-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_349

-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 5677, 5828
Sorry, prediction snap_scaffold_349-snap.3-T1 fails validation.
(ATG)	 TC	1566-1574	GT	AAG
(TGC)	 AG	1607-1826	GT	CGG
(GCG)	 AG	2147-2420	GT	GGG
(GCT)	 AG	2925-3062	GT	TCG
(GTG)	 AG	3255-3380	GT	AGG
(GTA)	 AG	3803-3884	GT	AGG
(GAA)	 AG	4565-4711	GT	GGG
(TCG)	 AG	5677-5828	GT	TCG
-recovered snap_scaffold_349-snap.3-T1, initial, 1566, 1574
-recovered snap_scaffold_349-snap.3-T1, internal, 1607, 1826
-recovered snap_scaffold_349-snap.3-T1, internal, 2147, 2420
-recovered snap_scaffold_349-snap.3-T1, internal, 2925, 3062
-recovered snap_scaffold_349-snap.3-T1, internal, 3255, 3380
-recovered snap_scaffold_349-snap.3-T1, internal, 3803, 3884
-recovered snap_scaffold_349-snap.3-T1, internal, 4565, 4711
-recovered snap_scaffold_349-snap.3-T1, internal, 5677, 5828
Valid prediction for GeneMark_model.107381_t
Valid prediction for GeneMark_model.107383_t
Couldn't classify 57, 167
Sorry, prediction snap_scaffold_349-snap.2-T1 fails validation.
(GGT)	 AG	57-167	GT	GGG
(ATG)	 AG	553-678	GT	TGG
(AAT)	 AG	1285-1446	GA	GAG
-recovered snap_scaffold_349-snap.2-T1, initial, 553, 678
-recovered snap_scaffold_349-snap.2-T1, terminal, 1285, 1446
-recovered snap_scaffold_349-snap.2-T1, internal, 57, 167
-recovered snap_scaffold_349-snap.2-T1, internal, 553, 678

-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 7664, 7807
Sorry, prediction GeneMark_model.107380_t fails validation.
(ATG)	 AC	4369-4389	GT	TGG
(ATC)	 AG	4436-4635	GC	AGG
(AGG)	 AG	4660-4741	GT	GGG
(GTG)	 AG	4859-4939	GT	AGG
(GTG)	 AG	5488-5722	GT	CCG
(GAA)	 AG	5977-6293	GT	AGG
(GTG)	 AG	6485-6671	GT	GGG
(GTG)	 AG	7167-7309	GT	AGG
(GCC)	 AG	7664-7807	GT	AGG
-recovered GeneMark_model.107380_t, initial, 4369, 4389
-recovered GeneMark_model.107380_t, internal, 4436, 4635
-recovered GeneMark_model.107380_t, internal, 4660, 4741
-recovered GeneMark_model.107380_t, internal, 4859, 4939
-recovered GeneMark_model.107380_t, internal, 5488, 5722
-recovered GeneMark_model.107380_t, internal, 5977, 6293
-recovered GeneMark_model.107380_t, internal, 6485, 6671
-recovered GeneMark_model.107380_t, internal, 7167, 7309
-recovered GeneMark_model.107380_t, internal, 7664, 7807
Couldn't classify 7664, 7807
Sorry, prediction Augustus_model.g41037.t1 fails validation.
(ATG)	 GG	1790-1814	GT	GGG
(GGT)	 AG	2013-2221	GT	AGG
(ATC)	 AG	2759-2861	GT	AGG
(GTG)	 AG	3166-3353	GT	AGG
(GGG)	 AG	3935-4057	GT	AGG
(ATC)	 AG	4436-4642	GT	AGG
(GTG)	 AG	4859-4939	GT	AGG
(GTG)	 AG	5488-5722	GT	CCG
(GAA)	 AG	5977-6293	GT	AGG
(GTG)	 AG	6485-6671	GT	GGG
(GTG)	 AG	7167-7309	GT	AGG
(GCC)	 AG	7664-7807	GT	AGG
-recovered Augustus_model.g41037.t1, initial, 1790, 1814
-recovered Augustus_model.g41037.t1, internal, 2013, 2221
-recovered Augustus_model.g41037.t1, internal, 2759, 2861
-recovered Augustus_model.g41037.t1, internal, 3166, 3353
-recovered Augustus_model.g41037.t1, internal, 3935, 4057
-recovered Augustus_model.g41037.t1, internal, 4436, 4642
-recovered Augustus_model.g41037.t1, internal, 4859, 4939
-recovered Augustus_model.g41037.t1, internal, 5488, 5722
-recovered Augustus_model.g41037.t1, internal, 5977, 6293
-recovered Augustus_model.g41037.t1, internal, 6485, 6671
-recovered Augustus_model.g41037.t1, internal, 7167, 7309
-recovered Augustus_model.g41037.t1, internal, 7664, 7807
Couldn't classify 2013, 2221
Sorry, prediction GlimmerHMM_glimmerT_61739-T1 fails validation.
(GGT)	 AG	2013-2221	GT	AGG
(ATC)	 AG	2759-2861	GT	AGG
(GTG)	 AG	3166-3353	GT	AGG
(GGG)	 AG	3935-4057	GT	AGG
(ATC)	 AG	4436-4642	GT	AGG
(GTG)	 AG	4859-4939	GT	AGG
(GTG)	 AG	5488-5722	GT	CCG
(GAA)	 AG	5977-6293	GT	AGG
(GTG)	 AG	6485-6649	GT	TGG
(GTG)	 AG	7167-7175	CC	AAC
-recovered GlimmerHMM_glimmerT_61739-T1, terminal, 7167, 7175
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 2013, 2221
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 2759, 2861
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 3166, 3353
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 3935, 4057
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 4436, 4642
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 4859, 4939
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 5488, 5722
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 5977, 6293
-recovered GlimmerHMM_glimmerT_61739-T1, internal, 6485, 6649
Valid prediction for GeneMark_model.107382_t
Couldn't classify 2013, 2221
Couldn't classify 7664, 7807
Sorry, prediction snap_scaffold_349-snap.1-T1 fails validation.
(GGT)	 AG	2013-2221	GT	AGG
(ATC)	 AG	2759-2861	GT	AGG
(GTG)	 AG	3166-3353	GT	AGG
(GGG)	 AG	3935-4057	GT	AGG
(ATC)	 AG	4436-4642	GT	AGG
(GTG)	 AG	4859-4939	GT	AGG
(GTG)	 AG	5488-5722	GT	CCG
(GAA)	 AG	5977-6293	GT	AGG
(GTG)	 AG	6485-6671	GT	GGG
(GTG)	 AG	7167-7309	GT	AGG
(GCC)	 AG	7664-7807	GT	AGG
-recovered snap_scaffold_349-snap.1-T1, internal, 2013, 2221
-recovered snap_scaffold_349-snap.1-T1, internal, 2759, 2861
-recovered snap_scaffold_349-snap.1-T1, internal, 3166, 3353
-recovered snap_scaffold_349-snap.1-T1, internal, 3935, 4057
-recovered snap_scaffold_349-snap.1-T1, internal, 4436, 4642
-recovered snap_scaffold_349-snap.1-T1, internal, 4859, 4939
-recovered snap_scaffold_349-snap.1-T1, internal, 5488, 5722
-recovered snap_scaffold_349-snap.1-T1, internal, 5977, 6293
-recovered snap_scaffold_349-snap.1-T1, internal, 6485, 6671
-recovered snap_scaffold_349-snap.1-T1, internal, 7167, 7309
-recovered snap_scaffold_349-snap.1-T1, internal, 7664, 7807
Couldn't classify 2804, 2861
Couldn't classify 7664, 7807
Sorry, prediction pasa_asmbl_40978.p1 fails validation.
(AGT)	 AC	2804-2861	GT	AGG
(GTG)	 AG	3166-3353	GT	AGG
(GGG)	 AG	3935-4057	GT	AGG
(ATC)	 AG	4436-4642	GT	AGG
(GTG)	 AG	4859-4939	GT	AGG
(GTG)	 AG	5488-5722	GT	CCG
(GAA)	 AG	5977-6293	GT	AGG
(GTG)	 AG	6485-6671	GT	GGG
(GTG)	 AG	7167-7309	GT	AGG
(GCC)	 AG	7664-7807	GT	AGG
-recovered pasa_asmbl_40978.p1, internal, 3166, 3353
-recovered pasa_asmbl_40978.p1, internal, 3935, 4057
-recovered pasa_asmbl_40978.p1, internal, 4436, 4642
-recovered pasa_asmbl_40978.p1, internal, 4859, 4939
-recovered pasa_asmbl_40978.p1, internal, 5488, 5722
-recovered pasa_asmbl_40978.p1, internal, 5977, 6293
-recovered pasa_asmbl_40978.p1, internal, 6485, 6671
-recovered pasa_asmbl_40978.p1, internal, 7167, 7309
-recovered pasa_asmbl_40978.p1, internal, 7664, 7807

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5842, rend_intergenic: 57  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7854
-exon list size: 74


building trellis

1.3    
2.6    
3.9    
5.3    
6.6    
7.9    
9.2    
10.5    
11.8    
13.2    
14.5    
15.8    
17.1    
18.4    
19.7    
21.1    
22.4    
23.7    
25.0    
26.3    
27.6    
28.9    
30.3    
31.6    
32.9    
34.2    
35.5    
36.8    
38.2    
39.5    
40.8    
42.1    
43.4    
44.7    
46.1    
47.4    
48.7    
50.0    
51.3    
52.6    
53.9    
55.3    
56.6    
57.9    
59.2    
60.5    
61.8    
63.2    
64.5    
65.8    
67.1    
68.4    
69.7    
71.1    
72.4    
73.7    
75.0    
76.3    
77.6    
78.9    
80.3    
81.6    
82.9    
84.2    
85.5    
86.8    
88.2    
89.5    
90.8    
92.1    
93.4    
94.7    
96.1    
97.4    
98.7    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5842, rend_intergenic: 57  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