[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557026 sequences (80000165 bp)...
[M::process] read 557030 sequences (80000112 bp)...
[M::mem_process_seqs] Processed 557026 reads in 146.755 CPU sec, 18.245 real sec
[M::process] read 557052 sequences (80000271 bp)...
[M::mem_process_seqs] Processed 557030 reads in 151.418 CPU sec, 18.595 real sec
[M::process] read 557016 sequences (80000041 bp)...
[M::mem_process_seqs] Processed 557052 reads in 149.610 CPU sec, 18.349 real sec
[M::process] read 557026 sequences (80000137 bp)...
[M::mem_process_seqs] Processed 557016 reads in 151.470 CPU sec, 18.562 real sec
[M::process] read 39890 sequences (5726239 bp)...
[M::mem_process_seqs] Processed 557026 reads in 148.350 CPU sec, 18.315 real sec
[M::mem_process_seqs] Processed 39890 reads in 12.792 CPU sec, 1.515 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_FG144\tSM:CypressIslandWA_FG144\tPL:Illumina reference.fasta CypressIslandWA_FG144.R1.fq.gz
[main] Real time: 97.582 sec; CPU: 763.120 sec