[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555916 sequences (80000044 bp)...
[M::process] read 555982 sequences (80000138 bp)...
[M::mem_process_seqs] Processed 555916 reads in 178.564 CPU sec, 22.273 real sec
[M::process] read 555840 sequences (80000267 bp)...
[M::mem_process_seqs] Processed 555982 reads in 180.460 CPU sec, 22.193 real sec
[M::process] read 555874 sequences (80000003 bp)...
[M::mem_process_seqs] Processed 555840 reads in 184.243 CPU sec, 22.671 real sec
[M::process] read 26966 sequences (3880118 bp)...
[M::mem_process_seqs] Processed 555874 reads in 182.183 CPU sec, 22.571 real sec
[M::mem_process_seqs] Processed 26966 reads in 10.386 CPU sec, 1.225 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_391\tSM:CatalinaCA_391\tPL:Illumina reference.fasta CatalinaCA_391.R1.fq.gz
[main] Real time: 95.321 sec; CPU: 738.597 sec