[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556016 sequences (80000007 bp)...
[M::process] read 556012 sequences (80000186 bp)...
[M::mem_process_seqs] Processed 556016 reads in 166.602 CPU sec, 20.770 real sec
[M::process] read 362412 sequences (52145358 bp)...
[M::mem_process_seqs] Processed 556012 reads in 172.957 CPU sec, 21.329 real sec
[M::mem_process_seqs] Processed 362412 reads in 112.097 CPU sec, 13.784 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_378\tSM:CatalinaCA_378\tPL:Illumina reference.fasta CatalinaCA_378.R1.fq.gz
[main] Real time: 59.651 sec; CPU: 453.981 sec