[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556388 sequences (80000062 bp)...
[M::process] read 556426 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 556388 reads in 169.778 CPU sec, 21.174 real sec
[M::process] read 556384 sequences (80000174 bp)...
[M::mem_process_seqs] Processed 556426 reads in 171.727 CPU sec, 21.128 real sec
[M::process] read 192899 sequences (27729437 bp)...
[M::mem_process_seqs] Processed 556384 reads in 171.389 CPU sec, 21.171 real sec
[M::mem_process_seqs] Processed 192899 reads in 64.082 CPU sec, 7.759 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_376\tSM:CatalinaCA_376\tPL:Illumina reference.fasta CatalinaCA_376.R1.fq.gz
[main] Real time: 73.934 sec; CPU: 578.932 sec