Question: Segmentation Fault (Core Dumped)-Bwa Indexing Ref Genome
gravatar for Z-F
7.8 years ago by
Z-F20 wrote:

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

The OS and its version is Linux 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.

bwa • 4.2k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 7.8 years ago by Z-F20

wg.fa is 3.2GB and the available RAM memory of my computer is 3980 MB in total.However,used memory is about 3056MB and I have only 924MB free memory! Is this the problem?

ADD REPLYlink modified 7.8 years ago • written 7.8 years ago by Z-F20
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

what's the size of wg.fa ? it is the correct compression algorithm (bwtsw?) are you allowed to read wg.fa ? to you have the permission to write in that folder ? to you have enough free space ?

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum130k
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