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Old 12-15-2012, 05:36 AM   #1
zgene
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Location: Asia

Join Date: Sep 2012
Posts: 7
Default Segmentation fault (core dumped)-BWA indexing ref genome

Dear All,

I am working with program: bwa (alignment via Burrows-Wheeler transformation),Version: 0.6.2

The OS and its version is Linux Linux-Pc.LabDomain.com 3.3.4-5.fc17.i686.PAE #1 SMP Mon May 7 17:37:39 UTC 2012 i686 i686 i386 GNU/Linux.

I used the following command to index my ref genome( I have downloaded,unzipped and concatenated the chromosome files) : bwa index -p hg19bwaidx -a bwtsw wg.fa

and I got the error as following: Pack FASTA... Segmentation fault (core dumped)

Since I am new in working with BWA and even Linux system,I do not understand that what the problem is exactly and how I can solve it. Would you please kindly help me in this matter? I am looking forward to hearing from you.
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Old 12-16-2012, 06:17 AM   #2
AJERYC
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Location: Spain

Join Date: Jan 2012
Posts: 26
Default

Quote:
Originally Posted by zgene View Post
Dear All,

I am working with program: bwa (alignment via Burrows-Wheeler transformation),Version: 0.6.2

The OS and its version is Linux Linux-Pc.LabDomain.com 3.3.4-5.fc17.i686.PAE #1 SMP Mon May 7 17:37:39 UTC 2012 i686 i686 i386 GNU/Linux.

I used the following command to index my ref genome( I have downloaded,unzipped and concatenated the chromosome files) : bwa index -p hg19bwaidx -a bwtsw wg.fa

and I got the error as following: Pack FASTA... Segmentation fault (core dumped)

Since I am new in working with BWA and even Linux system,I do not understand that what the problem is exactly and how I can solve it. Would you please kindly help me in this matter? I am looking forward to hearing from you.

That its an error that appears when you are working with very large files. It has to do with linux or windows handling of ram memory
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