[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556322 sequences (80000053 bp)...
[M::process] read 556324 sequences (80000236 bp)...
[M::mem_process_seqs] Processed 556322 reads in 152.843 CPU sec, 19.044 real sec
[M::process] read 556322 sequences (80000185 bp)...
[M::mem_process_seqs] Processed 556324 reads in 157.731 CPU sec, 19.359 real sec
[M::process] read 556350 sequences (80000221 bp)...
[M::mem_process_seqs] Processed 556322 reads in 158.213 CPU sec, 19.425 real sec
[M::process] read 556308 sequences (80000146 bp)...
[M::mem_process_seqs] Processed 556350 reads in 157.347 CPU sec, 19.238 real sec
[M::process] read 191031 sequences (27468343 bp)...
[M::mem_process_seqs] Processed 556308 reads in 158.261 CPU sec, 19.519 real sec
[M::mem_process_seqs] Processed 191031 reads in 58.420 CPU sec, 7.078 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_FG130\tSM:CypressIslandWA_FG130\tPL:Illumina reference.fasta CypressIslandWA_FG130.R1.fq.gz
[main] Real time: 107.013 sec; CPU: 845.115 sec