[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556130 sequences (80000097 bp)...
[M::process] read 556190 sequences (80000081 bp)...
[M::mem_process_seqs] Processed 556130 reads in 165.507 CPU sec, 20.620 real sec
[M::process] read 556100 sequences (80000009 bp)...
[M::mem_process_seqs] Processed 556190 reads in 169.890 CPU sec, 20.858 real sec
[M::process] read 385877 sequences (55503434 bp)...
[M::mem_process_seqs] Processed 556100 reads in 171.413 CPU sec, 21.116 real sec
[M::mem_process_seqs] Processed 385877 reads in 118.573 CPU sec, 14.615 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_395\tSM:CatalinaCA_395\tPL:Illumina reference.fasta CatalinaCA_395.R1.fq.gz
[main] Real time: 81.344 sec; CPU: 628.239 sec