[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555900 sequences (80000033 bp)...
[M::process] read 555956 sequences (80000061 bp)...
[M::mem_process_seqs] Processed 555900 reads in 174.258 CPU sec, 21.726 real sec
[M::process] read 555898 sequences (80000153 bp)...
[M::mem_process_seqs] Processed 555956 reads in 177.634 CPU sec, 21.848 real sec
[M::process] read 555850 sequences (80000125 bp)...
[M::mem_process_seqs] Processed 555898 reads in 180.775 CPU sec, 22.263 real sec
[M::process] read 350189 sequences (50393034 bp)...
[M::mem_process_seqs] Processed 555850 reads in 177.887 CPU sec, 21.901 real sec
[M::mem_process_seqs] Processed 350189 reads in 112.689 CPU sec, 13.879 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_388\tSM:CatalinaCA_388\tPL:Illumina reference.fasta CatalinaCA_388.R1.fq.gz
[main] Real time: 105.406 sec; CPU: 825.719 sec