[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556736 sequences (80000096 bp)...
[M::process] read 556766 sequences (80000115 bp)...
[M::mem_process_seqs] Processed 556736 reads in 146.690 CPU sec, 18.267 real sec
[M::process] read 370265 sequences (53204919 bp)...
[M::mem_process_seqs] Processed 556766 reads in 151.434 CPU sec, 18.665 real sec
[M::mem_process_seqs] Processed 370265 reads in 101.979 CPU sec, 12.538 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_FG113\tSM:CypressIslandWA_FG113\tPL:Illumina reference.fasta CypressIslandWA_FG113.R1.fq.gz
[main] Real time: 53.175 sec; CPU: 402.666 sec