[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556522 sequences (80000227 bp)...
[M::process] read 556496 sequences (80000132 bp)...
[M::mem_process_seqs] Processed 556522 reads in 158.572 CPU sec, 19.736 real sec
[M::process] read 556482 sequences (80000068 bp)...
[M::mem_process_seqs] Processed 556496 reads in 163.543 CPU sec, 20.076 real sec
[M::process] read 380875 sequences (54750827 bp)...
[M::mem_process_seqs] Processed 556482 reads in 163.389 CPU sec, 20.095 real sec
[M::mem_process_seqs] Processed 380875 reads in 113.933 CPU sec, 14.014 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_FG136\tSM:CypressIslandWA_FG136\tPL:Illumina reference.fasta CypressIslandWA_FG136.R1.fq.gz
[main] Real time: 77.837 sec; CPU: 601.966 sec