[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556126 sequences (80000254 bp)...
[M::process] read 556096 sequences (80000281 bp)...
[M::mem_process_seqs] Processed 556126 reads in 160.714 CPU sec, 20.023 real sec
[M::process] read 332180 sequences (47789388 bp)...
[M::mem_process_seqs] Processed 556096 reads in 165.705 CPU sec, 20.461 real sec
[M::mem_process_seqs] Processed 332180 reads in 100.300 CPU sec, 12.334 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_380\tSM:CatalinaCA_380\tPL:Illumina reference.fasta CatalinaCA_380.R1.fq.gz
[main] Real time: 56.524 sec; CPU: 429.233 sec