[MacPorts] #29131: bowtie cannot align to large genomes
MacPorts
noreply at macports.org
Thu Apr 14 06:58:20 PDT 2011
#29131: bowtie cannot align to large genomes
-------------------------------------+--------------------------------------
Reporter: pchines@… | Owner: macports-tickets@…
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 1.9.2
Keywords: malloc mmap nomem 64bit | Port: bowtie
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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}
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Ticket URL: <https://trac.macports.org/ticket/29131>
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