[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556232 sequences (80000184 bp)...
[M::process] read 555940 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 556232 reads in 165.854 CPU sec, 20.662 real sec
[M::process] read 555970 sequences (80000187 bp)...
[M::mem_process_seqs] Processed 555940 reads in 173.555 CPU sec, 21.350 real sec
[M::process] read 555918 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 555970 reads in 172.805 CPU sec, 21.206 real sec
[M::process] read 555838 sequences (80000165 bp)...
[M::mem_process_seqs] Processed 555918 reads in 172.400 CPU sec, 21.168 real sec
[M::process] read 125029 sequences (17996599 bp)...
[M::mem_process_seqs] Processed 555838 reads in 171.604 CPU sec, 21.189 real sec
[M::mem_process_seqs] Processed 125029 reads in 43.966 CPU sec, 5.269 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_433-SEQREP\tSM:MontereyBayCA_433-SEQREP\tPL:Illumina reference.fasta MontereyBayCA_433-SEQREP.R1.fq.gz
[main] Real time: 113.289 sec; CPU: 901.985 sec