Executing align2.BBMap [build=1, overwrite=true, match=long, fastareadlen=500, ref=aclum.TNOH/spades/scaffolds.fasta, in=aclum.TNOH/spades/corrected/TNOH.7707.1.80834.GGTAG.nophix.contam.artifact.clean_1.fastq.00.cor.fastq.gz, in2=aclum.TNOH/spades/corrected/TNOH.7707.1.80834.GGTAG.nophix.contam.artifact.clean_2.fastq.00.cor.fastq.gz]

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:	0.204 seconds.
Generated Index:	4.718 seconds.
Analyzed Index:   	3.030 seconds.
Cleared Memory:    	0.561 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7

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

Genome:                	1
Key Length:            	13
Max Indel:             	16000
Minimum Score Ratio:  	0.56
Mapping Mode:         	normal
Reads Used:           	6341616	(1554598833 bases)

Mapping:          	6051.486 seconds.
Reads/sec:       	523.97
kBases/sec:      	256.90


Read 1 data:

mapped:          	 98.9402%	3137204 reads
unambiguous:     	 80.0404%	2537928 reads

Mated pairs:     	58.6827%
bad pairs:       	39.143% (of all reads)
rescued:         	 2.786%
avg insert size: 	527.24

perfect best site:	37.3204%
semiperfect site:	58.7257%
ambiguousMapping:	18.8998%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 24.3643% 	722038568
Error Rate:      	 74.0435% 	2194284691
Sub Rate:        	  0.3783% 	11210862
Del Rate:        	 73.0937% 	2166138332
Ins Rate:        	  0.5715% 	16935497
N Rate:          	  1.5922% 	47185487


Read 2 data:

mapped:          	 98.8319%	3133771 reads
unambiguous:     	 79.1614%	2510056 reads

rescued:         	 2.975%

perfect best site:	30.9901%
semiperfect site:	49.2505%
ambiguousMapping:	19.6705%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 25.0796% 	697146033
Error Rate:      	 73.3613% 	2039251904
Sub Rate:        	  0.4636% 	12885497
Del Rate:        	 72.2622% 	2008699490
Ins Rate:        	  0.6356% 	17666917
N Rate:          	  1.5592% 	43340584

Total time:     	6063.019 seconds.