[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556338 sequences (80000162 bp)...
[M::process] read 556354 sequences (80000081 bp)...
[M::mem_process_seqs] Processed 556338 reads in 161.679 CPU sec, 20.170 real sec
[M::process] read 232476 sequences (33423044 bp)...
[M::mem_process_seqs] Processed 556354 reads in 164.221 CPU sec, 20.291 real sec
[M::mem_process_seqs] Processed 232476 reads in 72.036 CPU sec, 8.772 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_373\tSM:CatalinaCA_373\tPL:Illumina reference.fasta CatalinaCA_373.R1.fq.gz
[main] Real time: 52.344 sec; CPU: 400.105 sec