-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_243

-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 snap_scaffold_243-snap.3-T1
Valid prediction for GeneMark_model.107057_t
Couldn't classify 96, 376
Sorry, prediction snap_scaffold_243-snap.1-T1 fails validation.
(AGA)	 AG	96-376	GT	CTG
(GGC)	 AG	2833-3181	GT	AGG
(GTG)	 AG	3613-3698	GG	GAG
-recovered snap_scaffold_243-snap.1-T1, terminal, 3613, 3698
-recovered snap_scaffold_243-snap.1-T1, internal, 96, 376
-recovered snap_scaffold_243-snap.1-T1, internal, 2833, 3181
Couldn't classify 73, 183
Sorry, prediction GeneMark_model.107055_t fails validation.
(ACA)	 AG	73-183	GC	GAG
(GAG)	 AG	209-331	GT	GAG
(GAG)	 AG	359-380	CT	AGC
-recovered GeneMark_model.107055_t, terminal, 359, 380
-recovered GeneMark_model.107055_t, internal, 73, 183
-recovered GeneMark_model.107055_t, internal, 209, 331
Valid prediction for GeneMark_model.107059_t
Valid prediction for GlimmerHMM_glimmerT_61564-T1

-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 147, 235
Sorry, prediction GlimmerHMM_glimmerT_61565-T1 fails validation.
(GGT)	 AG	147-235	GT	AGG
(AGA)	 AG	2217-2672	CC	GAC
-recovered GlimmerHMM_glimmerT_61565-T1, terminal, 2217, 2672
-recovered GlimmerHMM_glimmerT_61565-T1, internal, 147, 235
Valid prediction for GeneMark_model.107056_t
Couldn't classify 147, 266
Sorry, prediction Augustus_model.g40939.t1 fails validation.
(GGT)	 AG	147-266	GT	AGG
(AGA)	 AG	758-851	GT	ATG
(TGT)	 AG	1292-1388	GG	GAG
-recovered Augustus_model.g40939.t1, terminal, 1292, 1388
-recovered Augustus_model.g40939.t1, internal, 147, 266
-recovered Augustus_model.g40939.t1, internal, 758, 851
Valid prediction for Augustus_model.g40938.t1
Couldn't classify 147, 235
Sorry, prediction snap_scaffold_243-snap.4-T1 fails validation.
(GGT)	 AG	147-235	GT	AGG
(AGA)	 AG	2217-2672	CC	GAC
-recovered snap_scaffold_243-snap.4-T1, terminal, 2217, 2672
-recovered snap_scaffold_243-snap.4-T1, internal, 147, 235
Valid prediction for GeneMark_model.107058_t
Couldn't classify 6022, 6350
Sorry, prediction snap_scaffold_243-snap.2-T1 fails validation.
(ATG)	 TC	2842-2851	GT	TGG
(GTA)	 AG	3252-3547	GT	AGG
(GGC)	 AG	4563-4662	GT	GCG
(AAA)	 AG	4729-5014	GT	GAG
(CTG)	 AG	5739-5808	GT	GGG
(CCC)	 AG	6022-6350	GT	GGG
-recovered snap_scaffold_243-snap.2-T1, initial, 2842, 2851
-recovered snap_scaffold_243-snap.2-T1, internal, 3252, 3547
-recovered snap_scaffold_243-snap.2-T1, internal, 4563, 4662
-recovered snap_scaffold_243-snap.2-T1, internal, 4729, 5014
-recovered snap_scaffold_243-snap.2-T1, internal, 5739, 5808
-recovered snap_scaffold_243-snap.2-T1, internal, 6022, 6350
Couldn't classify 147, 288
Sorry, prediction GeneMark_model.107060_t fails validation.
(GGT)	 AG	147-288	GT	CTG
(TGT)	 AG	1292-1388	GG	GAG
-recovered GeneMark_model.107060_t, terminal, 1292, 1388
-recovered GeneMark_model.107060_t, internal, 147, 288

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3698, rend_intergenic: 2815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6323, rend_intergenic: 4316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6960, rend_intergenic: 6493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9164
-exon list size: 87


building trellis

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3.4    
4.5    
5.6    
6.7    
7.9    
9.0    
10.1    
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12.4    
13.5    
14.6    
15.7    
16.9    
18.0    
19.1    
20.2    
21.3    
22.5    
23.6    
24.7    
25.8    
27.0    
28.1    
29.2    
30.3    
31.5    
32.6    
33.7    
34.8    
36.0    
37.1    
38.2    
39.3    
40.4    
41.6    
42.7    
43.8    
44.9    
46.1    
47.2    
48.3    
49.4    
50.6    
51.7    
52.8    
53.9    
55.1    
56.2    
57.3    
58.4    
59.6    
60.7    
61.8    
62.9    
64.0    
65.2    
66.3    
67.4    
68.5    
69.7    
70.8    
71.9    
73.0    
74.2    
75.3    
76.4    
77.5    
78.7    
79.8    
80.9    
82.0    
83.1    
84.3    
85.4    
86.5    
87.6    
88.8    
89.9    
91.0    
92.1    
93.3    
94.4    
95.5    
96.6    
97.8    
98.9    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 3698, rend_intergenic: 2815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6323, rend_intergenic: 4316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6960, rend_intergenic: 6493  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