[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000163 bp)...
[M::process] read 555560 sequences (80000193 bp)...
[M::mem_process_seqs] Processed 555560 reads in 152.582 CPU sec, 19.004 real sec
[M::process] read 555560 sequences (80000178 bp)...
[M::mem_process_seqs] Processed 555560 reads in 158.642 CPU sec, 19.538 real sec
[M::process] read 555560 sequences (80000203 bp)...
[M::mem_process_seqs] Processed 555560 reads in 160.252 CPU sec, 19.723 real sec
[M::process] read 555560 sequences (80000218 bp)...
[M::mem_process_seqs] Processed 555560 reads in 157.290 CPU sec, 19.289 real sec
[M::process] read 555560 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555560 reads in 158.738 CPU sec, 19.488 real sec
[M::process] read 351916 sequences (50675660 bp)...
[M::mem_process_seqs] Processed 555560 reads in 156.517 CPU sec, 19.257 real sec
[M::mem_process_seqs] Processed 351916 reads in 101.288 CPU sec, 12.472 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_Q330\tSM:CatalinaCA_Q330\tPL:Illumina reference.fasta CatalinaCA_Q330.R1.fq.gz
[main] Real time: 132.129 sec; CPU: 1047.676 sec