[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556248 sequences (80000042 bp)...
[M::process] read 556026 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 556248 reads in 166.458 CPU sec, 20.780 real sec
[M::process] read 555888 sequences (80000183 bp)...
[M::mem_process_seqs] Processed 556026 reads in 170.995 CPU sec, 21.028 real sec
[M::process] read 555896 sequences (80000082 bp)...
[M::mem_process_seqs] Processed 555888 reads in 172.188 CPU sec, 21.155 real sec
[M::process] read 555984 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555896 reads in 172.476 CPU sec, 21.168 real sec
[M::process] read 555892 sequences (80000190 bp)...
[M::mem_process_seqs] Processed 555984 reads in 172.947 CPU sec, 21.247 real sec
[M::process] read 555820 sequences (80000098 bp)...
[M::mem_process_seqs] Processed 555892 reads in 172.116 CPU sec, 21.165 real sec
[M::process] read 555828 sequences (80000080 bp)...
[M::mem_process_seqs] Processed 555820 reads in 171.896 CPU sec, 21.079 real sec
[M::process] read 63394 sequences (9125196 bp)...
[M::mem_process_seqs] Processed 555828 reads in 168.830 CPU sec, 20.868 real sec
[M::mem_process_seqs] Processed 63394 reads in 23.093 CPU sec, 2.725 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_423\tSM:MontereyBayCA_423\tPL:Illumina reference.fasta MontereyBayCA_423.R1.fq.gz
[main] Real time: 174.783 sec; CPU: 1393.469 sec