[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557408 sequences (80000060 bp)...
[M::process] read 557396 sequences (80000133 bp)...
[M::mem_process_seqs] Processed 557408 reads in 148.748 CPU sec, 18.521 real sec
[M::process] read 557426 sequences (80000146 bp)...
[M::mem_process_seqs] Processed 557396 reads in 156.982 CPU sec, 19.304 real sec
[M::process] read 557338 sequences (80000187 bp)...
[M::mem_process_seqs] Processed 557426 reads in 153.218 CPU sec, 18.754 real sec
[M::process] read 263578 sequences (37826294 bp)...
[M::mem_process_seqs] Processed 557338 reads in 152.709 CPU sec, 18.801 real sec
[M::mem_process_seqs] Processed 263578 reads in 75.164 CPU sec, 9.197 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_FG112\tSM:CypressIslandWA_FG112\tPL:Illumina reference.fasta CypressIslandWA_FG112.R1.fq.gz
[main] Real time: 87.871 sec; CPU: 689.162 sec