[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000246 bp)...
[M::process] read 555560 sequences (80000138 bp)...
[M::mem_process_seqs] Processed 555560 reads in 163.925 CPU sec, 20.441 real sec
[M::process] read 555560 sequences (80000106 bp)...
[M::mem_process_seqs] Processed 555560 reads in 163.933 CPU sec, 20.128 real sec
[M::process] read 555560 sequences (80000252 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.503 CPU sec, 20.563 real sec
[M::process] read 555560 sequences (80000243 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.211 CPU sec, 20.435 real sec
[M::process] read 555558 sequences (80000068 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.109 CPU sec, 20.397 real sec
[M::process] read 161598 sequences (23270044 bp)...
[M::mem_process_seqs] Processed 555558 reads in 166.530 CPU sec, 20.539 real sec
[M::mem_process_seqs] Processed 161598 reads in 52.283 CPU sec, 6.321 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_FG108\tSM:CypressIslandWA_FG108\tPL:Illumina reference.fasta CypressIslandWA_FG108.R1.fq.gz
[main] Real time: 131.367 sec; CPU: 1048.251 sec