[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000150 bp)...
[M::process] read 555560 sequences (80000119 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.889 CPU sec, 21.299 real sec
[M::process] read 555562 sequences (80000204 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.927 CPU sec, 21.393 real sec
[M::process] read 555562 sequences (80000220 bp)...
[M::mem_process_seqs] Processed 555562 reads in 177.020 CPU sec, 21.769 real sec
[M::process] read 555560 sequences (80000100 bp)...
[M::mem_process_seqs] Processed 555562 reads in 174.291 CPU sec, 21.423 real sec
[M::process] read 555560 sequences (80000203 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.722 CPU sec, 21.505 real sec
[M::process] read 555560 sequences (80000043 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.527 CPU sec, 21.319 real sec
[M::process] read 555560 sequences (80000170 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.536 CPU sec, 21.467 real sec
[M::process] read 115626 sequences (16650096 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.042 CPU sec, 21.515 real sec
[M::mem_process_seqs] Processed 115626 reads in 40.785 CPU sec, 4.848 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_Q334\tSM:CatalinaCA_Q334\tPL:Illumina reference.fasta CatalinaCA_Q334.R1.fq.gz
[main] Real time: 178.784 sec; CPU: 1435.509 sec