[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555958 sequences (80000071 bp)...
[M::process] read 556042 sequences (80000086 bp)...
[M::mem_process_seqs] Processed 555958 reads in 171.911 CPU sec, 21.414 real sec
[M::process] read 556076 sequences (80000177 bp)...
[M::mem_process_seqs] Processed 556042 reads in 178.720 CPU sec, 21.969 real sec
[M::process] read 555904 sequences (80000240 bp)...
[M::mem_process_seqs] Processed 556076 reads in 176.101 CPU sec, 21.610 real sec
[M::process] read 555926 sequences (80000060 bp)...
[M::mem_process_seqs] Processed 555904 reads in 177.030 CPU sec, 21.730 real sec
[M::process] read 399374 sequences (57462290 bp)...
[M::mem_process_seqs] Processed 555926 reads in 176.724 CPU sec, 21.746 real sec
[M::mem_process_seqs] Processed 399374 reads in 127.701 CPU sec, 15.739 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_FG110\tSM:CypressIslandWA_FG110\tPL:Illumina reference.fasta CypressIslandWA_FG110.R1.fq.gz
[main] Real time: 128.098 sec; CPU: 1010.362 sec