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  • need help to solve bowtie2-inspect error

    Dear all bowtie users,

    I am new in NG-sequencing. I used following command to build index of repeat masked genome by repeatmasker.

    bowtie2-build genome_scaffolds.masked.fa my_genome_index

    during the execution of command I also faced the multiple warnings
    'Warning: Encountered reference sequence with only gaps'

    Furthermore, during using Tophat I got warning: could not find fasta file and error Error: bowtie-inspect returned an error log: bowtie2-inspect: bt2_inspect.cpp:218:

    So, after reading some blogs I thought to build fasta from index and used

    bowtie2-inspect my_genome_index

    assert_eq: expected (24026, 0x5dda) got (23330, 0x5b22)
    bt2_inspect.cpp:218
    bowtie2-inspect: bt2_inspect.cpp:218: void print_ref_sequences(std:stream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const uint32_t*, const std::string&): Assertion `0' failed.
    Aborted

    The command again failed with the above message. Could someone please help me to solve this problem

    below is the footer first bowtie execution
    len: 192701494
    bwtLen: 192701495
    sz: 48175374
    bwtSz: 48175374
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12043844
    offsSz: 48175376
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1003654
    numLines: 1003654
    ebwtTotLen: 64233856
    ebwtTotSz: 64233856
    color: 0
    reverse: 1


    Thank you for your HELP!

  • #2
    Did you fingure out what is the problem?

    Comment

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