-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_527

-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: +)Valid prediction for GlimmerHMM_glimmerT_61957-T1
Valid prediction for CodingQuarry_transcript_52376-T1
Couldn't classify 374, 470
Sorry, prediction GeneMark_model.107862_t fails validation.
(AAG)	 AG	374-470	GT	GTG
(GTG)	 AG	630-780	GT	AGG
(AGT)	 AG	2249-2413	GT	AGG
(AGG)	 AG	2541-2776	GA	GAG
-recovered GeneMark_model.107862_t, terminal, 2541, 2776
-recovered GeneMark_model.107862_t, internal, 374, 470
-recovered GeneMark_model.107862_t, internal, 630, 780
-recovered GeneMark_model.107862_t, internal, 2249, 2413
Couldn't classify 124, 343
Sorry, prediction Augustus_model.g41182.t1 fails validation.
(GTA)	 AG	124-343	GT	CTG
(GTG)	 AG	630-780	GT	AGG
(AGT)	 AG	2249-2413	GT	AGG
(AGG)	 AG	2541-2768	GT	AGG
(GTT)	 AG	2990-3149	GT	AGG
(GGT)	 AG	4769-5018	GT	AGG
(GTG)	 AG	5403-5565	GT	AGG
(ACT)	 AG	5808-5909	GT	AGG
add_exon() Sorry, Augustus_model.g41182.t1 5808-5909-terminal-1 is invalid.
-recovered Augustus_model.g41182.t1, terminal, 5808, 5909
-recovered Augustus_model.g41182.t1, internal, 124, 343
-recovered Augustus_model.g41182.t1, internal, 630, 780
-recovered Augustus_model.g41182.t1, internal, 2249, 2413
-recovered Augustus_model.g41182.t1, internal, 2541, 2768
-recovered Augustus_model.g41182.t1, internal, 2990, 3149
-recovered Augustus_model.g41182.t1, internal, 4769, 5018
-recovered Augustus_model.g41182.t1, internal, 5403, 5565
-recovered Augustus_model.g41182.t1, internal, 5808, 5909
Valid prediction for GeneMark_model.107864_t
Couldn't classify 134, 343
Couldn't classify 5403, 5549
Sorry, prediction pasa_asmbl_46490.p1 fails validation.
(CAT)	 GA	134-343	GT	CTG
(GTG)	 AG	630-780	GT	AGG
(AGT)	 AG	2249-2413	GT	AGG
(AGG)	 AG	2541-2768	GT	AGG
(GTT)	 AG	2990-3149	GT	AGG
(GGT)	 AG	4769-5018	GT	AGG
(GTG)	 AG	5403-5549	TA	TGT
-recovered pasa_asmbl_46490.p1, internal, 630, 780
-recovered pasa_asmbl_46490.p1, internal, 2249, 2413
-recovered pasa_asmbl_46490.p1, internal, 2541, 2768
-recovered pasa_asmbl_46490.p1, internal, 2990, 3149
-recovered pasa_asmbl_46490.p1, internal, 4769, 5018
Couldn't classify 162, 247
Sorry, prediction snap_scaffold_527-snap.1-T1 fails validation.
(GTT)	 AG	162-247	GT	GAG
(GTG)	 AG	630-780	GT	AGG
(AGT)	 AG	2249-2413	GT	AGG
(AGG)	 AG	2541-2768	GT	AGG
(GTT)	 AG	2990-3149	GT	AGG
(GGT)	 AG	4769-5018	GT	AGG
(GTG)	 AG	5403-5565	GT	AGG
(ACT)	 AG	5808-5909	GT	AGG
add_exon() Sorry, snap_scaffold_527-snap.1-T1 5808-5909-terminal-1 is invalid.
-recovered snap_scaffold_527-snap.1-T1, terminal, 5808, 5909
-recovered snap_scaffold_527-snap.1-T1, internal, 162, 247
-recovered snap_scaffold_527-snap.1-T1, internal, 630, 780
-recovered snap_scaffold_527-snap.1-T1, internal, 2249, 2413
-recovered snap_scaffold_527-snap.1-T1, internal, 2541, 2768
-recovered snap_scaffold_527-snap.1-T1, internal, 2990, 3149
-recovered snap_scaffold_527-snap.1-T1, internal, 4769, 5018
-recovered snap_scaffold_527-snap.1-T1, internal, 5403, 5565
-recovered snap_scaffold_527-snap.1-T1, internal, 5808, 5909
Couldn't classify 2645, 2768
Couldn't classify 2990, 3207
Sorry, prediction pasa_asmbl_46491.p2 fails validation.
(GGG)	 GT	2645-2768	GT	AGG
(GTT)	 AG	2990-3207	CA	CAC

-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 5328, 5469
Sorry, prediction snap_scaffold_527-snap.2-T1 fails validation.
(ATG)	 TC	1299-1474	GT	GGG
(CGT)	 AG	3363-3582	GT	AAG
(GTC)	 AG	3669-3874	GT	AGG
(CTG)	 AG	5328-5469	GT	GGG
-recovered snap_scaffold_527-snap.2-T1, initial, 1299, 1474
-recovered snap_scaffold_527-snap.2-T1, internal, 3363, 3582
-recovered snap_scaffold_527-snap.2-T1, internal, 3669, 3874
-recovered snap_scaffold_527-snap.2-T1, internal, 5328, 5469
Valid prediction for GeneMark_model.107863_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5909, rend_intergenic: 623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6091
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5909, rend_intergenic: 623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support