[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000188 bp)...
[M::process] read 555558 sequences (80000056 bp)...
[M::mem_process_seqs] Processed 555560 reads in 109.325 CPU sec, 13.587 real sec
[M::process] read 242239 sequences (34882270 bp)...
[M::mem_process_seqs] Processed 555558 reads in 113.891 CPU sec, 14.046 real sec
[M::mem_process_seqs] Processed 242239 reads in 51.113 CPU sec, 6.240 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -L 20,5 -t 8 -a -M -T 10 -A 1 -B 4 -O 6 -R @RG\tID:CatalinaCA_Q353\tSM:CatalinaCA_Q353\tPL:Illumina reference.fasta CatalinaCA_Q353.R1.fq.gz
[main] Real time: 36.186 sec; CPU: 276.099 sec