[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557172 sequences (80000262 bp)...
[M::process] read 557178 sequences (80000263 bp)...
[M::mem_process_seqs] Processed 557172 reads in 156.807 CPU sec, 19.541 real sec
[M::process] read 557174 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 557178 reads in 161.781 CPU sec, 19.856 real sec
[M::process] read 557130 sequences (80000041 bp)...
[M::mem_process_seqs] Processed 557174 reads in 162.171 CPU sec, 19.890 real sec
[M::process] read 130822 sequences (18780964 bp)...
[M::mem_process_seqs] Processed 557130 reads in 159.530 CPU sec, 19.681 real sec
[M::mem_process_seqs] Processed 130822 reads in 42.049 CPU sec, 5.037 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_FG147\tSM:CypressIslandWA_FG147\tPL:Illumina reference.fasta CypressIslandWA_FG147.R1.fq.gz
[main] Real time: 86.513 sec; CPU: 684.112 sec