[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555968 sequences (80000271 bp)...
[M::process] read 555986 sequences (80000151 bp)...
[M::mem_process_seqs] Processed 555968 reads in 161.945 CPU sec, 20.195 real sec
[M::process] read 555854 sequences (80000103 bp)...
[M::mem_process_seqs] Processed 555986 reads in 165.160 CPU sec, 20.323 real sec
[M::process] read 320033 sequences (46052890 bp)...
[M::mem_process_seqs] Processed 555854 reads in 164.620 CPU sec, 20.285 real sec
[M::mem_process_seqs] Processed 320033 reads in 96.363 CPU sec, 11.824 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_381\tSM:CatalinaCA_381\tPL:Illumina reference.fasta CatalinaCA_381.R1.fq.gz
[main] Real time: 76.211 sec; CPU: 590.699 sec