[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000015 bp)...
[M::process] read 555560 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555558 reads in 167.915 CPU sec, 20.929 real sec
[M::process] read 555560 sequences (80000242 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.536 CPU sec, 21.372 real sec
[M::process] read 555560 sequences (80000117 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.190 CPU sec, 21.288 real sec
[M::process] read 555560 sequences (80000221 bp)...
[M::mem_process_seqs] Processed 555560 reads in 172.660 CPU sec, 21.244 real sec
[M::process] read 555560 sequences (80000180 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.689 CPU sec, 21.102 real sec
[M::process] read 555558 sequences (80000038 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.363 CPU sec, 21.296 real sec
[M::process] read 555558 sequences (80000058 bp)...
[M::mem_process_seqs] Processed 555558 reads in 173.271 CPU sec, 21.312 real sec
[M::process] read 555560 sequences (80000226 bp)...
[M::mem_process_seqs] Processed 555558 reads in 172.681 CPU sec, 21.219 real sec
[M::process] read 555558 sequences (80000036 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.807 CPU sec, 21.362 real sec
[M::process] read 509868 sequences (73420700 bp)...
[M::mem_process_seqs] Processed 555558 reads in 175.510 CPU sec, 21.598 real sec
[M::mem_process_seqs] Processed 509868 reads in 157.373 CPU sec, 19.465 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_Q332\tSM:CatalinaCA_Q332\tPL:Illumina reference.fasta CatalinaCA_Q332.R1.fq.gz
[main] Real time: 236.845 sec; CPU: 1887.945 sec