Hi, I'm running bwa mem (v. 0.7.15) on some whole exome sequencing fastqs (paired end, illumina) and I'm getting a segmentation fault very early on in the run. Here's the command:
bwa mem -t 8 -M -R "@RG\tID:D658\tPL:ILLUMINA\tSM:D658" localDir/human_g1k_v37.fasta localDir/D658_S6_L001_R1_001.fastq.gz localDir/D658_S6_L001_R2_001.fastq.gz
Here's the last part of the output:
@SQ SN:GL000200.1 LN:187035 @SQ SN:GL000193.1 LN:189789 @SQ SN:GL000194.1 LN:191469 @SQ SN:GL000225.1 LN:211173 @SQ SN:GL000192.1 LN:547496 @RG ID:D658 PL:ILLUMINA SM:D658 @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -M -R @RG\tID:D658\tPL:ILLUMINA\tSM:D658 localDir/human_g1k_v37.fasta localDir/D658_S6_L001_R1_001.fastq.gz localDir/D658_S6_L001_R2_001.fastq.gz [M::process] read 800000 sequences (80000000 bp)... Segmentation fault
I'm actually running this on an AWS ec2 instance m4.2xlarge, so there's 8 vCPUs and 32Gb of memory. So I don't think a lack of resources is a problem.
Any feedback would be much appreciated!