[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556856 sequences (80000204 bp)...
[M::process] read 556856 sequences (80000033 bp)...
[M::mem_process_seqs] Processed 556856 reads in 154.574 CPU sec, 19.226 real sec
[M::process] read 556834 sequences (80000097 bp)...
[M::mem_process_seqs] Processed 556856 reads in 153.458 CPU sec, 18.870 real sec
[M::process] read 556778 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 556834 reads in 154.491 CPU sec, 18.919 real sec
[M::process] read 444393 sequences (63844667 bp)...
[M::mem_process_seqs] Processed 556778 reads in 154.250 CPU sec, 18.977 real sec
[M::mem_process_seqs] Processed 444393 reads in 123.987 CPU sec, 15.320 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_Q357\tSM:CatalinaCA_Q357\tPL:Illumina reference.fasta CatalinaCA_Q357.R1.fq.gz
[main] Real time: 95.354 sec; CPU: 743.615 sec