[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000030 bp)...
[M::process] read 555558 sequences (80000054 bp)...
[M::mem_process_seqs] Processed 555558 reads in 176.579 CPU sec, 22.014 real sec
[M::process] read 555560 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.272 CPU sec, 21.896 real sec
[M::process] read 555560 sequences (80000219 bp)...
[M::mem_process_seqs] Processed 555560 reads in 178.544 CPU sec, 21.982 real sec
[M::process] read 555560 sequences (80000217 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.775 CPU sec, 22.068 real sec
[M::process] read 555558 sequences (80000019 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.108 CPU sec, 22.041 real sec
[M::process] read 555558 sequences (80000124 bp)...
[M::mem_process_seqs] Processed 555558 reads in 180.387 CPU sec, 22.152 real sec
[M::process] read 555558 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 555558 reads in 177.557 CPU sec, 21.839 real sec
[M::process] read 555560 sequences (80000180 bp)...
[M::mem_process_seqs] Processed 555558 reads in 177.121 CPU sec, 21.784 real sec
[M::process] read 555558 sequences (80000137 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.646 CPU sec, 22.229 real sec
[M::process] read 555558 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 555558 reads in 180.726 CPU sec, 22.239 real sec
[M::process] read 143505 sequences (20664652 bp)...
[M::mem_process_seqs] Processed 555558 reads in 177.981 CPU sec, 22.013 real sec
[M::mem_process_seqs] Processed 143505 reads in 51.237 CPU sec, 6.191 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_Q352\tSM:CatalinaCA_Q352\tPL:Illumina reference.fasta CatalinaCA_Q352.R1.fq.gz
[main] Real time: 251.028 sec; CPU: 2019.775 sec