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  • bowtie index problem (bowtie-build and then bowtie-inspect)

    I used bowtie-build to build an index:
    Code:
    ~/bin/bowtie/bowtie-build human_g1k_v37.fa human_g1k_v37
    It seemed to complete just fine:
    ebwtTotLen: 818510080
    ebwtTotSz: 818510080
    reverse: 0
    Total time for backward call to driver() for mirror index: 05:24:17
    Created these files:
    -rw-r--r-- 1 akurdogl asiniard 684M Dec 25 09:33 human_g1k_v37.4.ebwt
    -rw-r--r-- 1 akurdogl asiniard 3.7K Dec 25 09:33 human_g1k_v37.3.ebwt
    -rw-r--r-- 1 akurdogl asiniard 829M Dec 25 16:58 human_g1k_v37.1.ebwt
    -rw-r--r-- 1 akurdogl asiniard 361M Dec 25 16:58 human_g1k_v37.2.ebwt
    -rw-r--r-- 1 akurdogl asiniard 785M Dec 25 22:23 human_g1k_v37.rev.1.ebwt
    -rw-r--r-- 1 akurdogl asiniard 342M Dec 25 22:23 human_g1k_v37.rev.2.ebwt
    But when I run bowtie-inspect:
    Code:
    bowtie-inspect human_g1k_v37
    It immediately crashes with this error:
    assert_eq: expected (1, 0x1) got (84, 0x54)
    bowtie_inspect.cpp:242
    bowtie-inspect: bowtie_inspect.cpp:242: void print_ref_sequences(std:stream&, bool, const std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, const uint32_t*, const std::string&): Assertion `0' failed.
    Aborted
    Or if I run:
    Code:
    bowtie-inspect -s human_g1k_v37
    I get this:
    Colorspace 0
    SA-Sample 1 in 32
    FTab-Chars 10
    Sequence-1 ?M???F=?w?Q???!~? /m?_}u?????w??}?????_o?C_Q??stߕ[5?{d??]?q??w?t?}g?>0 249250621
    Sequence-2 x??x?????????????????????????????...
    Any help is appreciated.

  • #2
    Query

    I am getting the same problem . Could you please let me know how you solved this?

    Thanks

    Comment


    • #3
      Bowtie_build - internal exception#1

      Hello All!

      I am having troubles running bowtie_build.
      I am running:
      bowtie2-build /scratch/annet/Sdata/SSURefSilva.fa SSURef \
      > /scratch/annet/Sdata/SSURefSilva.fa

      And I am getting this error message:
      Reference file does not seem to be a FASTA file
      Error: Encountered internal Bowtie 2 exception (#1)
      Command: /opt/local/software/Genome/bowtie2/2.0.0-beta7/bin/bowtie2-build /scratch/annet/Sdata/SSURefSilva.fa SSURef

      But my fasta file is ok, I know it!

      Does anybody know what can be the problem???
      Please!!!!!!

      Comment


      • #4
        according to the Bowtie2 manual,
        the format of the bowtie-build statement should be

        Code:
        bowtie2-build [options]* <reference_in> <bt2_base>
        You might want to use the option -f to specify that your reference is in fasta format.

        Comment


        • #5
          Ok! Thank you very much!!!

          Comment

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