Executing align2.BBMap [build=1, overwrite=true, match=long, fastareadlen=500, in=phixscreen_jigsaw_norm/spades/corrected/TNOC.7707.1.80834.CGTAC.nophix.contam.artifact.clean.norm.paired_1.fastq.00.cor.fastq.gz, in2=phixscreen_jigsaw_norm/spades/corrected/TNOC.7707.1.80834.CGTAC.nophix.contam.artifact.clean.norm.paired_2.fastq.00.cor.fastq.gz, ref=phixscreen_jigsaw_norm/spades/scaffolds.fasta]

BBMap version 31.26
Set OVERWRITE to true
Cigar strings enabled.
Retaining first best site only for ambiguous mappings.
No output file.
Writing reference.
Set genome to 1

Loaded Reference:	0.015 seconds.
Generated Index:	2.416 seconds.
Analyzed Index:   	2.573 seconds.
Cleared Memory:    	1.034 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 4 mapping threads.
Detecting finished threads: 0, 1, 2, 3

   ------------------   Results   ------------------   

Genome:                	1
Key Length:            	13
Max Indel:             	16000
Minimum Score Ratio:  	0.56
Mapping Mode:         	normal
Reads Used:           	14974	(3697653 bases)

Mapping:          	5.640 seconds.
Reads/sec:       	1327.58
kBases/sec:      	655.66


Read 1 data:

mapped:          	 99.4524%	7446 reads
unambiguous:     	 78.9368%	5910 reads

Mated pairs:     	93.0546%
bad pairs:       	 5.770% (of all reads)
rescued:         	 0.080%
avg insert size: 	470.33

perfect best site:	80.6064%
semiperfect site:	81.7150%
ambiguousMapping:	20.5156%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 81.9021% 	1839834
Error Rate:      	 17.9141% 	402418
Sub Rate:        	  0.2786% 	6258
Del Rate:        	 17.3694% 	390184
Ins Rate:        	  0.2660% 	5976
N Rate:          	  0.1838% 	4129


Read 2 data:

mapped:          	 99.2387%	7430 reads
unambiguous:     	 78.7765%	5898 reads

rescued:         	 0.120%

perfect best site:	69.3469%
semiperfect site:	70.5490%
ambiguousMapping:	20.4621%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 77.8301% 	1796906
Error Rate:      	 21.9446% 	506647
Sub Rate:        	  0.4696% 	10841
Del Rate:        	 21.2002% 	489460
Ins Rate:        	  0.2749% 	6346
N Rate:          	  0.2253% 	5201

Total time:     	11.855 seconds.