[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556334 sequences (80000279 bp)...
[M::process] read 556346 sequences (80000160 bp)...
[M::mem_process_seqs] Processed 556334 reads in 148.252 CPU sec, 18.430 real sec
[M::process] read 556332 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 556346 reads in 151.112 CPU sec, 18.549 real sec
[M::process] read 556348 sequences (80000002 bp)...
[M::mem_process_seqs] Processed 556332 reads in 150.520 CPU sec, 18.468 real sec
[M::process] read 556336 sequences (80000091 bp)...
[M::mem_process_seqs] Processed 556348 reads in 150.535 CPU sec, 18.459 real sec
[M::process] read 106694 sequences (15341427 bp)...
[M::mem_process_seqs] Processed 556336 reads in 152.122 CPU sec, 18.792 real sec
[M::mem_process_seqs] Processed 106694 reads in 33.192 CPU sec, 3.911 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_FG146\tSM:CypressIslandWA_FG146\tPL:Illumina reference.fasta CypressIslandWA_FG146.R1.fq.gz
[main] Real time: 98.663 sec; CPU: 787.333 sec