[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556016 sequences (80000189 bp)...
[M::process] read 556104 sequences (80000101 bp)...
[M::mem_process_seqs] Processed 556016 reads in 157.924 CPU sec, 19.644 real sec
[M::process] read 555974 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 556104 reads in 159.907 CPU sec, 19.663 real sec
[M::process] read 556006 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 555974 reads in 160.946 CPU sec, 19.763 real sec
[M::process] read 70047 sequences (10077025 bp)...
[M::mem_process_seqs] Processed 556006 reads in 159.586 CPU sec, 19.681 real sec
[M::mem_process_seqs] Processed 70047 reads in 23.404 CPU sec, 2.751 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_FG133-SEQREP\tSM:CypressIslandWA_FG133-SEQREP\tPL:Illumina reference.fasta CypressIslandWA_FG133-SEQREP.R1.fq.gz
[main] Real time: 84.301 sec; CPU: 663.852 sec