-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_557

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Couldn't classify 598, 650
Couldn't classify 1844, 1999
Sorry, prediction snap_scaffold_557-snap.2-T1 fails validation.
(GCG)	 AG	598-650	GT	CGG
(CTT)	 AG	927-1010	GT	AGG
(AGC)	 AG	1661-1714	GT	AGG
(GTG)	 AG	1844-1999	GT	CCG
-recovered snap_scaffold_557-snap.2-T1, internal, 598, 650
-recovered snap_scaffold_557-snap.2-T1, internal, 927, 1010
-recovered snap_scaffold_557-snap.2-T1, internal, 1661, 1714
-recovered snap_scaffold_557-snap.2-T1, internal, 1844, 1999

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Couldn't classify 5802, 5870
Sorry, prediction Augustus_model.g41201.t1 fails validation.
(ATG)	 GA	4160-4270	GT	AGG
(GTG)	 AG	4490-4662	GT	CAG
(ATT)	 AG	4914-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5870	GT	AGG
-recovered Augustus_model.g41201.t1, initial, 4160, 4270
-recovered Augustus_model.g41201.t1, internal, 4490, 4662
-recovered Augustus_model.g41201.t1, internal, 4914, 4989
-recovered Augustus_model.g41201.t1, internal, 5188, 5361
-recovered Augustus_model.g41201.t1, internal, 5533, 5658
-recovered Augustus_model.g41201.t1, internal, 5802, 5870
Valid prediction for GlimmerHMM_glimmerT_61985-T1
Couldn't classify 4927, 4989
Couldn't classify 5802, 5867
Sorry, prediction pasa_asmbl_46519.p1 fails validation.
(AAG)	 AG	4927-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5867	GA	CCG
-recovered pasa_asmbl_46519.p1, internal, 4927, 4989
-recovered pasa_asmbl_46519.p1, internal, 5188, 5361
-recovered pasa_asmbl_46519.p1, internal, 5533, 5658
Couldn't classify 5802, 5870
Sorry, prediction snap_scaffold_557-snap.1-T1 fails validation.
(ATG)	 GA	4160-4270	GT	AGG
(GTG)	 AG	4490-4662	GT	CAG
(ATT)	 AG	4914-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5658	GT	AGG
(GTT)	 AG	5802-5870	GT	AGG
-recovered snap_scaffold_557-snap.1-T1, initial, 4160, 4270
-recovered snap_scaffold_557-snap.1-T1, internal, 4490, 4662
-recovered snap_scaffold_557-snap.1-T1, internal, 4914, 4989
-recovered snap_scaffold_557-snap.1-T1, internal, 5188, 5361
-recovered snap_scaffold_557-snap.1-T1, internal, 5533, 5658
-recovered snap_scaffold_557-snap.1-T1, internal, 5802, 5870
Couldn't classify 20, 196
Sorry, prediction GeneMark_model.107927_t fails validation.
(GAT)	 AG	20-196	GT	AGG
(TCT)	 AG	495-527	CA	GAC
-recovered GeneMark_model.107927_t, terminal, 495, 527
-recovered GeneMark_model.107927_t, internal, 20, 196
Couldn't classify 1, 196
Sorry, prediction Augustus_model.g41202.t1 fails validation.
(TCC)	 CA	1-196	GT	AGG
(GTT)	 AG	3914-3955	CC	AAC
-recovered Augustus_model.g41202.t1, terminal, 3914, 3955
Couldn't classify 5732, 5870
Sorry, prediction GeneMark_model.107926_t fails validation.
(ATG)	 GA	4160-4270	GT	AGG
(GTG)	 AG	4490-4662	GT	CAG
(ATT)	 AG	4914-4989	GT	AGG
(GTG)	 AG	5188-5361	GT	AGG
(CTG)	 AG	5533-5678	GT	GAG
(GGA)	 AG	5732-5870	GT	AGG
-recovered GeneMark_model.107926_t, initial, 4160, 4270
-recovered GeneMark_model.107926_t, internal, 4490, 4662
-recovered GeneMark_model.107926_t, internal, 4914, 4989
-recovered GeneMark_model.107926_t, internal, 5188, 5361
-recovered GeneMark_model.107926_t, internal, 5533, 5678
-recovered GeneMark_model.107926_t, internal, 5732, 5870
Couldn't classify 20, 196
Sorry, prediction GlimmerHMM_glimmerT_61986-T1 fails validation.
(GAT)	 AG	20-196	GT	AGG
(GTT)	 AG	3914-3955	CC	AAC
-recovered GlimmerHMM_glimmerT_61986-T1, terminal, 3914, 3955
-recovered GlimmerHMM_glimmerT_61986-T1, internal, 20, 196
Couldn't classify 20, 196
Sorry, prediction snap_scaffold_557-snap.3-T1 fails validation.
(GAT)	 AG	20-196	GT	AGG
(GAG)	 AG	3329-3352	AT	AAA
-recovered snap_scaffold_557-snap.3-T1, terminal, 3329, 3352
-recovered snap_scaffold_557-snap.3-T1, internal, 20, 196

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 1732, rend_intergenic: 598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5891
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 1732, rend_intergenic: 598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support