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Old 07-28-2011, 09:12 AM   #1
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Default segmentation fault in BWA sampe

Hi all,
i am using bwa-0.5.9 for illumina output.

i have reads from 2 samples of same organism.
So i have 2 databases.

when i run BWA on the first, everything went well. the SAM file is 3.3GB.

On the second, i got segmentation fault in the last part, when converting to *.sam.
it succeed to convert 2.2GB , and then seg` fault.

My steps are:
bwa index -a is database.fasta

bwa aln database.fasta read_1.fastq > database_aln_sa_1.sai
bwa aln database.fasta read_2.fastq > database_aln_sa_2.sai

bwa sampe database.fasta database_aln_sa_1.sai database_aln_sa_2.sai read_1.fastq read_2.fastq > database_aln.sam

When i run bwa with samse on each end separately , i got 2 sam file , each in size 1.6GB , as expected.

My questions are:
How can i solve the Segmentation fault?
Or, Can i merge the 2 sam files that have been resulted separately to one sam?without loosing any data?

Thanks in advance..
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