[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556298 sequences (80000106 bp)...
[M::process] read 556342 sequences (80000254 bp)...
[M::mem_process_seqs] Processed 556298 reads in 157.961 CPU sec, 19.685 real sec
[M::process] read 459304 sequences (66045384 bp)...
[M::mem_process_seqs] Processed 556342 reads in 163.994 CPU sec, 20.176 real sec
[M::mem_process_seqs] Processed 459304 reads in 133.494 CPU sec, 16.485 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_370\tSM:CatalinaCA_370\tPL:Illumina reference.fasta CatalinaCA_370.R1.fq.gz
[main] Real time: 60.487 sec; CPU: 458.099 sec