[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556238 sequences (80000094 bp)...
[M::process] read 556304 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 556238 reads in 172.346 CPU sec, 21.481 real sec
[M::process] read 556236 sequences (80000196 bp)...
[M::mem_process_seqs] Processed 556304 reads in 177.455 CPU sec, 21.850 real sec
[M::process] read 556252 sequences (80000195 bp)...
[M::mem_process_seqs] Processed 556236 reads in 177.629 CPU sec, 21.812 real sec
[M::process] read 171615 sequences (24676528 bp)...
[M::mem_process_seqs] Processed 556252 reads in 176.883 CPU sec, 21.856 real sec
[M::mem_process_seqs] Processed 171615 reads in 59.441 CPU sec, 7.203 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_389\tSM:CatalinaCA_389\tPL:Illumina reference.fasta CatalinaCA_389.R1.fq.gz
[main] Real time: 96.532 sec; CPU: 765.361 sec