[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555864 sequences (80000256 bp)...
[M::process] read 555874 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 555864 reads in 168.671 CPU sec, 21.029 real sec
[M::process] read 555760 sequences (80000109 bp)...
[M::mem_process_seqs] Processed 555874 reads in 173.501 CPU sec, 21.350 real sec
[M::process] read 348077 sequences (50099721 bp)...
[M::mem_process_seqs] Processed 555760 reads in 175.949 CPU sec, 21.664 real sec
[M::mem_process_seqs] Processed 348077 reads in 110.299 CPU sec, 13.555 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_390\tSM:CatalinaCA_390\tPL:Illumina reference.fasta CatalinaCA_390.R1.fq.gz
[main] Real time: 80.923 sec; CPU: 630.793 sec