bowtie does not obey build_arch

[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}

[pchines@…]

Cc Me!

[jmroot (Joshua Root)]

What OS are you running? 10.5? I assume you have build_arch set to x86_64 in macports.conf?

[jmroot (Joshua Root)]

r91309