[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556346 sequences (80000186 bp)...
[M::process] read 556376 sequences (80000214 bp)...
[M::mem_process_seqs] Processed 556346 reads in 163.772 CPU sec, 20.386 real sec
[M::process] read 393720 sequences (56614126 bp)...
[M::mem_process_seqs] Processed 556376 reads in 166.824 CPU sec, 20.558 real sec
[M::mem_process_seqs] Processed 393720 reads in 118.556 CPU sec, 14.631 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_385\tSM:CatalinaCA_385\tPL:Illumina reference.fasta CatalinaCA_385.R1.fq.gz
[main] Real time: 59.537 sec; CPU: 451.969 sec