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Old 01-29-2013, 05:15 AM   #1
JMFA
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Default BWA index segmentation fault

Dear all,

I'm having some difficulties trying to index a reference genome using BWA -a bwtsw.
I am using BWA 0.6.2 version and I tried to index the Hg19 but BWA fails to complete the index.

The error looks like this:

Quote:
[BWTIncConstructFromPacked] 620 iterations done. 1697352406 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 1740074246 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 1778041526 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 1811782918 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 1841768294 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
[bwt_gen] Finished constructing BWT in 688 iterations.
[bwa_index] 886.42 seconds elapse.
[bwa_index] Update BWT... Segmentation fault (core dumped)
I am currently using a 4 CPU server with 8Gb RAM.
In the BWA manual it says that BWA uses approx. 2.5 Gb of memory to align the whole human genome, so I wasn't expecting this type of error.
I checked the memory usage (using system monitor) during BWA index and in fact it showed that only 2.4 Gb out of 7.9Gb were being used in the process.

Do you have any idea of what might be the problem?
I tried looking at the different seqanswers threads reporting "segmentation fault" with BWA but none of them had an answer to my question.
I have 250Gb of disk space left so I don't think that this is the problem.
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Old 01-29-2013, 11:55 AM   #2
xied75
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Is this a 64 bit Linux? Did you compile the BWA on it? 680 iterations done, 1892095270 doesn't look correct, it should be 6 billion something. Check your config or make file for 64 bit file access switches.

Best,

dong
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Old 01-30-2013, 02:44 AM   #3
JMFA
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dear xied75,

Thanks for the reply!
No. I'm running a 32-bit version of ubuntu 12.04.1 LTS

Code:
file bwa
gives this output

Quote:
bwa: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.24, BuildID[sha1]=0x4292d216c6a53bd4d44bbb70b5e2dd5e81c1e2bd, not stripped
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Old 01-30-2013, 02:47 AM   #4
xied75
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Oh dear, I've no idea if a 32 bit BWA can process hg19. Anyone?
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Old 01-30-2013, 03:41 AM   #5
GenoMax
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Is there a reason to run 32-bit linux on this machine? Though in theory ubuntu likely supports PAE you are going to run into some problem or other down the road (http://askubuntu.com/questions/20049...t-installation). If at all possible you should consider switching to 64-bit version of the OS.
You have 8 GB of RAM and "4 CPU's" (I assume that refers to either a dual-core multi-threaded or a quad-core singe-threaded physical CPU) which will support that 64-bit OS.

Back on the topic of your original question: One thing to check is the size of swap partition. It is quite possible that either swap (or /tmp) is filling up completely causing bwa to crash.
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Old 01-30-2013, 03:53 PM   #6
RDW
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Quote:
Originally Posted by xied75 View Post
Oh dear, I've no idea if a 32 bit BWA can process hg19. Anyone?
As far as I recall, it can't. Time to upgrade the OS!
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Old 01-31-2013, 08:06 AM   #7
JMFA
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Dear all,
thank you very much for the comments!

I decided to upgrade the OS to 64-bit!
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