-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_314

-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.107275_t
Valid prediction for snap_scaffold_314-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61682-T1
Valid prediction for GlimmerHMM_glimmerT_61681-T1
Couldn't classify 1049, 1144
Sorry, prediction GeneMark_model.107274_t fails validation.
(GCA)	 AG	1049-1144	GT	AGG
(GAG)	 AG	1169-1252	GC	GGG
(AGA)	 AG	1275-1286	GT	AGG
(ACC)	 AG	1311-1337	GT	AGG
(AGA)	 AG	1358-1417	GC	AAG
(AGG)	 AG	1440-1499	GT	AGG
(GAG)	 AG	1536-1547	GT	AGG
(AGG)	 AG	1570-1611	GT	AGG
(AGA)	 AG	1632-1643	GT	AGG
(GAC)	 AG	1668-1754	GT	AAG
(ACA)	 AG	1779-1793	GT	AGG
(GAA)	 AG	1816-1821	GT	AGG
(GAC)	 AG	1846-1917	GT	AGG
(GAC)	 AG	1942-1965	GT	AGG
(GAG)	 AG	1990-2013	GT	AGG
(GTA)	 AG	2048-2059	GT	AGG
(AGA)	 AG	2080-2121	GT	AAG
(AGG)	 AG	2161-2235	GT	GAG
(AGA)	 AG	2257-2277	GT	AGG
(AGG)	 AG	2303-2311	GT	AGG
(AGG)	 AG	2335-2394	GT	CGG
(AGG)	 AG	2419-2445	GT	AGG
(AGA)	 AG	2468-2794	GT	AGG
(AGG)	 AG	2817-2825	GT	AGG
(AGC)	 AG	2848-2922	GT	GGG
(GAG)	 AG	2954-2995	GT	AGG
(GAC)	 AG	3024-3092	GT	AGG
(AAG)	 AG	3123-3218	GC	AGG
(AGG)	 AG	3241-3279	GT	CAG
(AGA)	 AG	3304-3339	GT	AGG
(GAG)	 AG	3372-3536	GT	AGG
(AGA)	 AG	3557-3568	GT	AGG
(AGG)	 AG	3591-3632	GC	AGG
(GAG)	 AG	3657-3728	GT	AGG
(AGG)	 AG	3751-3870	GT	AGG
(GAG)	 AG	3895-3984	GT	AGG
(GAG)	 AG	4009-4032	GT	AGG
(AGA)	 AG	4053-4193	GT	AGG
(AGG)	 AG	4216-4272	GT	AGG
(AGG)	 AG	4295-4336	GT	AGG
(GAC)	 AG	4361-4432	GT	AGG
(AGG)	 AG	4455-4496	GT	AGG
(GAG)	 AG	4521-4544	GT	AGG
(AGA)	 AG	4565-4576	GT	AGG
(GAC)	 AG	4601-4624	GT	AGG
(ACA)	 AG	4647-4700	GT	AGG
(AGA)	 AG	4721-4732	GT	AGG
(ACA)	 AG	4758-4763	GT	CGG
(GAG)	 AG	4788-4796	GT	GCG
(GAC)	 AG	4823-4870	GT	AGG
(AAG)	 AG	4892-5068	GT	GGG
(AGA)	 AG	5098-5151	GT	AGG
(GCA)	 AG	5203-5436	GT	AAG
(GAC)	 AG	5511-5570	GT	AGG
(AGG)	 AG	5593-5646	GT	AGG
(AGG)	 AG	5669-5680	GT	AGG
(AGA)	 AG	5702-5728	GT	AGG
(GAC)	 AG	5749-5838	GT	AGG
(AGA)	 AG	5861-5902	GT	AAG
(AGA)	 AG	5923-5934	GT	AGG
(AGA)	 AG	5955-5970	TT	GAT
-recovered GeneMark_model.107274_t, terminal, 5955, 5970
-recovered GeneMark_model.107274_t, internal, 1049, 1144
-recovered GeneMark_model.107274_t, internal, 1169, 1252
-recovered GeneMark_model.107274_t, internal, 1275, 1286
-recovered GeneMark_model.107274_t, internal, 1311, 1337
-recovered GeneMark_model.107274_t, internal, 1358, 1417
-recovered GeneMark_model.107274_t, internal, 1440, 1499
-recovered GeneMark_model.107274_t, internal, 1536, 1547
-recovered GeneMark_model.107274_t, internal, 1570, 1611
-recovered GeneMark_model.107274_t, internal, 1632, 1643
-recovered GeneMark_model.107274_t, internal, 1668, 1754
-recovered GeneMark_model.107274_t, internal, 1779, 1793
-recovered GeneMark_model.107274_t, internal, 1816, 1821
-recovered GeneMark_model.107274_t, internal, 1846, 1917
-recovered GeneMark_model.107274_t, internal, 1942, 1965
-recovered GeneMark_model.107274_t, internal, 1990, 2013
-recovered GeneMark_model.107274_t, internal, 2048, 2059
-recovered GeneMark_model.107274_t, internal, 2080, 2121
-recovered GeneMark_model.107274_t, internal, 2161, 2235
-recovered GeneMark_model.107274_t, internal, 2257, 2277
-recovered GeneMark_model.107274_t, internal, 2303, 2311
-recovered GeneMark_model.107274_t, internal, 2335, 2394
-recovered GeneMark_model.107274_t, internal, 2419, 2445
-recovered GeneMark_model.107274_t, internal, 2468, 2794
-recovered GeneMark_model.107274_t, internal, 2817, 2825
-recovered GeneMark_model.107274_t, internal, 2848, 2922
-recovered GeneMark_model.107274_t, internal, 2954, 2995
-recovered GeneMark_model.107274_t, internal, 3024, 3092
-recovered GeneMark_model.107274_t, internal, 3123, 3218
-recovered GeneMark_model.107274_t, internal, 3241, 3279
-recovered GeneMark_model.107274_t, internal, 3304, 3339
-recovered GeneMark_model.107274_t, internal, 3372, 3536
-recovered GeneMark_model.107274_t, internal, 3557, 3568
-recovered GeneMark_model.107274_t, internal, 3591, 3632
-recovered GeneMark_model.107274_t, internal, 3657, 3728
-recovered GeneMark_model.107274_t, internal, 3751, 3870
-recovered GeneMark_model.107274_t, internal, 3895, 3984
-recovered GeneMark_model.107274_t, internal, 4009, 4032
-recovered GeneMark_model.107274_t, internal, 4053, 4193
-recovered GeneMark_model.107274_t, internal, 4216, 4272
-recovered GeneMark_model.107274_t, internal, 4295, 4336
-recovered GeneMark_model.107274_t, internal, 4361, 4432
-recovered GeneMark_model.107274_t, internal, 4455, 4496
-recovered GeneMark_model.107274_t, internal, 4521, 4544
-recovered GeneMark_model.107274_t, internal, 4565, 4576
-recovered GeneMark_model.107274_t, internal, 4601, 4624
-recovered GeneMark_model.107274_t, internal, 4647, 4700
-recovered GeneMark_model.107274_t, internal, 4721, 4732
-recovered GeneMark_model.107274_t, internal, 4758, 4763
-recovered GeneMark_model.107274_t, internal, 4788, 4796
-recovered GeneMark_model.107274_t, internal, 4823, 4870
-recovered GeneMark_model.107274_t, internal, 4892, 5068
-recovered GeneMark_model.107274_t, internal, 5098, 5151
-recovered GeneMark_model.107274_t, internal, 5203, 5436
-recovered GeneMark_model.107274_t, internal, 5511, 5570
-recovered GeneMark_model.107274_t, internal, 5593, 5646
-recovered GeneMark_model.107274_t, internal, 5669, 5680
-recovered GeneMark_model.107274_t, internal, 5702, 5728
-recovered GeneMark_model.107274_t, internal, 5749, 5838
-recovered GeneMark_model.107274_t, internal, 5861, 5902
-recovered GeneMark_model.107274_t, internal, 5923, 5934

-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 212, 361
Sorry, prediction snap_scaffold_314-snap.2-T1 fails validation.
(CGC)	 AG	212-361	GT	CTG
(GGG)	 AG	1387-1536	GT	TGG
(ATG)	 AG	7247-7285	CA	GAC
-recovered snap_scaffold_314-snap.2-T1, terminal, 7247, 7285
-recovered snap_scaffold_314-snap.2-T1, internal, 212, 361
-recovered snap_scaffold_314-snap.2-T1, internal, 1387, 1536
Couldn't classify 8064, 8195
Sorry, prediction snap_scaffold_314-snap.1-T1 fails validation.
(ATG)	 AC	7940-8003	GT	AGG
(CTC)	 AG	8064-8195	GT	GGG
-recovered snap_scaffold_314-snap.1-T1, initial, 7940, 8003
-recovered snap_scaffold_314-snap.1-T1, internal, 8064, 8195
Valid prediction for GlimmerHMM_glimmerT_61683-T1
Couldn't classify 127, 182
Sorry, prediction GeneMark_model.107276_t fails validation.
(AGA)	 AG	127-182	GT	CAG
(CGC)	 AG	212-361	GT	CTG
(GCC)	 AG	544-641	GT	CTG
(GCC)	 AG	755-813	GT	AGG
(GGC)	 AG	849-889	GT	CTG
(GCC)	 AG	967-1052	GT	CTG
(GGG)	 AG	1107-1170	GT	CTG
(GCC)	 AG	1225-1293	GG	AGG
-recovered GeneMark_model.107276_t, terminal, 755, 813
-recovered GeneMark_model.107276_t, terminal, 1225, 1293
-recovered GeneMark_model.107276_t, internal, 127, 182
-recovered GeneMark_model.107276_t, internal, 212, 361
-recovered GeneMark_model.107276_t, internal, 544, 641
-recovered GeneMark_model.107276_t, internal, 755, 813
-recovered GeneMark_model.107276_t, internal, 849, 889
-recovered GeneMark_model.107276_t, internal, 967, 1052
-recovered GeneMark_model.107276_t, internal, 1107, 1170

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8047, rend_intergenic: 2145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8258
-exon list size: 195


building trellis

0.5    
1.0    
1.5    
2.0    
2.5    
3.0    
3.6    
4.1    
4.6    
5.1    
5.6    
6.1    
6.6    
7.1    
7.6    
8.1    
8.6    
9.1    
9.6    
10.2    
10.7    
11.2    
11.7    
12.2    
12.7    
13.2    
13.7    
14.2    
14.7    
15.2    
15.7    
16.2    
16.8    
17.3    
17.8    
18.3    
18.8    
19.3    
19.8    
20.3    
20.8    
21.3    
21.8    
22.3    
22.8    
23.4    
23.9    
24.4    
24.9    
25.4    
25.9    
26.4    
26.9    
27.4    
27.9    
28.4    
28.9    
29.4    
29.9    
30.5    
31.0    
31.5    
32.0    
32.5    
33.0    
33.5    
34.0    
34.5    
35.0    
35.5    
36.0    
36.5    
37.1    
37.6    
38.1    
38.6    
39.1    
39.6    
40.1    
40.6    
41.1    
41.6    
42.1    
42.6    
43.1    
43.7    
44.2    
44.7    
45.2    
45.7    
46.2    
46.7    
47.2    
47.7    
48.2    
48.7    
49.2    
49.7    
50.3    
50.8    
51.3    
51.8    
52.3    
52.8    
53.3    
53.8    
54.3    
54.8    
55.3    
55.8    
56.3    
56.9    
57.4    
57.9    
58.4    
58.9    
59.4    
59.9    
60.4    
60.9    
61.4    
61.9    
62.4    
62.9    
63.5    
64.0    
64.5    
65.0    
65.5    
66.0    
66.5    
67.0    
67.5    
68.0    
68.5    
69.0    
69.5    
70.1    
70.6    
71.1    
71.6    
72.1    
72.6    
73.1    
73.6    
74.1    
74.6    
75.1    
75.6    
76.1    
76.6    
77.2    
77.7    
78.2    
78.7    
79.2    
79.7    
80.2    
80.7    
81.2    
81.7    
82.2    
82.7    
83.2    
83.8    
84.3    
84.8    
85.3    
85.8    
86.3    
86.8    
87.3    
87.8    
88.3    
88.8    
89.3    
89.8    
90.4    
90.9    
91.4    
91.9    
92.4    
92.9    
93.4    
93.9    
94.4    
94.9    
95.4    
95.9    
96.4    
97.0    
97.5    
98.0    
98.5    
99.0    
99.5    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 8047, rend_intergenic: 2145  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