[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000188 bp)...
[M::process] read 555560 sequences (80000136 bp)...
[M::mem_process_seqs] Processed 555560 reads in 165.127 CPU sec, 20.593 real sec
[M::process] read 555560 sequences (80000064 bp)...
[M::mem_process_seqs] Processed 555560 reads in 166.773 CPU sec, 20.470 real sec
[M::process] read 555560 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.170 CPU sec, 20.576 real sec
[M::process] read 555558 sequences (80000047 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.732 CPU sec, 20.597 real sec
[M::process] read 555560 sequences (80000258 bp)...
[M::mem_process_seqs] Processed 555558 reads in 166.292 CPU sec, 20.393 real sec
[M::process] read 524079 sequences (75467092 bp)...
[M::mem_process_seqs] Processed 555560 reads in 167.205 CPU sec, 20.548 real sec
[M::mem_process_seqs] Processed 524079 reads in 158.346 CPU sec, 19.620 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_FG107\tSM:CypressIslandWA_FG107\tPL:Illumina reference.fasta CypressIslandWA_FG107.R1.fq.gz
[main] Real time: 147.669 sec; CPU: 1161.987 sec