[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556308 sequences (80000277 bp)...
[M::process] read 556364 sequences (80000150 bp)...
[M::mem_process_seqs] Processed 556308 reads in 150.242 CPU sec, 18.690 real sec
[M::process] read 556368 sequences (80000063 bp)...
[M::mem_process_seqs] Processed 556364 reads in 155.516 CPU sec, 19.100 real sec
[M::process] read 556318 sequences (80000216 bp)...
[M::mem_process_seqs] Processed 556368 reads in 155.980 CPU sec, 19.121 real sec
[M::process] read 556320 sequences (80000192 bp)...
[M::mem_process_seqs] Processed 556318 reads in 155.684 CPU sec, 19.059 real sec
[M::process] read 556322 sequences (80000042 bp)...
[M::mem_process_seqs] Processed 556320 reads in 156.789 CPU sec, 19.206 real sec
[M::process] read 240592 sequences (34594226 bp)...
[M::mem_process_seqs] Processed 556322 reads in 153.055 CPU sec, 18.860 real sec
[M::mem_process_seqs] Processed 240592 reads in 69.849 CPU sec, 8.519 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_FG148\tSM:CypressIslandWA_FG148\tPL:Illumina reference.fasta CypressIslandWA_FG148.R1.fq.gz
[main] Real time: 125.639 sec; CPU: 999.357 sec