[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556802 sequences (80000218 bp)...
[M::process] read 556784 sequences (80000173 bp)...
[M::mem_process_seqs] Processed 556802 reads in 149.950 CPU sec, 18.635 real sec
[M::process] read 556744 sequences (80000267 bp)...
[M::mem_process_seqs] Processed 556784 reads in 153.430 CPU sec, 18.853 real sec
[M::process] read 437554 sequences (62865670 bp)...
[M::mem_process_seqs] Processed 556744 reads in 150.086 CPU sec, 18.450 real sec
[M::mem_process_seqs] Processed 437554 reads in 119.711 CPU sec, 14.754 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_FG142\tSM:CypressIslandWA_FG142\tPL:Illumina reference.fasta CypressIslandWA_FG142.R1.fq.gz
[main] Real time: 74.980 sec; CPU: 576.240 sec