[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556056 sequences (80000015 bp)...
[M::process] read 556120 sequences (80000253 bp)...
[M::mem_process_seqs] Processed 556056 reads in 165.758 CPU sec, 20.645 real sec
[M::process] read 555998 sequences (80000016 bp)...
[M::mem_process_seqs] Processed 556120 reads in 171.464 CPU sec, 21.099 real sec
[M::process] read 556034 sequences (80000036 bp)...
[M::mem_process_seqs] Processed 555998 reads in 171.924 CPU sec, 21.135 real sec
[M::process] read 86269 sequences (12410271 bp)...
[M::mem_process_seqs] Processed 556034 reads in 170.784 CPU sec, 21.086 real sec
[M::mem_process_seqs] Processed 86269 reads in 30.333 CPU sec, 3.571 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_383\tSM:CatalinaCA_383\tPL:Illumina reference.fasta CatalinaCA_383.R1.fq.gz
[main] Real time: 89.604 sec; CPU: 711.962 sec