20:48 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Mon Jan 10 22:20:48 2011] Checking for Samtools
    Samtools version: 0.1.11.0
    [Mon Jan 10 22:20:55 2011] Checking reads
    min read length: 76bp, max read length: 76bp
    format: fastq
    quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
    [Mon Jan 10 22:34:39 2011] Mapping reads against ensembl_human_v60 with Bowtie
    [Mon Jan 10 23:10:25 2011] Joining segment hits
    [Tue Jan 11 01:24:08 2011] Mapping reads against ensembl_human_v60 with Bowtie(1/3)
    [Tue Jan 11 01:49:37 2011] Mapping reads against ensembl_human_v60 with Bowtie(2/3)
    [Tue Jan 11 02:04:24 2011] Mapping reads against ensembl_human_v60 with Bowtie(3/3)
    [Tue Jan 11 02:15:54 2011] Searching for junctions via segment mapping
    [Tue Jan 11 03:26:00 2011] Retrieving sequences for splices
    [Tue Jan 11 03:50:25 2011] Indexing splices
    [Tue Jan 11 04:38:27 2011] Mapping reads against segment_juncs with Bowtie
    [Tue Jan 11 05:01:24 2011] Mapping reads against segment_juncs with Bowtie
    [Tue Jan 11 05:19:07 2011] Mapping reads against segment_juncs with Bowtie
    [Tue Jan 11 05:32:35 2011] Joining segment hits
    Traceback (most recent call last):
    File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2223, in <module>
    sys.exit(main())
    File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2181, in main
    user_supplied_juncs)
    File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2053, in spliced_alignment
    os.rename(merged_map, mapped_reads)
    OSError: [Errno 1] Operation not permitted

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