[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557534 sequences (80000068 bp)...
[M::process] read 557620 sequences (80000096 bp)...
[M::mem_process_seqs] Processed 557534 reads in 157.342 CPU sec, 19.596 real sec
[M::process] read 557576 sequences (80000253 bp)...
[M::mem_process_seqs] Processed 557620 reads in 159.707 CPU sec, 19.612 real sec
[M::process] read 557554 sequences (80000240 bp)...
[M::mem_process_seqs] Processed 557576 reads in 158.666 CPU sec, 19.432 real sec
[M::process] read 557510 sequences (80000139 bp)...
[M::mem_process_seqs] Processed 557554 reads in 160.295 CPU sec, 19.659 real sec
[M::process] read 353469 sequences (50710624 bp)...
[M::mem_process_seqs] Processed 557510 reads in 157.886 CPU sec, 19.423 real sec
[M::mem_process_seqs] Processed 353469 reads in 102.173 CPU sec, 12.541 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_FG139\tSM:CypressIslandWA_FG139\tPL:Illumina reference.fasta CypressIslandWA_FG139.R1.fq.gz
[main] Real time: 113.921 sec; CPU: 898.484 sec