[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000230 bp)...
[M::process] read 555560 sequences (80000074 bp)...
[M::mem_process_seqs] Processed 555560 reads in 177.873 CPU sec, 22.157 real sec
[M::process] read 555560 sequences (80000101 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.408 CPU sec, 22.311 real sec
[M::process] read 555558 sequences (80000020 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.372 CPU sec, 22.142 real sec
[M::process] read 555558 sequences (80000094 bp)...
[M::mem_process_seqs] Processed 555558 reads in 180.425 CPU sec, 22.181 real sec
[M::process] read 555560 sequences (80000272 bp)...
[M::mem_process_seqs] Processed 555558 reads in 181.065 CPU sec, 22.251 real sec
[M::process] read 425541 sequences (61277707 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.811 CPU sec, 22.280 real sec
[M::mem_process_seqs] Processed 425541 reads in 138.273 CPU sec, 17.083 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_FG102-B\tSM:CypressIslandWA_FG102-B\tPL:Illumina reference.fasta CypressIslandWA_FG102-B.R1.fq.gz
[main] Real time: 154.699 sec; CPU: 1223.029 sec