[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000213 bp)...
[M::process] read 555560 sequences (80000040 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.618 CPU sec, 22.525 real sec
[M::process] read 555560 sequences (80000008 bp)...
[M::mem_process_seqs] Processed 555560 reads in 187.071 CPU sec, 23.033 real sec
[M::process] read 555560 sequences (80000263 bp)...
[M::mem_process_seqs] Processed 555560 reads in 184.698 CPU sec, 22.706 real sec
[M::process] read 555560 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 555560 reads in 187.206 CPU sec, 22.983 real sec
[M::process] read 386249 sequences (55619613 bp)...
[M::mem_process_seqs] Processed 555560 reads in 187.445 CPU sec, 23.074 real sec
[M::mem_process_seqs] Processed 386249 reads in 131.304 CPU sec, 16.198 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_Q338\tSM:CatalinaCA_Q338\tPL:Illumina reference.fasta CatalinaCA_Q338.R1.fq.gz
[main] Real time: 134.653 sec; CPU: 1060.950 sec