-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_644

-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 Augustus_model.g41266.t1
Valid prediction for GlimmerHMM_glimmerT_62078-T1
add_exon() Sorry, GlimmerHMM_glimmerT_62078-T1 4361-4773-terminal-1 is invalid.
Couldn't classify 4760, 5195
Sorry, prediction snap_scaffold_644-snap.2-T1 fails validation.
(ATG)	 GA	2194-2386	GT	TTG
(GTG)	 AG	4249-4292	GT	AGG
(GAC)	 AG	4471-4637	GT	TTG
(AGG)	 AG	4760-5195	GT	GAG
-recovered snap_scaffold_644-snap.2-T1, initial, 2194, 2386
-recovered snap_scaffold_644-snap.2-T1, internal, 4249, 4292
-recovered snap_scaffold_644-snap.2-T1, internal, 4471, 4637
-recovered snap_scaffold_644-snap.2-T1, internal, 4760, 5195
Couldn't classify 4795, 5195
Sorry, prediction GeneMark_model.108117_t fails validation.
(ATG)	 TC	1775-1815	GT	GCG
(ACA)	 AG	1930-1950	GT	GGG
(ACC)	 AG	2080-2088	GT	AGG
(GCT)	 AG	2187-2351	GT	AAG
(GCG)	 AG	3075-3119	GT	GGG
(GGA)	 AG	3143-3157	GT	AGG
(AAT)	 AG	3182-3208	GT	ATG
(GCC)	 AG	3945-3971	GT	AGG
(GGA)	 AG	4401-4599	GT	AGG
(ACC)	 AG	4795-5195	GT	GAG
-recovered GeneMark_model.108117_t, initial, 1775, 1815
add_exon() Sorry, GeneMark_model.108117_t 2187-2351-terminal-1 is invalid.
-recovered GeneMark_model.108117_t, terminal, 2187, 2351
-recovered GeneMark_model.108117_t, internal, 1930, 1950
-recovered GeneMark_model.108117_t, internal, 2080, 2088
-recovered GeneMark_model.108117_t, internal, 2187, 2351
-recovered GeneMark_model.108117_t, internal, 3075, 3119
-recovered GeneMark_model.108117_t, internal, 3143, 3157
-recovered GeneMark_model.108117_t, internal, 3182, 3208
-recovered GeneMark_model.108117_t, internal, 3945, 3971
-recovered GeneMark_model.108117_t, internal, 4401, 4599
-recovered GeneMark_model.108117_t, internal, 4795, 5195
Couldn't classify 698, 721
Sorry, prediction GeneMark_model.108116_t fails validation.
(GAG)	 AG	698-721	GT	ATG
(GAA)	 AG	753-785	GT	GGG
(GAG)	 AG	806-820	GT	GGG
(GGG)	 AG	843-926	GT	GGG
(GAG)	 AG	950-961	GT	AGG
(GAG)	 AG	992-1006	GT	GGG
(ATG)	 AG	1027-1089	GT	AGG
(AGT)	 AG	1110-1184	GT	GGG
(AAG)	 AG	1217-1237	GT	GGG
(AGG)	 AG	1277-1328	GA	AAG
add_exon() Sorry, GeneMark_model.108116_t 1027-1089-initial-1 is invalid.
-recovered GeneMark_model.108116_t, initial, 1027, 1089
-recovered GeneMark_model.108116_t, terminal, 1277, 1328
-recovered GeneMark_model.108116_t, internal, 698, 721
-recovered GeneMark_model.108116_t, internal, 753, 785
-recovered GeneMark_model.108116_t, internal, 806, 820
-recovered GeneMark_model.108116_t, internal, 843, 926
-recovered GeneMark_model.108116_t, internal, 950, 961
-recovered GeneMark_model.108116_t, internal, 992, 1006
-recovered GeneMark_model.108116_t, internal, 1027, 1089
-recovered GeneMark_model.108116_t, internal, 1110, 1184
-recovered GeneMark_model.108116_t, internal, 1217, 1237

-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 32, 471
Couldn't classify 3230, 3297
Sorry, prediction snap_scaffold_644-snap.1-T1 fails validation.
(CAC)	 AG	32-471	GT	TGG
(GGG)	 AG	482-504	GT	AGG
(AAC)	 AG	626-771	GT	AGG
(GAG)	 AG	1716-1841	GT	TGG
(CCT)	 AG	2821-3039	GT	CAG
(GCA)	 AG	3230-3297	GT	TGG
-recovered snap_scaffold_644-snap.1-T1, internal, 32, 471
-recovered snap_scaffold_644-snap.1-T1, internal, 482, 504
-recovered snap_scaffold_644-snap.1-T1, internal, 626, 771
-recovered snap_scaffold_644-snap.1-T1, internal, 1716, 1841
-recovered snap_scaffold_644-snap.1-T1, internal, 2821, 3039
-recovered snap_scaffold_644-snap.1-T1, internal, 3230, 3297
Sorry, intron length (9) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5172, rend_intergenic: 2194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5203
-exon list size: 61


building trellis

1.6    
3.2    
4.8    
6.3    
7.9    
9.5    
11.1    
12.7    
14.3    
15.9    
17.5    
19.0    
20.6    
22.2    
23.8    
25.4    
27.0    
28.6    
30.2    
31.7    
33.3    
34.9    
36.5    
38.1    
39.7    
41.3    
42.9    
44.4    
46.0    
47.6    
49.2    
50.8    
52.4    
54.0    
55.6    
57.1    
58.7    
60.3    
61.9    
63.5    
65.1    
66.7    
68.3    
69.8    
71.4    
73.0    
74.6    
76.2    
77.8    
79.4    
81.0    
82.5    
84.1    
85.7    
87.3    
88.9    
90.5    
92.1    
93.7    
95.2    
96.8    
98.4    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 5172, rend_intergenic: 2194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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