[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557174 sequences (80000231 bp)...
[M::process] read 557144 sequences (80000145 bp)...
[M::mem_process_seqs] Processed 557174 reads in 151.672 CPU sec, 18.873 real sec
[M::process] read 557194 sequences (80000083 bp)...
[M::mem_process_seqs] Processed 557144 reads in 155.484 CPU sec, 19.112 real sec
[M::process] read 557058 sequences (80000165 bp)...
[M::mem_process_seqs] Processed 557194 reads in 157.524 CPU sec, 19.338 real sec
[M::process] read 405134 sequences (58162577 bp)...
[M::mem_process_seqs] Processed 557058 reads in 156.684 CPU sec, 19.248 real sec
[M::mem_process_seqs] Processed 405134 reads in 114.800 CPU sec, 14.148 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_FG143\tSM:CypressIslandWA_FG143\tPL:Illumina reference.fasta CypressIslandWA_FG143.R1.fq.gz
[main] Real time: 94.575 sec; CPU: 738.621 sec