[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556006 sequences (80000139 bp)...
[M::process] read 556102 sequences (80000102 bp)...
[M::mem_process_seqs] Processed 556006 reads in 166.085 CPU sec, 20.701 real sec
[M::process] read 556150 sequences (80000258 bp)...
[M::mem_process_seqs] Processed 556102 reads in 171.079 CPU sec, 21.053 real sec
[M::process] read 555948 sequences (80000060 bp)...
[M::mem_process_seqs] Processed 556150 reads in 168.451 CPU sec, 20.729 real sec
[M::process] read 555974 sequences (80000192 bp)...
[M::mem_process_seqs] Processed 555948 reads in 170.394 CPU sec, 20.928 real sec
[M::process] read 428108 sequences (61591354 bp)...
[M::mem_process_seqs] Processed 555974 reads in 168.145 CPU sec, 20.687 real sec
[M::mem_process_seqs] Processed 428108 reads in 131.115 CPU sec, 16.192 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_392\tSM:CatalinaCA_392\tPL:Illumina reference.fasta CatalinaCA_392.R1.fq.gz
[main] Real time: 124.539 sec; CPU: 978.233 sec