[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555952 sequences (80000281 bp)...
[M::process] read 556048 sequences (80000257 bp)...
[M::mem_process_seqs] Processed 555952 reads in 172.944 CPU sec, 21.560 real sec
[M::process] read 556146 sequences (80000085 bp)...
[M::mem_process_seqs] Processed 556048 reads in 176.979 CPU sec, 21.798 real sec
[M::process] read 556066 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 556146 reads in 177.975 CPU sec, 21.870 real sec
[M::process] read 556118 sequences (80000185 bp)...
[M::mem_process_seqs] Processed 556066 reads in 178.294 CPU sec, 21.924 real sec
[M::process] read 556212 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 556118 reads in 176.473 CPU sec, 21.711 real sec
[M::process] read 555958 sequences (80000093 bp)...
[M::mem_process_seqs] Processed 556212 reads in 177.477 CPU sec, 21.852 real sec
[M::process] read 555948 sequences (80000072 bp)...
[M::mem_process_seqs] Processed 555958 reads in 180.241 CPU sec, 22.169 real sec
[M::process] read 555972 sequences (80000148 bp)...
[M::mem_process_seqs] Processed 555948 reads in 180.513 CPU sec, 22.246 real sec
[M::process] read 555958 sequences (80000260 bp)...
[M::mem_process_seqs] Processed 555972 reads in 177.771 CPU sec, 21.887 real sec
[M::process] read 555954 sequences (80000201 bp)...
[M::mem_process_seqs] Processed 555958 reads in 177.842 CPU sec, 21.918 real sec
[M::process] read 556048 sequences (80000278 bp)...
[M::mem_process_seqs] Processed 555954 reads in 180.337 CPU sec, 22.213 real sec
[M::process] read 307473 sequences (44237019 bp)...
[M::mem_process_seqs] Processed 556048 reads in 176.918 CPU sec, 21.858 real sec
[M::mem_process_seqs] Processed 307473 reads in 99.890 CPU sec, 12.298 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_366\tSM:CatalinaCA_366\tPL:Illumina reference.fasta CatalinaCA_366.R1.fq.gz
[main] Real time: 279.088 sec; CPU: 2235.831 sec