[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556546 sequences (80000079 bp)...
[M::process] read 556548 sequences (80000115 bp)...
[M::mem_process_seqs] Processed 556546 reads in 146.868 CPU sec, 18.285 real sec
[M::process] read 556542 sequences (80000190 bp)...
[M::mem_process_seqs] Processed 556548 reads in 149.634 CPU sec, 18.359 real sec
[M::process] read 159186 sequences (22881031 bp)...
[M::mem_process_seqs] Processed 556542 reads in 148.903 CPU sec, 18.388 real sec
[M::mem_process_seqs] Processed 159186 reads in 46.064 CPU sec, 5.541 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_FG132\tSM:CypressIslandWA_FG132\tPL:Illumina reference.fasta CypressIslandWA_FG132.R1.fq.gz
[main] Real time: 63.328 sec; CPU: 493.386 sec