[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556304 sequences (80000136 bp)...
[M::process] read 556344 sequences (80000278 bp)...
[M::mem_process_seqs] Processed 556304 reads in 165.954 CPU sec, 20.677 real sec
[M::process] read 556242 sequences (80000045 bp)...
[M::mem_process_seqs] Processed 556344 reads in 172.573 CPU sec, 21.187 real sec
[M::process] read 277855 sequences (39951017 bp)...
[M::mem_process_seqs] Processed 556242 reads in 170.299 CPU sec, 20.999 real sec
[M::mem_process_seqs] Processed 277855 reads in 87.937 CPU sec, 10.744 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_FG149-SEQREP\tSM:CypressIslandWA_FG149-SEQREP\tPL:Illumina reference.fasta CypressIslandWA_FG149-SEQREP.R1.fq.gz
[main] Real time: 77.293 sec; CPU: 599.221 sec