[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556264 sequences (80000283 bp)...
[M::process] read 556336 sequences (80000156 bp)...
[M::mem_process_seqs] Processed 556264 reads in 170.765 CPU sec, 21.297 real sec
[M::process] read 556274 sequences (80000021 bp)...
[M::mem_process_seqs] Processed 556336 reads in 173.906 CPU sec, 21.386 real sec
[M::process] read 556222 sequences (80000070 bp)...
[M::mem_process_seqs] Processed 556274 reads in 177.415 CPU sec, 21.810 real sec
[M::process] read 379442 sequences (54561807 bp)...
[M::mem_process_seqs] Processed 556222 reads in 175.046 CPU sec, 21.550 real sec
[M::mem_process_seqs] Processed 379442 reads in 118.841 CPU sec, 14.642 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_FG180\tSM:PortGambleWA_FG180\tPL:Illumina reference.fasta PortGambleWA_FG180.R1.fq.gz
[main] Real time: 105.699 sec; CPU: 818.858 sec