[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557238 sequences (80000016 bp)...
[M::process] read 557256 sequences (80000044 bp)...
[M::mem_process_seqs] Processed 557238 reads in 160.108 CPU sec, 19.944 real sec
[M::process] read 321496 sequences (46153739 bp)...
[M::mem_process_seqs] Processed 557256 reads in 164.178 CPU sec, 20.215 real sec
[M::mem_process_seqs] Processed 321496 reads in 97.519 CPU sec, 11.967 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_FG135\tSM:CypressIslandWA_FG135\tPL:Illumina reference.fasta CypressIslandWA_FG135.R1.fq.gz
[main] Real time: 55.965 sec; CPU: 424.229 sec