[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555858 sequences (80000208 bp)...
[M::process] read 555932 sequences (80000027 bp)...
[M::mem_process_seqs] Processed 555858 reads in 172.878 CPU sec, 21.553 real sec
[M::process] read 555816 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555932 reads in 176.916 CPU sec, 21.769 real sec
[M::process] read 555776 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 555816 reads in 179.840 CPU sec, 22.116 real sec
[M::process] read 294944 sequences (42450194 bp)...
[M::mem_process_seqs] Processed 555776 reads in 178.030 CPU sec, 21.954 real sec
[M::mem_process_seqs] Processed 294944 reads in 96.027 CPU sec, 11.783 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:CatalinaCA_387\tSM:CatalinaCA_387\tPL:Illumina reference.fasta CatalinaCA_387.R1.fq.gz
[main] Real time: 102.406 sec; CPU: 805.812 sec