Getting Index Error 12 When Attempting To Index A Genome With Bwa

Question

[sindhuri.prakash]

Hello everyone,

I am trying to index human genome build 37. I am using a Mac OS 10.5.8, 64 bit, 8GB of RAM and 280GB of space. And using the latest version of BWA 0.6.2. When I run the command:

bwa index -a bwtsw -p human_g1k_v37 human_g1k_v37.fasta

BWA starts indexing the genome but stops and provides an error message (error code=12)

[BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
[bwt_gen] Finished constructing BWT in 688 iterations.
[bwa_index] 2010.81 seconds elapse.
[bwa_index] Update BWT... bwa(3627) malloc: *** mmap(size=3101806592) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Bus error

Any help with this will be greatly appreciated.

Thanks!

[lh3]

Sounds like insufficient memory. Not sure. Never indexed human genome on my mac laptop.

Answer 1

[Istvan Albert]

Based on the error that you get

Bus error

You are most likely running a 32 bit application on a 64 bit machine or viceversa. Make sure that you compile the application on the machine that you are running it on.

[sindhuri.prakash]

THanks so much for getting back to me so promptly! So according to the makefile it says its 64 bit. Below is a line from the makefile:

DFLAGS= -DHAVEPTHREAD #-DNOSSE2 #-DFILEOFFSETBITS=64

My computer has a 64 bit processor : 3.06 GHz Intel Core 2 Duo..

Let me know if I can do anything else...

[Istvan Albert]

that second thing that comes to mind is that Macs have radically changed their GCC software and went from 'regular' to an LLVM architecture (not sure what the right words are) - but look for concepts such as clang vs gcc vs xcode. See if you can index smaller genomes and whether bwa works otherwise. I still believe that you have a problem at infrastructure level and not in the software.