[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555888 sequences (80000240 bp)...
[M::process] read 555950 sequences (80000070 bp)...
[M::mem_process_seqs] Processed 555888 reads in 167.906 CPU sec, 20.917 real sec
[M::process] read 555824 sequences (80000012 bp)...
[M::mem_process_seqs] Processed 555950 reads in 172.838 CPU sec, 21.256 real sec
[M::process] read 555842 sequences (80000114 bp)...
[M::mem_process_seqs] Processed 555824 reads in 177.885 CPU sec, 21.851 real sec
[M::process] read 96897 sequences (13944469 bp)...
[M::mem_process_seqs] Processed 555842 reads in 172.564 CPU sec, 21.296 real sec
[M::mem_process_seqs] Processed 96897 reads in 34.678 CPU sec, 4.103 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_386\tSM:CatalinaCA_386\tPL:Illumina reference.fasta CatalinaCA_386.R1.fq.gz
[main] Real time: 91.489 sec; CPU: 727.489 sec