[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556010 sequences (80000060 bp)...
[M::process] read 555914 sequences (80000279 bp)...
[M::mem_process_seqs] Processed 556010 reads in 162.613 CPU sec, 20.254 real sec
[M::process] read 180976 sequences (26042305 bp)...
[M::mem_process_seqs] Processed 555914 reads in 166.775 CPU sec, 20.595 real sec
[M::mem_process_seqs] Processed 180976 reads in 59.558 CPU sec, 7.217 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_371\tSM:CatalinaCA_371\tPL:Illumina reference.fasta CatalinaCA_371.R1.fq.gz
[main] Real time: 50.499 sec; CPU: 390.736 sec