[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555982 sequences (80000019 bp)...
[M::process] read 556040 sequences (80000265 bp)...
[M::mem_process_seqs] Processed 555982 reads in 159.516 CPU sec, 19.855 real sec
[M::process] read 555894 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 556040 reads in 163.223 CPU sec, 20.063 real sec
[M::process] read 555932 sequences (80000096 bp)...
[M::mem_process_seqs] Processed 555894 reads in 166.295 CPU sec, 20.418 real sec
[M::process] read 11787 sequences (1695862 bp)...
[M::mem_process_seqs] Processed 555932 reads in 160.317 CPU sec, 19.827 real sec
[M::mem_process_seqs] Processed 11787 reads in 4.402 CPU sec, 0.515 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_367\tSM:CatalinaCA_367\tPL:Illumina reference.fasta CatalinaCA_367.R1.fq.gz
[main] Real time: 85.183 sec; CPU: 656.750 sec