[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555906 sequences (80000110 bp)...
[M::process] read 555932 sequences (80000198 bp)...
[M::mem_process_seqs] Processed 555906 reads in 162.242 CPU sec, 20.205 real sec
[M::process] read 555804 sequences (80000254 bp)...
[M::mem_process_seqs] Processed 555932 reads in 165.304 CPU sec, 20.317 real sec
[M::process] read 296754 sequences (42708046 bp)...
[M::mem_process_seqs] Processed 555804 reads in 165.519 CPU sec, 20.395 real sec
[M::mem_process_seqs] Processed 296754 reads in 89.805 CPU sec, 11.020 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_372\tSM:CatalinaCA_372\tPL:Illumina reference.fasta CatalinaCA_372.R1.fq.gz
[main] Real time: 75.206 sec; CPU: 585.133 sec