Executing align2.BBMap [build=1, overwrite=true, match=long, fastareadlen=500, ref=aclum.TNNW/spades/scaffolds.fasta, in=/global/projectb/scratch/aclum/gaa-691/TNNW/phixscreen_jigsaw/spades/corrected/TNNW.7707.1.80834.CCGTC.nophix.contam.artifact.clean_1.fastq.00.cor.fastq.gz, in2=/global/projectb/scratch/aclum/gaa-691/TNNW/phixscreen_jigsaw/spades/corrected/TNNW.7707.1.80834.CCGTC.nophix.contam.artifact.clean_2.fastq.00.cor.fastq.gz, out=TNNW.spades.assembled.reads]

BBMap version 31.26
Set OVERWRITE to true
Cigar strings enabled.
Retaining first best site only for ambiguous mappings.
Writing reference.
Set genome to 1

Loaded Reference:	0.169 seconds.
Generated Index:	3.717 seconds.
Analyzed Index:   	2.592 seconds.
Started output stream:	3.634 seconds.
Cleared Memory:    	0.380 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 32 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31

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

Genome:                	1
Key Length:            	13
Max Indel:             	16000
Minimum Score Ratio:  	0.56
Mapping Mode:         	normal
Reads Used:           	5821332	(1444859929 bases)

Mapping:          	347.361 seconds.
Reads/sec:       	8379.37
kBases/sec:      	4159.53


Read 1 data:

mapped:          	 80.7900%	2351526 reads
unambiguous:     	 75.1913%	2188567 reads

Mated pairs:     	21.6109%
bad pairs:       	46.710% (of all reads)
rescued:         	 3.579%
avg insert size: 	370.83

perfect best site:	12.4676%
semiperfect site:	48.6671%
ambiguousMapping:	 5.5987%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 91.9817% 	541438788
Error Rate:      	  1.0515% 	6189617
Sub Rate:        	  0.8630% 	5079655
Del Rate:        	  0.0655% 	385624
Ins Rate:        	  0.1231% 	724338
N Rate:          	  6.9668% 	41009298


Read 2 data:

mapped:          	 81.8837%	2383361 reads
unambiguous:     	 75.1152%	2186353 reads

rescued:         	 3.480%

perfect best site:	10.8262%
semiperfect site:	42.0086%
ambiguousMapping:	 6.7685%	(Kept)
low-Q discards:  	 0.0000%

Match Rate:      	 92.0471% 	539588840
Error Rate:      	  1.3109% 	7684686
Sub Rate:        	  1.1125% 	6521757
Del Rate:        	  0.0729% 	427257
Ins Rate:        	  0.1255% 	735672
N Rate:          	  6.6420% 	38936052

Total time:     	359.313 seconds.