[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556564 sequences (80000073 bp)...
[M::process] read 556584 sequences (80000094 bp)...
[M::mem_process_seqs] Processed 556564 reads in 148.049 CPU sec, 18.423 real sec
[M::process] read 556592 sequences (80000273 bp)...
[M::mem_process_seqs] Processed 556584 reads in 152.754 CPU sec, 18.777 real sec
[M::process] read 556602 sequences (80000227 bp)...
[M::mem_process_seqs] Processed 556592 reads in 153.134 CPU sec, 18.805 real sec
[M::process] read 556566 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 556602 reads in 155.428 CPU sec, 19.049 real sec
[M::process] read 243716 sequences (35027280 bp)...
[M::mem_process_seqs] Processed 556566 reads in 151.140 CPU sec, 18.620 real sec
[M::mem_process_seqs] Processed 243716 reads in 68.554 CPU sec, 8.363 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_FG125\tSM:CypressIslandWA_FG125\tPL:Illumina reference.fasta CypressIslandWA_FG125.R1.fq.gz
[main] Real time: 105.026 sec; CPU: 831.254 sec