[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556588 sequences (80000218 bp)...
[M::process] read 556642 sequences (80000024 bp)...
[M::mem_process_seqs] Processed 556588 reads in 149.621 CPU sec, 18.581 real sec
[M::process] read 556624 sequences (80000218 bp)...
[M::mem_process_seqs] Processed 556642 reads in 151.084 CPU sec, 18.558 real sec
[M::process] read 556562 sequences (80000053 bp)...
[M::mem_process_seqs] Processed 556624 reads in 150.968 CPU sec, 18.482 real sec
[M::process] read 556532 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 556562 reads in 151.032 CPU sec, 18.479 real sec
[M::process] read 463266 sequences (66580480 bp)...
[M::mem_process_seqs] Processed 556532 reads in 151.828 CPU sec, 18.667 real sec
[M::mem_process_seqs] Processed 463266 reads in 125.827 CPU sec, 15.524 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_FG123\tSM:CypressIslandWA_FG123\tPL:Illumina reference.fasta CypressIslandWA_FG123.R1.fq.gz
[main] Real time: 112.715 sec; CPU: 883.453 sec