[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555958 sequences (80000159 bp)...
[M::process] read 556026 sequences (80000078 bp)...
[M::mem_process_seqs] Processed 555958 reads in 165.717 CPU sec, 20.658 real sec
[M::process] read 555904 sequences (80000099 bp)...
[M::mem_process_seqs] Processed 556026 reads in 167.535 CPU sec, 20.614 real sec
[M::process] read 555890 sequences (80000179 bp)...
[M::mem_process_seqs] Processed 555904 reads in 167.808 CPU sec, 20.621 real sec
[M::process] read 205054 sequences (29504847 bp)...
[M::mem_process_seqs] Processed 555890 reads in 167.490 CPU sec, 20.649 real sec
[M::mem_process_seqs] Processed 205054 reads in 64.426 CPU sec, 7.851 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_384\tSM:CatalinaCA_384\tPL:Illumina reference.fasta CatalinaCA_384.R1.fq.gz
[main] Real time: 93.156 sec; CPU: 734.928 sec