[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555938 sequences (80000019 bp)...
[M::process] read 555990 sequences (80000065 bp)...
[M::mem_process_seqs] Processed 555938 reads in 164.734 CPU sec, 20.507 real sec
[M::process] read 555856 sequences (80000057 bp)...
[M::mem_process_seqs] Processed 555990 reads in 169.740 CPU sec, 20.883 real sec
[M::process] read 555896 sequences (80000138 bp)...
[M::mem_process_seqs] Processed 555856 reads in 172.301 CPU sec, 21.179 real sec
[M::process] read 26506 sequences (3813987 bp)...
[M::mem_process_seqs] Processed 555896 reads in 167.676 CPU sec, 20.745 real sec
[M::mem_process_seqs] Processed 26506 reads in 8.984 CPU sec, 1.068 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:SewardAK_304\tSM:SewardAK_304\tPL:Illumina reference.fasta SewardAK_304.R1.fq.gz
[main] Real time: 89.152 sec; CPU: 686.138 sec