[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556222 sequences (80000152 bp)...
[M::process] read 556248 sequences (80000177 bp)...
[M::mem_process_seqs] Processed 556222 reads in 159.372 CPU sec, 19.831 real sec
[M::process] read 556178 sequences (80000224 bp)...
[M::mem_process_seqs] Processed 556248 reads in 165.647 CPU sec, 20.386 real sec
[M::process] read 139366 sequences (20042009 bp)...
[M::mem_process_seqs] Processed 556178 reads in 164.468 CPU sec, 20.316 real sec
[M::mem_process_seqs] Processed 139366 reads in 46.871 CPU sec, 5.651 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_382\tSM:CatalinaCA_382\tPL:Illumina reference.fasta CatalinaCA_382.R1.fq.gz
[main] Real time: 68.363 sec; CPU: 537.953 sec