[MacPorts] #29131: bowtie cannot align to large genomes

[MacPorts]

#29131: bowtie cannot align to large genomes
----------------------------------+-----------------------------------------
 Reporter:  pchines@…             |       Owner:  haroldpimentel@…        
     Type:  defect                |      Status:  new                     
 Priority:  Normal                |   Milestone:                          
Component:  ports                 |     Version:  1.9.2                   
 Keywords:                        |        Port:  bowtie                  
----------------------------------+-----------------------------------------
Changes (by macsforever2000@…):

  * keywords:  malloc mmap nomem 64bit =>
 * cc: haroldpimentel@…, pchines@… (removed)
  * owner:  macports-tickets@… => haroldpimentel@…


Old description:

> 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}

New description:

 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}
 }}}

--

-- 
Ticket URL: <https://trac.macports.org/ticket/29131#comment:2>
MacPorts <http://www.macports.org/>
Ports system for Mac OS