bowtie cannot align to large genomes

[pchines@…]

Running bowtie on an Xserve with 24Gb RAM, aligning against Human reference (build 37/hg19) I get this message:

bowtie(16525) malloc: * mmap(size=716197888) failed (error code=12) * error: can't allocate region * set a breakpoint in malloc_error_break to debug Error: Ran out of memory allocating space for the bitpacked reference. Please re-run on a computer with more memory.

I believe this is because the -m64 (or -arch x86_64) parameter needs to be provided during compilation in order for the program to be in 64-bit, rather than 32-bit mode. The stock version of bowtie from UMD works for me. Below are the results of --version run on each:

/opt/local/bin/bowtie version 0.12.7 32-bit Built on zeus.nhgri.nih.gov Tue Apr 12 10:33:33 EDT 2011 Compiler: gcc version 4.0.1 (Apple Inc. build 5490) Options: -O3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 4, 8, 4, 4, 8}

/usr/local/bin/bowtie version 0.12.7 64-bit Built on Franklin.local Tue Sep 7 14:27:57 PDT 2010 Compiler: gcc version 4.0.1 (Apple Inc. build 5493) Options: -O3 -m64 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}