-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_142

-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 GeneMark_model.106719_t
Valid prediction for GeneMark_model.106720_t
Couldn't classify 12769, 12804
Sorry, prediction GeneMark_model.106721_t fails validation.
(ATG)	 AG	11716-11768	GT	GTG
(GGG)	 AG	11793-11955	GC	AAG
(CCT)	 AG	12382-12525	GT	ATG
(GAG)	 AG	12567-12739	GT	AGG
(AGA)	 AG	12769-12804	GT	AAG
-recovered GeneMark_model.106721_t, initial, 11716, 11768
-recovered GeneMark_model.106721_t, internal, 11716, 11768
-recovered GeneMark_model.106721_t, internal, 11793, 11955
-recovered GeneMark_model.106721_t, internal, 12382, 12525
-recovered GeneMark_model.106721_t, internal, 12567, 12739
-recovered GeneMark_model.106721_t, internal, 12769, 12804
Valid prediction for GeneMark_model.106717_t
Valid prediction for snap_scaffold_142-snap.3-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: -)Valid prediction for snap_scaffold_142-snap.2-T1
Valid prediction for Augustus_model.g40821.t1
Couldn't classify 12821, 12892
Sorry, prediction GeneMark_model.106716_t fails validation.
(ATG)	 TG	8114-8162	GT	CGG
(GTG)	 AG	8198-8353	GT	GGG
(AGG)	 AG	9317-9421	GT	AGG
(GTC)	 AG	10164-10383	GT	CGG
(AGT)	 AG	11333-11343	GT	AGG
(GGT)	 AG	12344-12536	GT	AGG
(AGC)	 AG	12821-12892	GT	GAG
-recovered GeneMark_model.106716_t, initial, 8114, 8162
add_exon() Sorry, GeneMark_model.106716_t 9317-9421-terminal-1 is invalid.
-recovered GeneMark_model.106716_t, terminal, 9317, 9421
-recovered GeneMark_model.106716_t, terminal, 11333, 11343
-recovered GeneMark_model.106716_t, internal, 8198, 8353
-recovered GeneMark_model.106716_t, internal, 9317, 9421
-recovered GeneMark_model.106716_t, internal, 10164, 10383
-recovered GeneMark_model.106716_t, internal, 11333, 11343
-recovered GeneMark_model.106716_t, internal, 12344, 12536
-recovered GeneMark_model.106716_t, internal, 12821, 12892
Couldn't classify 4638, 4752
Sorry, prediction GlimmerHMM_glimmerT_61376-T1 fails validation.
(AGG)	 AG	4638-4752	GT	AGG
(GAG)	 AG	4807-4860	GT	AGG
(TTG)	 AG	8072-8191	CC	GAC
-recovered GlimmerHMM_glimmerT_61376-T1, terminal, 8072, 8191
-recovered GlimmerHMM_glimmerT_61376-T1, internal, 4638, 4752
-recovered GlimmerHMM_glimmerT_61376-T1, internal, 4807, 4860
Valid prediction for snap_scaffold_142-snap.1-T1
Valid prediction for GeneMark_model.106718_t
Valid prediction for GlimmerHMM_glimmerT_61375-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9209, rend_intergenic: 4583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 12906
-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 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 9209, rend_intergenic: 4583  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