[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000266 bp)...
[M::process] read 555560 sequences (80000136 bp)...
[M::mem_process_seqs] Processed 555560 reads in 164.364 CPU sec, 20.493 real sec
[M::process] read 555560 sequences (80000020 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.523 CPU sec, 20.600 real sec
[M::process] read 555558 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.236 CPU sec, 20.911 real sec
[M::process] read 555560 sequences (80000259 bp)...
[M::mem_process_seqs] Processed 555558 reads in 168.031 CPU sec, 20.634 real sec
[M::process] read 555560 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.168 CPU sec, 21.023 real sec
[M::process] read 423000 sequences (60911708 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.743 CPU sec, 20.471 real sec
[M::mem_process_seqs] Processed 423000 reads in 128.232 CPU sec, 15.818 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_Q356\tSM:CatalinaCA_Q356\tPL:Illumina reference.fasta CatalinaCA_Q356.R1.fq.gz
[main] Real time: 143.750 sec; CPU: 1138.942 sec