[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555866 sequences (80000099 bp)...
[M::process] read 555960 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 555866 reads in 162.782 CPU sec, 20.288 real sec
[M::process] read 556012 sequences (80000172 bp)...
[M::mem_process_seqs] Processed 555960 reads in 170.183 CPU sec, 20.925 real sec
[M::process] read 555790 sequences (80000239 bp)...
[M::mem_process_seqs] Processed 556012 reads in 167.577 CPU sec, 20.558 real sec
[M::process] read 555812 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 555790 reads in 172.197 CPU sec, 21.155 real sec
[M::process] read 555864 sequences (80000070 bp)...
[M::mem_process_seqs] Processed 555812 reads in 167.844 CPU sec, 20.604 real sec
[M::process] read 38942 sequences (5603146 bp)...
[M::mem_process_seqs] Processed 555864 reads in 165.951 CPU sec, 20.521 real sec
[M::mem_process_seqs] Processed 38942 reads in 13.806 CPU sec, 1.622 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\tSM:CypressIslandWA_FG149\tPL:Illumina reference.fasta CypressIslandWA_FG149.R1.fq.gz
[main] Real time: 129.423 sec; CPU: 1022.639 sec