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  • Please help with newbie Bowtie2 question (Mac)!

    Hello everyone,

    I've just downloaded "bowtie2-2.1.0-macos-x86_64.zip" on my mac. Put the unzipped file directly under Users/Behr.

    The file seems to contain all necessary files:
    (sequence.fasta is lambda phage sequence for practice).

    Behrs-MacBook-Pro:bt2_home Behr$ ls -p
    AUTHORS
    LICENSE
    MANUAL
    MANUAL.markdown
    MAPK10.fasta
    NEWS
    TUTORIAL
    VERSION
    bowtie2
    bowtie2-align
    bowtie2-align-debug
    bowtie2-build
    bowtie2-build-debug
    bowtie2-inspect
    bowtie2-inspect-debug
    doc/
    example/
    scripts/
    sequence.fasta

    However when I ran the command, I got 2 error messages:
    Behrs-MacBook-Pro:bt2_home Behr$ /Users/Behr/BT2_home/bowtie2-build /Users/Behr/BT2_home/sequence.fa blah
    Settings:
    Output files: "blah.*.bt2"
    Line rate: 6 (line is 64 bytes)
    Lines per side: 1 (side is 64 bytes)
    Offset rate: 4 (one in 16)
    FTable chars: 10
    Strings: unpacked
    Max bucket size: default
    Max bucket size, sqrt multiplier: default
    Max bucket size, len divisor: 4
    Difference-cover sample period: 1024
    Endianness: little
    Actual local endianness: little
    Sanity checking: disabled
    Assertions: disabled
    Random seed: 0
    Sizeofs: void*:8, int:4, long:8, size_t:8
    Input files DNA, FASTA:
    /Users/Behr/BT2_home/sequence.fa
    Error: could not open /Users/Behr/BT2_home/sequence.fa
    Total time for call to driver() for forward index: 00:00:00
    Error: Encountered internal Bowtie 2 exception (#1)
    Command: /Users/Behr/BT2_home/bowtie2-build /Users/Behr/BT2_home/sequence.fa blah

    Can someone help me with this, please?

    Thank you very much in advance!
    Joyce

  • #2
    The directory for your fa file may not be right. You can try ~/ to indicate your fa file direct

    Comment


    • #3
      Thank you, that fixed the problem - it's indeed the .fa! (should be .fasta).
      Joyce :P

      Comment

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