[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557396 sequences (80000138 bp)...
[M::process] read 557374 sequences (80000215 bp)...
[M::mem_process_seqs] Processed 557396 reads in 149.527 CPU sec, 18.614 real sec
[M::process] read 557424 sequences (80000249 bp)...
[M::mem_process_seqs] Processed 557374 reads in 149.337 CPU sec, 18.337 real sec
[M::process] read 557288 sequences (80000204 bp)...
[M::mem_process_seqs] Processed 557424 reads in 151.781 CPU sec, 18.595 real sec
[M::process] read 340225 sequences (48829779 bp)...
[M::mem_process_seqs] Processed 557288 reads in 150.223 CPU sec, 18.490 real sec
[M::mem_process_seqs] Processed 340225 reads in 92.358 CPU sec, 11.348 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_FG115\tSM:CypressIslandWA_FG115\tPL:Illumina reference.fasta CypressIslandWA_FG115.R1.fq.gz
[main] Real time: 89.254 sec; CPU: 695.607 sec