[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556018 sequences (80000025 bp)...
[M::process] read 556010 sequences (80000147 bp)...
[M::mem_process_seqs] Processed 556018 reads in 158.725 CPU sec, 19.766 real sec
[M::process] read 555934 sequences (80000173 bp)...
[M::mem_process_seqs] Processed 556010 reads in 161.406 CPU sec, 19.828 real sec
[M::process] read 128811 sequences (18532753 bp)...
[M::mem_process_seqs] Processed 555934 reads in 160.202 CPU sec, 19.786 real sec
[M::mem_process_seqs] Processed 128811 reads in 42.009 CPU sec, 5.024 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_375\tSM:CatalinaCA_375\tPL:Illumina reference.fasta CatalinaCA_375.R1.fq.gz
[main] Real time: 66.611 sec; CPU: 524.073 sec