[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000015 bp)...
[M::process] read 555560 sequences (80000260 bp)...
[M::mem_process_seqs] Processed 555558 reads in 160.187 CPU sec, 19.970 real sec
[M::process] read 555560 sequences (80000220 bp)...
[M::mem_process_seqs] Processed 555560 reads in 165.463 CPU sec, 20.359 real sec
[M::process] read 555558 sequences (80000008 bp)...
[M::mem_process_seqs] Processed 555560 reads in 163.179 CPU sec, 20.050 real sec
[M::process] read 555558 sequences (80000080 bp)...
[M::mem_process_seqs] Processed 555558 reads in 165.299 CPU sec, 20.288 real sec
[M::process] read 555558 sequences (80000003 bp)...
[M::mem_process_seqs] Processed 555558 reads in 165.723 CPU sec, 20.377 real sec
[M::process] read 240275 sequences (34599459 bp)...
[M::mem_process_seqs] Processed 555558 reads in 164.156 CPU sec, 20.270 real sec
[M::mem_process_seqs] Processed 240275 reads in 72.417 CPU sec, 8.854 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_FG111\tSM:CypressIslandWA_FG111\tPL:Illumina reference.fasta CypressIslandWA_FG111.R1.fq.gz
[main] Real time: 133.073 sec; CPU: 1058.383 sec