[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556316 sequences (80000278 bp)...
[M::process] read 556106 sequences (80000045 bp)...
[M::mem_process_seqs] Processed 556316 reads in 162.576 CPU sec, 20.235 real sec
[M::process] read 555954 sequences (80000054 bp)...
[M::mem_process_seqs] Processed 556106 reads in 167.184 CPU sec, 20.548 real sec
[M::process] read 555930 sequences (80000191 bp)...
[M::mem_process_seqs] Processed 555954 reads in 171.297 CPU sec, 21.060 real sec
[M::process] read 555980 sequences (80000102 bp)...
[M::mem_process_seqs] Processed 555930 reads in 170.377 CPU sec, 20.939 real sec
[M::process] read 555984 sequences (80000222 bp)...
[M::mem_process_seqs] Processed 555980 reads in 167.924 CPU sec, 20.591 real sec
[M::process] read 555902 sequences (80000080 bp)...
[M::mem_process_seqs] Processed 555984 reads in 167.593 CPU sec, 20.573 real sec
[M::process] read 555856 sequences (80000189 bp)...
[M::mem_process_seqs] Processed 555902 reads in 170.441 CPU sec, 20.930 real sec
[M::process] read 555864 sequences (80000238 bp)...
[M::mem_process_seqs] Processed 555856 reads in 168.377 CPU sec, 20.668 real sec
[M::process] read 43554 sequences (6269056 bp)...
[M::mem_process_seqs] Processed 555864 reads in 168.682 CPU sec, 20.861 real sec
[M::mem_process_seqs] Processed 43554 reads in 16.061 CPU sec, 1.879 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:MontereyBayCA_448\tSM:MontereyBayCA_448\tPL:Illumina reference.fasta MontereyBayCA_448.R1.fq.gz
[main] Real time: 191.923 sec; CPU: 1532.925 sec