-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/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: +)Couldn't classify 2645, 2768
Couldn't classify 2990, 3207
Sorry, prediction pasa_asmbl_46538.p2 fails validation.
(GGG)	 GT	2645-2768	GT	AGG
(GTT)	 AG	2990-3207	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_60454-T1
Valid prediction for CodingQuarry_transcript_52508-T1
Couldn't classify 134, 343
Couldn't classify 5403, 5549
Sorry, prediction pasa_asmbl_46537.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_46537.p1, internal, 630, 780
-recovered pasa_asmbl_46537.p1, internal, 2249, 2413
-recovered pasa_asmbl_46537.p1, internal, 2541, 2768
-recovered pasa_asmbl_46537.p1, internal, 2990, 3149
-recovered pasa_asmbl_46537.p1, internal, 4769, 5018
Couldn't classify 124, 343
Sorry, prediction Augustus_model.g40020.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.g40020.t1 5808-5909-terminal-1 is invalid.
-recovered Augustus_model.g40020.t1, terminal, 5808, 5909
-recovered Augustus_model.g40020.t1, internal, 124, 343
-recovered Augustus_model.g40020.t1, internal, 630, 780
-recovered Augustus_model.g40020.t1, internal, 2249, 2413
-recovered Augustus_model.g40020.t1, internal, 2541, 2768
-recovered Augustus_model.g40020.t1, internal, 2990, 3149
-recovered Augustus_model.g40020.t1, internal, 4769, 5018
-recovered Augustus_model.g40020.t1, internal, 5403, 5565
-recovered Augustus_model.g40020.t1, internal, 5808, 5909
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

-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 3669, 3874
Sorry, prediction snap_scaffold_527-snap.2-T1 fails validation.
(ATG)	 TC	1299-1474	GT	GGG
(CGT)	 AG	3363-3534	GT	TCG
(GTC)	 AG	3669-3874	GT	AGG
-recovered snap_scaffold_527-snap.2-T1, initial, 1299, 1474
-recovered snap_scaffold_527-snap.2-T1, internal, 3363, 3534
-recovered snap_scaffold_527-snap.2-T1, internal, 3669, 3874

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5909, rend_intergenic: 2218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6091
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5909, rend_intergenic: 2218  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