[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000185 bp)...
[M::process] read 555560 sequences (80000256 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.769 CPU sec, 21.419 real sec
[M::process] read 555560 sequences (80000036 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.048 CPU sec, 21.044 real sec
[M::process] read 555560 sequences (80000030 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.891 CPU sec, 21.100 real sec
[M::process] read 555560 sequences (80000129 bp)...
[M::mem_process_seqs] Processed 555560 reads in 168.886 CPU sec, 20.754 real sec
[M::process] read 555560 sequences (80000163 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.671 CPU sec, 20.855 real sec
[M::process] read 555560 sequences (80000238 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.428 CPU sec, 20.849 real sec
[M::process] read 555560 sequences (80000127 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.759 CPU sec, 20.888 real sec
[M::process] read 555560 sequences (80000158 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.566 CPU sec, 20.818 real sec
[M::process] read 555560 sequences (80000269 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.863 CPU sec, 20.990 real sec
[M::process] read 503137 sequences (72451324 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.577 CPU sec, 20.955 real sec
[M::mem_process_seqs] Processed 503137 reads in 153.648 CPU sec, 19.004 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_Q339\tSM:CatalinaCA_Q339\tPL:Illumina reference.fasta CatalinaCA_Q339.R1.fq.gz
[main] Real time: 232.896 sec; CPU: 1859.580 sec