I am having problems with bwa, and would like some direction. I am running on some
454 reads for Salmonella.
I have converted the reads to fastq format.
I index with the command:
bwa index -p sal_chr sal.fa
I then align with the command:
bwa aln -t 4 sal_chr 454Reads.MID1.sff.fq sal.sam
and get:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... Segmentation fault
Ideas on what I am doing wrong?
I am requesting 10GB memory, is this insufficient?
Thank you.
454 reads for Salmonella.
I have converted the reads to fastq format.
I index with the command:
bwa index -p sal_chr sal.fa
I then align with the command:
bwa aln -t 4 sal_chr 454Reads.MID1.sff.fq sal.sam
and get:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... Segmentation fault
Ideas on what I am doing wrong?
I am requesting 10GB memory, is this insufficient?
Thank you.
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