-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_460

-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 6244, 6431
Sorry, prediction snap_scaffold_460-snap.2-T1 fails validation.
(ATG)	 AA	46-153	GT	AGG
(GGA)	 AG	198-694	GT	TGG
(TCT)	 AG	2571-2748	GT	CTG
(GTT)	 AG	3657-3800	GT	ACG
(ACC)	 AG	4724-4868	GT	CTG
(GCC)	 AG	5695-5833	GT	GAG
(GAG)	 AG	6244-6431	GT	AGG
-recovered snap_scaffold_460-snap.2-T1, initial, 46, 153
-recovered snap_scaffold_460-snap.2-T1, internal, 198, 694
-recovered snap_scaffold_460-snap.2-T1, internal, 2571, 2748
-recovered snap_scaffold_460-snap.2-T1, internal, 3657, 3800
-recovered snap_scaffold_460-snap.2-T1, internal, 4724, 4868
-recovered snap_scaffold_460-snap.2-T1, internal, 5695, 5833
-recovered snap_scaffold_460-snap.2-T1, internal, 6244, 6431
Couldn't classify 6360, 6431
Sorry, prediction GeneMark_model.107686_t fails validation.
(ATG)	 CC	5770-5816	GT	GAG
(GAG)	 AG	5842-5856	GT	TGG
(GAG)	 AG	5882-5923	GT	GAG
(GAG)	 AG	5959-5982	GT	GAG
(GAG)	 AG	6011-6034	GT	GAG
(GGA)	 AG	6062-6094	GT	GAG
(TGA)	 AG	6116-6154	GT	GAG
(AGA)	 AG	6185-6193	GT	GAG
(GAG)	 AG	6222-6245	GT	GAG
(ACC)	 AG	6296-6331	GT	GAG
(AGG)	 AG	6360-6431	GT	AGG
-recovered GeneMark_model.107686_t, initial, 5770, 5816
-recovered GeneMark_model.107686_t, internal, 5842, 5856
-recovered GeneMark_model.107686_t, internal, 5882, 5923
-recovered GeneMark_model.107686_t, internal, 5959, 5982
-recovered GeneMark_model.107686_t, internal, 6011, 6034
-recovered GeneMark_model.107686_t, internal, 6062, 6094
-recovered GeneMark_model.107686_t, internal, 6116, 6154
-recovered GeneMark_model.107686_t, internal, 6185, 6193
-recovered GeneMark_model.107686_t, internal, 6222, 6245
-recovered GeneMark_model.107686_t, internal, 6296, 6331
-recovered GeneMark_model.107686_t, internal, 6360, 6431

-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 GlimmerHMM_glimmerT_61875-T1
Couldn't classify 1052, 1123
Sorry, prediction GlimmerHMM_glimmerT_61876-T1 fails validation.
(GTC)	 AG	1052-1123	GT	AGG
(ACG)	 AG	1999-2099	GT	GAG
(AGG)	 AG	3014-3185	AC	AGA
-recovered GlimmerHMM_glimmerT_61876-T1, terminal, 3014, 3185
-recovered GlimmerHMM_glimmerT_61876-T1, internal, 1052, 1123
-recovered GlimmerHMM_glimmerT_61876-T1, internal, 1999, 2099
Couldn't classify 6129, 6800
Sorry, prediction GeneMark_model.107685_t fails validation.
(ATG)	 CG	1089-1095	GT	GAG
(AGA)	 AG	1389-1419	GT	CTG
(ACA)	 AG	1457-1495	GT	CAG
(AGA)	 AG	1523-1531	GT	CAG
(ACT)	 AG	1569-1607	GT	CAG
(AGA)	 AG	1647-1667	GT	CAG
(AGT)	 AG	1693-1731	GT	GAG
(AGA)	 AG	1767-1781	GT	CAG
(AGA)	 AG	1805-1819	GT	CAG
(AGA)	 AG	1845-1859	GT	CAG
(AGA)	 AG	1885-1899	GT	CAG
(TGC)	 AG	1923-2099	GT	GAG
(TGG)	 AG	2532-2544	GT	AGG
(ACG)	 AG	3027-3181	GT	AAG
(ATT)	 AG	4113-4189	GT	AGG
(AAG)	 AG	4219-4273	GT	AAG
(GAA)	 AG	4464-4554	GT	AGG
(TGC)	 AG	4792-4897	GT	GGG
(ATT)	 AG	5278-5432	GT	ATG
(ACC)	 AG	5581-5710	GT	AGG
(ACA)	 AG	6129-6800	GT	CAG
-recovered GeneMark_model.107685_t, initial, 1089, 1095
-recovered GeneMark_model.107685_t, internal, 1389, 1419
-recovered GeneMark_model.107685_t, internal, 1457, 1495
-recovered GeneMark_model.107685_t, internal, 1523, 1531
-recovered GeneMark_model.107685_t, internal, 1569, 1607
-recovered GeneMark_model.107685_t, internal, 1647, 1667
-recovered GeneMark_model.107685_t, internal, 1693, 1731
-recovered GeneMark_model.107685_t, internal, 1767, 1781
-recovered GeneMark_model.107685_t, internal, 1805, 1819
-recovered GeneMark_model.107685_t, internal, 1845, 1859
-recovered GeneMark_model.107685_t, internal, 1885, 1899
-recovered GeneMark_model.107685_t, internal, 1923, 2099
-recovered GeneMark_model.107685_t, internal, 2532, 2544
-recovered GeneMark_model.107685_t, internal, 3027, 3181
-recovered GeneMark_model.107685_t, internal, 4113, 4189
-recovered GeneMark_model.107685_t, internal, 4219, 4273
-recovered GeneMark_model.107685_t, internal, 4464, 4554
-recovered GeneMark_model.107685_t, internal, 4792, 4897
-recovered GeneMark_model.107685_t, internal, 5278, 5432
-recovered GeneMark_model.107685_t, internal, 5581, 5710
-recovered GeneMark_model.107685_t, internal, 6129, 6800
Couldn't classify 1052, 1123
Couldn't classify 6129, 6800
Sorry, prediction snap_scaffold_460-snap.1-T1 fails validation.
(GTC)	 AG	1052-1123	GT	AGG
(ACG)	 AG	1999-2122	GT	GGG
(GAA)	 AG	2509-2544	GT	AGG
(GCC)	 AG	3016-3181	GT	AAG
(ATT)	 AG	4113-4189	GT	AGG
(AAG)	 AG	4219-4266	GT	TGG
(ACT)	 AG	4418-4554	GT	AGG
(TGC)	 AG	4792-4897	GT	GGG
(ATT)	 AG	5278-5432	GT	ATG
(ACC)	 AG	5581-5710	GT	AGG
(ACA)	 AG	6129-6800	GT	CAG
-recovered snap_scaffold_460-snap.1-T1, internal, 1052, 1123
-recovered snap_scaffold_460-snap.1-T1, internal, 1999, 2122
-recovered snap_scaffold_460-snap.1-T1, internal, 2509, 2544
-recovered snap_scaffold_460-snap.1-T1, internal, 3016, 3181
-recovered snap_scaffold_460-snap.1-T1, internal, 4113, 4189
-recovered snap_scaffold_460-snap.1-T1, internal, 4219, 4266
-recovered snap_scaffold_460-snap.1-T1, internal, 4418, 4554
-recovered snap_scaffold_460-snap.1-T1, internal, 4792, 4897
-recovered snap_scaffold_460-snap.1-T1, internal, 5278, 5432
-recovered snap_scaffold_460-snap.1-T1, internal, 5581, 5710
-recovered snap_scaffold_460-snap.1-T1, internal, 6129, 6800
Couldn't classify 1052, 1123
Sorry, prediction Augustus_model.g41129.t1 fails validation.
(GTC)	 AG	1052-1123	GT	AGG
(ACG)	 AG	1999-2122	GT	GGG
(GAA)	 AG	2509-2533	GT	TGG
(AGG)	 AG	3014-3185	AC	AGA
-recovered Augustus_model.g41129.t1, terminal, 3014, 3185
-recovered Augustus_model.g41129.t1, internal, 1052, 1123
-recovered Augustus_model.g41129.t1, internal, 1999, 2122
-recovered Augustus_model.g41129.t1, internal, 2509, 2533
Couldn't classify 6638, 6799
Sorry, prediction pasa_asmbl_43700.p1 fails validation.
(ATG)	 CA	3900-3904	GT	ACG
(ATT)	 AG	4113-4189	GT	AGG
(ACT)	 AG	4418-4554	GT	AGG
(TGC)	 AG	4792-4897	GT	GGG
(ATT)	 AG	5278-5432	GT	ATG
(ACC)	 AG	5581-5710	GT	AGG
(ACA)	 AG	6129-6349	GT	ACG
(GAG)	 AG	6638-6799	AG	ACA
-recovered pasa_asmbl_43700.p1, initial, 3900, 3904
-recovered pasa_asmbl_43700.p1, internal, 4113, 4189
-recovered pasa_asmbl_43700.p1, internal, 4418, 4554
-recovered pasa_asmbl_43700.p1, internal, 4792, 4897
-recovered pasa_asmbl_43700.p1, internal, 5278, 5432
-recovered pasa_asmbl_43700.p1, internal, 5581, 5710
-recovered pasa_asmbl_43700.p1, internal, 6129, 6349
Couldn't classify 6638, 6800
Sorry, prediction Augustus_model.g41128.t1 fails validation.
(ATG)	 CA	3900-3904	GT	ACG
(ATT)	 AG	4113-4189	GT	AGG
(ACT)	 AG	4418-4554	GT	AGG
(TGC)	 AG	4792-4897	GT	GGG
(ATT)	 AG	5278-5432	GT	ATG
(ACC)	 AG	5581-5710	GT	AGG
(ACA)	 AG	6129-6349	GT	ACG
(GAG)	 AG	6638-6800	GT	CAG
-recovered Augustus_model.g41128.t1, initial, 3900, 3904
-recovered Augustus_model.g41128.t1, internal, 4113, 4189
-recovered Augustus_model.g41128.t1, internal, 4418, 4554
-recovered Augustus_model.g41128.t1, internal, 4792, 4897
-recovered Augustus_model.g41128.t1, internal, 5278, 5432
-recovered Augustus_model.g41128.t1, internal, 5581, 5710
-recovered Augustus_model.g41128.t1, internal, 6129, 6349
-recovered Augustus_model.g41128.t1, internal, 6638, 6800

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5777, rend_intergenic: 46  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6828
-exon list size: 99


building trellis

1.0    
2.0    
3.0    
4.0    
5.0    
5.9    
6.9    
7.9    
8.9    
9.9    
10.9    
11.9    
12.9    
13.9    
14.9    
15.8    
16.8    
17.8    
18.8    
19.8    
20.8    
21.8    
22.8    
23.8    
24.8    
25.7    
26.7    
27.7    
28.7    
29.7    
30.7    
31.7    
32.7    
33.7    
34.7    
35.6    
36.6    
37.6    
38.6    
39.6    
40.6    
41.6    
42.6    
43.6    
44.6    
45.5    
46.5    
47.5    
48.5    
49.5    
50.5    
51.5    
52.5    
53.5    
54.5    
55.4    
56.4    
57.4    
58.4    
59.4    
60.4    
61.4    
62.4    
63.4    
64.4    
65.3    
66.3    
67.3    
68.3    
69.3    
70.3    
71.3    
72.3    
73.3    
74.3    
75.2    
76.2    
77.2    
78.2    
79.2    
80.2    
81.2    
82.2    
83.2    
84.2    
85.1    
86.1    
87.1    
88.1    
89.1    
90.1    
91.1    
92.1    
93.1    
94.1    
95.0    
96.0    
97.0    
98.0    
99.0    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5777, rend_intergenic: 46  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