I've been running bwa mem to do pair wise alignment to a reference. I have already indexed my reference and it resulted in 5 output files with the following extensions: .pac, .sa, .amb, .ann, .bwt. I have run bwa men with 60G multiple times now and all the jobs never finish. They take over 20 hours and often time out at 24 hours. I have run it as:
bwa mem -t 24 ref read1.fq.gz read2.fq.gz > output.sam bwa mem -1 -t 1 ref read1.fq.gz read2.fq.gz > output.sam bwa mem ref read1.fq.gz read2.fq.gz > output.sam
Regardless of how I run it or with which parameters standard error files end with the following:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 834) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 66668 reads in 251.152 CPU sec, 251.145 real sec
[M::mem_process_seqs] Processed 66668 reads in 187.866 CPU sec, 187.859 real sec [M::process] read 66668 sequences (10000200 bp)..
I'm confused on what this error is? Why doesn't the job ever finish? When I google it no one else has this issue.
Any constructive help is great!! I'm honestly fed up with bwa, it seems I'm not the only one that experiences this problem. It's funny how it is so popular when it doesn't work. Are there any other platforms that you would suggest?