#287 bowtie2-build 64-bit not able to build more than 32bit


I have tried both the x86_64 binaries as well as building from source of bowtie2-2.1.0, but bowtie2-build was unable to build a large database:

/usr/local/bin/bowtie2-2.1.0-source/bowtie2-build version 2.1.0
Built on cooler
Tue Jul 16 13:34:57 EST 2013
Compiler: gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1)
Options: -O3 -m64 -msse2 -funroll-loops -g3
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

==> and the error when running this bowtie2-build:

Error: Reference sequence has more than 2^32-1 characters! Please divide the
reference into batches or chunks of about 3.6 billion characters or less each
and index each independently.

Do I still need to divide the reference into smaller chunks for 64bit bowtie2-build?


  • ken

    ken - 2013-07-16

    In addition, here is an excerpt from seqanswers about being able to align to multiple indexes at one time:

    As far as I know you can only use one index at a time. You can run bowtie2 three times and should be able to merge the resulting BAM files. On the other hand this multi-index may create multiple mappings that you would not find with a single index.

    Can you recommend any way to get a 'single index' from a very large reference without having to split it up?

    thank you

  • Val

    Val - 2013-07-17

    Hi Ken,

    To quickly answer your question, yes, you will have to divide the reference into smaller chunks for now. We will extend the size of the index bowtie2 can use and you can expect this feature to make it into bowtie2 in the next 2 following releases.


  • Val

    Val - 2013-07-29
    • Priority: 5 --> 1
  • Val

    Val - 2014-01-30

    Fixed this for the next release.

  • Val

    Val - 2014-01-30
    • status: open --> closed
    • assigned_to: Val

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