[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555846 sequences (80000219 bp)...
[M::process] read 555962 sequences (80000031 bp)...
[M::mem_process_seqs] Processed 555846 reads in 169.885 CPU sec, 21.172 real sec
[M::process] read 555932 sequences (80000198 bp)...
[M::mem_process_seqs] Processed 555962 reads in 175.108 CPU sec, 21.527 real sec
[M::process] read 555936 sequences (80000140 bp)...
[M::mem_process_seqs] Processed 555932 reads in 175.379 CPU sec, 21.522 real sec
[M::process] read 555792 sequences (80000245 bp)...
[M::mem_process_seqs] Processed 555936 reads in 173.459 CPU sec, 21.291 real sec
[M::process] read 555804 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 555792 reads in 174.207 CPU sec, 21.413 real sec
[M::process] read 555832 sequences (80000135 bp)...
[M::mem_process_seqs] Processed 555804 reads in 173.983 CPU sec, 21.356 real sec
[M::process] read 235997 sequences (33963058 bp)...
[M::mem_process_seqs] Processed 555832 reads in 173.160 CPU sec, 21.359 real sec
[M::mem_process_seqs] Processed 235997 reads in 77.955 CPU sec, 9.512 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_FG134\tSM:CypressIslandWA_FG134\tPL:Illumina reference.fasta CypressIslandWA_FG134.R1.fq.gz
[main] Real time: 162.420 sec; CPU: 1295.476 sec