[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557040 sequences (80000276 bp)...
[M::process] read 557020 sequences (80000275 bp)...
[M::mem_process_seqs] Processed 557040 reads in 157.666 CPU sec, 19.639 real sec
[M::process] read 556986 sequences (80000172 bp)...
[M::mem_process_seqs] Processed 557020 reads in 162.532 CPU sec, 19.982 real sec
[M::process] read 533192 sequences (76581326 bp)...
[M::mem_process_seqs] Processed 556986 reads in 164.283 CPU sec, 20.147 real sec
[M::mem_process_seqs] Processed 533192 reads in 153.162 CPU sec, 18.946 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_FG119\tSM:CypressIslandWA_FG119\tPL:Illumina reference.fasta CypressIslandWA_FG119.R1.fq.gz
[main] Real time: 83.920 sec; CPU: 640.707 sec