[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556112 sequences (80000257 bp)...
[M::process] read 556184 sequences (80000152 bp)...
[M::mem_process_seqs] Processed 556112 reads in 170.532 CPU sec, 21.262 real sec
[M::process] read 556100 sequences (80000137 bp)...
[M::mem_process_seqs] Processed 556184 reads in 171.865 CPU sec, 21.077 real sec
[M::process] read 556074 sequences (80000018 bp)...
[M::mem_process_seqs] Processed 556100 reads in 173.668 CPU sec, 21.337 real sec
[M::process] read 269078 sequences (38702524 bp)...
[M::mem_process_seqs] Processed 556074 reads in 173.514 CPU sec, 21.405 real sec
[M::mem_process_seqs] Processed 269078 reads in 86.658 CPU sec, 10.609 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_393\tSM:CatalinaCA_393\tPL:Illumina reference.fasta CatalinaCA_393.R1.fq.gz
[main] Real time: 98.749 sec; CPU: 778.261 sec