[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556116 sequences (80000282 bp)...
[M::process] read 556084 sequences (80000084 bp)...
[M::mem_process_seqs] Processed 556116 reads in 157.058 CPU sec, 19.580 real sec
[M::process] read 260118 sequences (37417525 bp)...
[M::mem_process_seqs] Processed 556084 reads in 161.697 CPU sec, 19.929 real sec
[M::mem_process_seqs] Processed 260118 reads in 78.901 CPU sec, 9.645 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_394\tSM:CatalinaCA_394\tPL:Illumina reference.fasta CatalinaCA_394.R1.fq.gz
[main] Real time: 52.240 sec; CPU: 400.046 sec