[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000001 bp)...
[M::process] read 555560 sequences (80000260 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.350 CPU sec, 21.095 real sec
[M::process] read 555560 sequences (80000230 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.017 CPU sec, 21.428 real sec
[M::process] read 555558 sequences (80000091 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.935 CPU sec, 21.495 real sec
[M::process] read 555558 sequences (80000049 bp)...
[M::mem_process_seqs] Processed 555558 reads in 172.419 CPU sec, 21.206 real sec
[M::process] read 555560 sequences (80000283 bp)...
[M::mem_process_seqs] Processed 555558 reads in 173.014 CPU sec, 21.275 real sec
[M::process] read 225761 sequences (32509428 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.575 CPU sec, 21.598 real sec
[M::mem_process_seqs] Processed 225761 reads in 73.783 CPU sec, 9.010 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_Q355\tSM:CatalinaCA_Q355\tPL:Illumina reference.fasta CatalinaCA_Q355.R1.fq.gz
[main] Real time: 140.100 sec; CPU: 1114.121 sec