[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556368 sequences (80000026 bp)...
[M::process] read 556376 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 556368 reads in 153.637 CPU sec, 19.131 real sec
[M::process] read 556394 sequences (80000174 bp)...
[M::mem_process_seqs] Processed 556376 reads in 156.868 CPU sec, 19.264 real sec
[M::process] read 556384 sequences (80000251 bp)...
[M::mem_process_seqs] Processed 556394 reads in 157.625 CPU sec, 19.346 real sec
[M::process] read 556396 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 556384 reads in 157.214 CPU sec, 19.279 real sec
[M::process] read 35492 sequences (5101552 bp)...
[M::mem_process_seqs] Processed 556396 reads in 156.974 CPU sec, 19.418 real sec
[M::mem_process_seqs] Processed 35492 reads in 12.495 CPU sec, 1.461 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_FG128\tSM:CypressIslandWA_FG128\tPL:Illumina reference.fasta CypressIslandWA_FG128.R1.fq.gz
[main] Real time: 101.785 sec; CPU: 797.347 sec