[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
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 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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