[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555890 sequences (80000233 bp)...
[M::process] read 555968 sequences (80000091 bp)...
[M::mem_process_seqs] Processed 555890 reads in 166.563 CPU sec, 20.746 real sec
[M::process] read 555980 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 555968 reads in 170.565 CPU sec, 20.948 real sec
[M::process] read 555812 sequences (80000173 bp)...
[M::mem_process_seqs] Processed 555980 reads in 171.533 CPU sec, 21.068 real sec
[M::process] read 555812 sequences (80000279 bp)...
[M::mem_process_seqs] Processed 555812 reads in 171.705 CPU sec, 21.105 real sec
[M::process] read 338307 sequences (48686644 bp)...
[M::mem_process_seqs] Processed 555812 reads in 170.073 CPU sec, 20.947 real sec
[M::mem_process_seqs] Processed 338307 reads in 104.486 CPU sec, 12.839 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:CypressIslandWA_FG150-SEQREP\tSM:CypressIslandWA_FG150-SEQREP\tPL:Illumina reference.fasta CypressIslandWA_FG150-SEQREP.R1.fq.gz
[main] Real time: 121.537 sec; CPU: 957.498 sec