[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556548 sequences (80000242 bp)...
[M::process] read 556532 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 556548 reads in 146.952 CPU sec, 18.293 real sec
[M::process] read 556524 sequences (80000147 bp)...
[M::mem_process_seqs] Processed 556532 reads in 151.230 CPU sec, 18.557 real sec
[M::process] read 397064 sequences (57072606 bp)...
[M::mem_process_seqs] Processed 556524 reads in 148.600 CPU sec, 18.257 real sec
[M::mem_process_seqs] Processed 397064 reads in 105.979 CPU sec, 13.033 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_FG141\tSM:CypressIslandWA_FG141\tPL:Illumina reference.fasta CypressIslandWA_FG141.R1.fq.gz
[main] Real time: 72.195 sec; CPU: 555.398 sec