[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556308 sequences (80000050 bp)...
[M::process] read 556012 sequences (80000274 bp)...
[M::mem_process_seqs] Processed 556308 reads in 160.098 CPU sec, 19.939 real sec
[M::process] read 556018 sequences (80000230 bp)...
[M::mem_process_seqs] Processed 556012 reads in 169.310 CPU sec, 20.788 real sec
[M::process] read 556010 sequences (80000107 bp)...
[M::mem_process_seqs] Processed 556018 reads in 170.073 CPU sec, 20.879 real sec
[M::process] read 555898 sequences (80000082 bp)...
[M::mem_process_seqs] Processed 556010 reads in 170.366 CPU sec, 20.911 real sec
[M::process] read 292726 sequences (42127379 bp)...
[M::mem_process_seqs] Processed 555898 reads in 169.551 CPU sec, 20.907 real sec
[M::mem_process_seqs] Processed 292726 reads in 93.617 CPU sec, 11.438 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_FG188\tSM:PortGambleWA_FG188\tPL:Illumina reference.fasta PortGambleWA_FG188.R1.fq.gz
[main] Real time: 118.655 sec; CPU: 935.624 sec