[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556372 sequences (80000055 bp)...
[M::process] read 556366 sequences (80000045 bp)...
[M::mem_process_seqs] Processed 556372 reads in 154.396 CPU sec, 19.237 real sec
[M::process] read 556380 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 556366 reads in 157.267 CPU sec, 19.331 real sec
[M::process] read 556360 sequences (80000075 bp)...
[M::mem_process_seqs] Processed 556380 reads in 158.135 CPU sec, 19.435 real sec
[M::process] read 541774 sequences (77897196 bp)...
[M::mem_process_seqs] Processed 556360 reads in 157.255 CPU sec, 19.291 real sec
[M::mem_process_seqs] Processed 541774 reads in 152.054 CPU sec, 18.825 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_FG120\tSM:CypressIslandWA_FG120\tPL:Illumina reference.fasta CypressIslandWA_FG120.R1.fq.gz
[main] Real time: 100.818 sec; CPU: 781.933 sec