[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000065 bp)...
[M::process] read 555560 sequences (80000182 bp)...
[M::mem_process_seqs] Processed 555558 reads in 177.048 CPU sec, 22.093 real sec
[M::process] read 555560 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.563 CPU sec, 22.083 real sec
[M::process] read 555560 sequences (80000077 bp)...
[M::mem_process_seqs] Processed 555560 reads in 184.589 CPU sec, 22.644 real sec
[M::process] read 555560 sequences (80000009 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.568 CPU sec, 22.236 real sec
[M::process] read 555560 sequences (80000017 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.600 CPU sec, 22.216 real sec
[M::process] read 555560 sequences (80000126 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.296 CPU sec, 22.030 real sec
[M::process] read 555560 sequences (80000275 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.501 CPU sec, 22.344 real sec
[M::process] read 555558 sequences (80000015 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.952 CPU sec, 22.354 real sec
[M::process] read 555558 sequences (80000057 bp)...
[M::mem_process_seqs] Processed 555558 reads in 180.367 CPU sec, 22.186 real sec
[M::process] read 555560 sequences (80000279 bp)...
[M::mem_process_seqs] Processed 555558 reads in 182.038 CPU sec, 22.406 real sec
[M::process] read 555558 sequences (80000005 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.846 CPU sec, 22.325 real sec
[M::process] read 555558 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555558 reads in 182.062 CPU sec, 22.395 real sec
[M::process] read 555560 sequences (80000285 bp)...
[M::mem_process_seqs] Processed 555558 reads in 183.599 CPU sec, 22.560 real sec
[M::process] read 74362 sequences (10708101 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.307 CPU sec, 22.413 real sec
[M::mem_process_seqs] Processed 74362 reads in 28.437 CPU sec, 3.346 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_Q351\tSM:CatalinaCA_Q351\tPL:Illumina reference.fasta CatalinaCA_Q351.R1.fq.gz
[main] Real time: 318.018 sec; CPU: 2566.545 sec