[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555924 sequences (80000231 bp)...
[M::process] read 555912 sequences (80000151 bp)...
[M::mem_process_seqs] Processed 555924 reads in 160.365 CPU sec, 19.967 real sec
[M::process] read 555808 sequences (80000092 bp)...
[M::mem_process_seqs] Processed 555912 reads in 164.131 CPU sec, 20.181 real sec
[M::process] read 194372 sequences (27973190 bp)...
[M::mem_process_seqs] Processed 555808 reads in 165.797 CPU sec, 20.452 real sec
[M::mem_process_seqs] Processed 194372 reads in 61.152 CPU sec, 7.421 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_377\tSM:CatalinaCA_377\tPL:Illumina reference.fasta CatalinaCA_377.R1.fq.gz
[main] Real time: 70.762 sec; CPU: 553.562 sec