[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556404 sequences (80000178 bp)...
[M::process] read 556406 sequences (80000219 bp)...
[M::mem_process_seqs] Processed 556404 reads in 152.779 CPU sec, 19.005 real sec
[M::process] read 556386 sequences (80000079 bp)...
[M::mem_process_seqs] Processed 556406 reads in 154.306 CPU sec, 18.946 real sec
[M::process] read 556366 sequences (80000022 bp)...
[M::mem_process_seqs] Processed 556386 reads in 157.117 CPU sec, 19.286 real sec
[M::process] read 207731 sequences (29868430 bp)...
[M::mem_process_seqs] Processed 556366 reads in 153.697 CPU sec, 18.899 real sec
[M::mem_process_seqs] Processed 207731 reads in 59.750 CPU sec, 7.275 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_FG118\tSM:CypressIslandWA_FG118\tPL:Illumina reference.fasta CypressIslandWA_FG118.R1.fq.gz
[main] Real time: 85.999 sec; CPU: 679.518 sec