[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556388 sequences (80000235 bp)...
[M::process] read 556396 sequences (80000237 bp)...
[M::mem_process_seqs] Processed 556388 reads in 144.040 CPU sec, 17.931 real sec
[M::process] read 556366 sequences (80000246 bp)...
[M::mem_process_seqs] Processed 556396 reads in 147.613 CPU sec, 18.123 real sec
[M::process] read 556362 sequences (80000202 bp)...
[M::mem_process_seqs] Processed 556366 reads in 147.614 CPU sec, 18.037 real sec
[M::process] read 63327 sequences (9104393 bp)...
[M::mem_process_seqs] Processed 556362 reads in 146.368 CPU sec, 18.034 real sec
[M::mem_process_seqs] Processed 63327 reads in 18.916 CPU sec, 2.205 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:CypressIslandWA_FG127\tSM:CypressIslandWA_FG127\tPL:Illumina reference.fasta CypressIslandWA_FG127.R1.fq.gz
[main] Real time: 77.663 sec; CPU: 606.751 sec