[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000167 bp)...
[M::process] read 555560 sequences (80000045 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.151 CPU sec, 20.208 real sec
[M::process] read 555560 sequences (80000124 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.786 CPU sec, 20.483 real sec
[M::process] read 555560 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.166 CPU sec, 20.541 real sec
[M::process] read 555560 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555560 reads in 168.267 CPU sec, 20.650 real sec
[M::process] read 117052 sequences (16855441 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.917 CPU sec, 20.731 real sec
[M::mem_process_seqs] Processed 117052 reads in 39.135 CPU sec, 4.657 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_FG103-B\tSM:CypressIslandWA_FG103-B\tPL:Illumina reference.fasta CypressIslandWA_FG103-B.R1.fq.gz
[main] Real time: 109.444 sec; CPU: 873.001 sec