[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556048 sequences (80000228 bp)...
[M::process] read 556128 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 556048 reads in 160.992 CPU sec, 20.033 real sec
[M::process] read 555942 sequences (80000130 bp)...
[M::mem_process_seqs] Processed 556128 reads in 163.318 CPU sec, 20.040 real sec
[M::process] read 555986 sequences (80000099 bp)...
[M::mem_process_seqs] Processed 555942 reads in 164.444 CPU sec, 20.202 real sec
[M::process] read 18048 sequences (2596244 bp)...
[M::mem_process_seqs] Processed 555986 reads in 164.289 CPU sec, 20.316 real sec
[M::mem_process_seqs] Processed 18048 reads in 6.906 CPU sec, 0.808 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_374\tSM:CatalinaCA_374\tPL:Illumina reference.fasta CatalinaCA_374.R1.fq.gz
[main] Real time: 85.463 sec; CPU: 662.432 sec