[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556660 sequences (80000102 bp)...
[M::process] read 556636 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 556660 reads in 151.199 CPU sec, 18.820 real sec
[M::process] read 556646 sequences (80000196 bp)...
[M::mem_process_seqs] Processed 556636 reads in 157.532 CPU sec, 19.343 real sec
[M::process] read 247579 sequences (35577613 bp)...
[M::mem_process_seqs] Processed 556646 reads in 154.708 CPU sec, 19.096 real sec
[M::mem_process_seqs] Processed 247579 reads in 71.950 CPU sec, 8.767 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_FG131\tSM:CypressIslandWA_FG131\tPL:Illumina reference.fasta CypressIslandWA_FG131.R1.fq.gz
[main] Real time: 68.921 sec; CPU: 537.420 sec