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..
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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