[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556354 sequences (80000192 bp)...
[M::process] read 556364 sequences (80000121 bp)...
[M::mem_process_seqs] Processed 556354 reads in 150.766 CPU sec, 18.777 real sec
[M::process] read 556362 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 556364 reads in 153.024 CPU sec, 18.786 real sec
[M::process] read 200776 sequences (28869074 bp)...
[M::mem_process_seqs] Processed 556362 reads in 154.771 CPU sec, 19.055 real sec
[M::mem_process_seqs] Processed 200776 reads in 59.501 CPU sec, 7.226 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_FG140\tSM:CypressIslandWA_FG140\tPL:Illumina reference.fasta CypressIslandWA_FG140.R1.fq.gz
[main] Real time: 66.513 sec; CPU: 519.880 sec