[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556520 sequences (80000024 bp)...
[M::process] read 556514 sequences (80000098 bp)...
[M::mem_process_seqs] Processed 556520 reads in 143.999 CPU sec, 17.923 real sec
[M::process] read 556514 sequences (80000217 bp)...
[M::mem_process_seqs] Processed 556514 reads in 148.559 CPU sec, 18.228 real sec
[M::process] read 176859 sequences (25423256 bp)...
[M::mem_process_seqs] Processed 556514 reads in 145.465 CPU sec, 17.965 real sec
[M::mem_process_seqs] Processed 176859 reads in 50.719 CPU sec, 6.132 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:DabobBayWA_Q361\tSM:DabobBayWA_Q361\tPL:Illumina reference.fasta DabobBayWA_Q361.R1.fq.gz
[main] Real time: 62.897 sec; CPU: 490.747 sec