[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000264 bp)...
[M::process] read 555560 sequences (80000188 bp)...
[M::mem_process_seqs] Processed 555560 reads in 164.283 CPU sec, 20.491 real sec
[M::process] read 555560 sequences (80000112 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.512 CPU sec, 20.860 real sec
[M::process] read 555558 sequences (80000085 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.457 CPU sec, 20.822 real sec
[M::process] read 555560 sequences (80000251 bp)...
[M::mem_process_seqs] Processed 555558 reads in 168.224 CPU sec, 20.634 real sec
[M::process] read 492635 sequences (70939207 bp)...
[M::mem_process_seqs] Processed 555560 reads in 168.206 CPU sec, 20.696 real sec
[M::mem_process_seqs] Processed 492635 reads in 148.673 CPU sec, 18.370 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_Q354\tSM:CatalinaCA_Q354\tPL:Illumina reference.fasta CatalinaCA_Q354.R1.fq.gz
[main] Real time: 127.149 sec; CPU: 991.884 sec