[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000211 bp)...
[M::process] read 555560 sequences (80000148 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.138 CPU sec, 20.213 real sec
[M::process] read 555562 sequences (80000267 bp)...
[M::mem_process_seqs] Processed 555560 reads in 164.313 CPU sec, 20.222 real sec
[M::process] read 555560 sequences (80000169 bp)...
[M::mem_process_seqs] Processed 555562 reads in 165.219 CPU sec, 20.303 real sec
[M::process] read 555560 sequences (80000249 bp)...
[M::mem_process_seqs] Processed 555560 reads in 164.135 CPU sec, 20.141 real sec
[M::process] read 555560 sequences (80000165 bp)...
[M::mem_process_seqs] Processed 555560 reads in 163.672 CPU sec, 20.116 real sec
[M::process] read 555560 sequences (80000268 bp)...
[M::mem_process_seqs] Processed 555560 reads in 165.684 CPU sec, 20.391 real sec
[M::process] read 253362 sequences (36483899 bp)...
[M::mem_process_seqs] Processed 555560 reads in 165.787 CPU sec, 20.441 real sec
[M::mem_process_seqs] Processed 253362 reads in 78.784 CPU sec, 9.624 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_Q347\tSM:CatalinaCA_Q347\tPL:Illumina reference.fasta CatalinaCA_Q347.R1.fq.gz
[main] Real time: 154.582 sec; CPU: 1232.001 sec