[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556526 sequences (80000013 bp)...
[M::process] read 556524 sequences (80000109 bp)...
[M::mem_process_seqs] Processed 556526 reads in 146.618 CPU sec, 18.225 real sec
[M::process] read 556500 sequences (80000056 bp)...
[M::mem_process_seqs] Processed 556524 reads in 149.384 CPU sec, 18.337 real sec
[M::process] read 556486 sequences (80000107 bp)...
[M::mem_process_seqs] Processed 556500 reads in 151.906 CPU sec, 18.621 real sec
[M::process] read 143594 sequences (20641021 bp)...
[M::mem_process_seqs] Processed 556486 reads in 149.197 CPU sec, 18.397 real sec
[M::mem_process_seqs] Processed 143594 reads in 42.294 CPU sec, 5.079 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_FG117\tSM:CypressIslandWA_FG117\tPL:Illumina reference.fasta CypressIslandWA_FG117.R1.fq.gz
[main] Real time: 81.060 sec; CPU: 641.208 sec