[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556166 sequences (80000171 bp)...
[M::process] read 555952 sequences (80000029 bp)...
[M::mem_process_seqs] Processed 556166 reads in 163.046 CPU sec, 20.318 real sec
[M::process] read 555910 sequences (80000252 bp)...
[M::mem_process_seqs] Processed 555952 reads in 166.115 CPU sec, 20.411 real sec
[M::process] read 276272 sequences (39761523 bp)...
[M::mem_process_seqs] Processed 555910 reads in 167.016 CPU sec, 20.593 real sec
[M::mem_process_seqs] Processed 276272 reads in 84.920 CPU sec, 10.380 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:PortGambleWA_FG193\tSM:PortGambleWA_FG193\tPL:Illumina reference.fasta PortGambleWA_FG193.R1.fq.gz
[main] Real time: 75.490 sec; CPU: 583.774 sec