[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556098 sequences (80000057 bp)...
[M::process] read 556204 sequences (80000155 bp)...
[M::mem_process_seqs] Processed 556098 reads in 164.654 CPU sec, 20.510 real sec
[M::process] read 556218 sequences (80000120 bp)...
[M::mem_process_seqs] Processed 556204 reads in 168.490 CPU sec, 20.687 real sec
[M::process] read 556018 sequences (80000237 bp)...
[M::mem_process_seqs] Processed 556218 reads in 166.899 CPU sec, 20.464 real sec
[M::process] read 556038 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 556018 reads in 169.013 CPU sec, 20.763 real sec
[M::process] read 368171 sequences (52960255 bp)...
[M::mem_process_seqs] Processed 556038 reads in 166.435 CPU sec, 20.487 real sec
[M::mem_process_seqs] Processed 368171 reads in 111.459 CPU sec, 13.719 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_FG150\tSM:CypressIslandWA_FG150\tPL:Illumina reference.fasta CypressIslandWA_FG150.R1.fq.gz
[main] Real time: 120.343 sec; CPU: 949.380 sec