Re: [Bio-bwa-help] Parallel BWA

[Mark K. <mk...@co...>]

Hi,
 
The problem is due to the reference index files being generated 
with bwa version 0.5.x
The reference index file format changed with bwa version 0.6.1
and is incompatible with earlier bwa 0.5.x versions.
 
thanks,
mark
 
From: Gregory Miles [mailto:mi...@um...] 
Sent: Tuesday, May 22, 2012 2:14 PM
To: bio...@li...
Subject: [Bio-bwa-help] Parallel BWA
 
Hi,
I was running BWA 0.6.1 sampe unpatched and the sam file was being generated
normally. I decided to try the patched parallel version that Mark Kelly has
posted and I get the following:

[bwa_sai2sam_pe_core] version: 0.6.1-r104-tpx-unknown (Tue May 22 13:34:30
EDT 2012)
[bwa_sai2sam_pe_core] num threads: 8 (max: 16)
Segmentation fault

I tried running the single thread version afterwards (the version that works
on the unpatched BWA), and got the same message (except num threads was 1).

Any help would be greatly appreciated. Thanks.

Greg


Dr. Gregory Miles
Bioinformatics Specialist
Cancer Institute of New Jersey @ UMDNJ
Office: (732) 235 8817

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