Re: [Bio-bwa-help] Segmentation fault

[Heng Li <lh...@sa...>]

The indexing has not been finished. You need about 5-6GB memory to index a human genome with bwa-0.6.x or bwa-0.7.x. Bwa-0.5.x requires less memory.

Heng

On Mar 15, 2013, at 11:29 AM, Wang, Zhiping wrote:

> Hi, I tried two different ways of pair end alignment using bwa-0.7.2
> 1)  bwa aln ref.fa read1.fq > aln_sa1.sai
> 
> bwa aln ref.fa read2.fq > aln_sa2.sai
> 
> bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
> 
> 2)      bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
>  
> However they both gave me this error within seconds: Segmentation fault (core dumped)
>  
> I am not sure if the index files generated by bwa-0.7.2 caused the trouble as the size of index files is really small as below,
> 3.0G Mar 13 15:52 hg19.fa
> 56 Mar 13 17:46 hg19.fa.sa
> 2 Mar 13 17:46 hg19.fa.pac
> 72 Mar 13 17:46 hg19.fa.bwt
> 7 Mar 13 17:46 hg19.fa.ann
> 6 Mar 13 17:46 hg19.fa.amb
>  
> While index files from bow-0.5.2 look like (BTW, same error occurred for this version of bwa using ‘sampe’),
> 3.0G Mar 12 14:47 hg19.fa
> 834K Mar 13 10:17 hg19.fa.amb
> 218K Mar 13 10:17 hg19.fa.ann
> 981K Mar 13 10:17 hg19.fa.bwt
> 654K Mar 13 10:17 hg19.fa.pac
> 981K Mar 13 10:17 hg19.fa.rbwt
> 654K Mar 13 10:17 hg19.fa.rpac
> 327K Mar 13 10:17 hg19.fa.rsa
> 327K Mar 13 10:17 hg19.fa.sa
> Please help… thanks a lot.
> Regards,
> Zhiping Paul Wang
> <>< <>< <>< <>< <>< <>< <>< <>< <>< <><
> Center of Computational Biology and Bioinformatics
> Indiana University School of Medicine
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> Indianapolis, IN 46202
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