-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_84

-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 18205, 18444
Sorry, prediction snap_scaffold_84-snap.3-T1 fails validation.
(ATG)	 CA	2969-2972	GT	GGG
(GTA)	 AG	3168-3325	GT	GGG
(GAC)	 AG	4704-5133	GT	GGG
(CTG)	 AG	10210-10316	GT	TAG
(GCA)	 AG	10564-10692	GT	TTG
(CAG)	 AG	18205-18444	GT	AGG
-recovered snap_scaffold_84-snap.3-T1, initial, 2969, 2972
-recovered snap_scaffold_84-snap.3-T1, internal, 3168, 3325
-recovered snap_scaffold_84-snap.3-T1, internal, 4704, 5133
-recovered snap_scaffold_84-snap.3-T1, internal, 10210, 10316
-recovered snap_scaffold_84-snap.3-T1, internal, 10564, 10692
-recovered snap_scaffold_84-snap.3-T1, internal, 18205, 18444
Valid prediction for GeneMark_model.106472_t
Couldn't classify 131, 152
Sorry, prediction snap_scaffold_84-snap.1-T1 fails validation.
(CGT)	 AG	131-152	GT	ATG
(AGG)	 AG	1792-2091	AA	GAA
-recovered snap_scaffold_84-snap.1-T1, terminal, 1792, 2091
-recovered snap_scaffold_84-snap.1-T1, internal, 131, 152

-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 7885, 7904
Sorry, prediction GeneMark_model.106473_t fails validation.
(CTT)	 AG	7885-7904	GT	AGG
(CCC)	 AG	8064-8146	GT	AAG
(CTG)	 AG	8277-8346	GT	CAG
(AAG)	 AG	8392-8403	GA	GAG
-recovered GeneMark_model.106473_t, terminal, 8392, 8403
-recovered GeneMark_model.106473_t, internal, 7885, 7904
-recovered GeneMark_model.106473_t, internal, 8064, 8146
-recovered GeneMark_model.106473_t, internal, 8277, 8346
Couldn't classify 14, 47
Couldn't classify 365, 497
Sorry, prediction GeneMark_model.106474_t fails validation.
(ATC)	 AG	14-47	GT	AGG
(CTG)	 AG	91-99	GT	TGG
(CTT)	 AG	224-286	GT	AGG
(ACC)	 AG	365-497	GT	CGG
-recovered GeneMark_model.106474_t, internal, 14, 47
-recovered GeneMark_model.106474_t, internal, 91, 99
-recovered GeneMark_model.106474_t, internal, 224, 286
-recovered GeneMark_model.106474_t, internal, 365, 497
Valid prediction for Augustus_model.g40732.t1
Couldn't classify 18509, 18634
Sorry, prediction GeneMark_model.106471_t fails validation.
(ATG)	 TT	14986-14996	GT	GTG
(AGA)	 AG	15176-15184	GC	GAG
(AGA)	 AG	15208-15246	GT	GAG
(ACG)	 AG	15444-15459	GT	CAG
(GTC)	 AG	16733-16958	GT	AGG
(GCG)	 AG	17732-17765	GT	GGG
(TGT)	 AG	18085-18111	GT	GAG
(TGT)	 AG	18201-18209	GT	GAG
(TGA)	 AG	18295-18309	GT	GAG
(TGA)	 AG	18331-18345	GT	GGG
(TTG)	 AG	18509-18634	GT	GGG
-recovered GeneMark_model.106471_t, initial, 14986, 14996
add_exon() Sorry, GeneMark_model.106471_t 16733-16958-terminal-3 is invalid.
-recovered GeneMark_model.106471_t, terminal, 16733, 16958
add_exon() Sorry, GeneMark_model.106471_t 18295-18309-terminal-1 is invalid.
-recovered GeneMark_model.106471_t, terminal, 18295, 18309
-recovered GeneMark_model.106471_t, internal, 15176, 15184
-recovered GeneMark_model.106471_t, internal, 15208, 15246
-recovered GeneMark_model.106471_t, internal, 15444, 15459
-recovered GeneMark_model.106471_t, internal, 16733, 16958
-recovered GeneMark_model.106471_t, internal, 17732, 17765
-recovered GeneMark_model.106471_t, internal, 18085, 18111
-recovered GeneMark_model.106471_t, internal, 18201, 18209
-recovered GeneMark_model.106471_t, internal, 18295, 18309
-recovered GeneMark_model.106471_t, internal, 18331, 18345
-recovered GeneMark_model.106471_t, internal, 18509, 18634
Valid prediction for snap_scaffold_84-snap.2-T1
Couldn't classify 224, 286
Sorry, prediction GlimmerHMM_glimmerT_61236-T1 fails validation.
(CTT)	 AG	224-286	GT	AGG
(ACC)	 AG	365-497	GT	CGG
(GTC)	 AG	9223-9329	GT	AGG
(GTC)	 AG	16733-16963	TA	AGT
-recovered GlimmerHMM_glimmerT_61236-T1, terminal, 16733, 16963
-recovered GlimmerHMM_glimmerT_61236-T1, internal, 224, 286
-recovered GlimmerHMM_glimmerT_61236-T1, internal, 365, 497
-recovered GlimmerHMM_glimmerT_61236-T1, internal, 9223, 9329
Valid prediction for Augustus_model.g40731.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2091, rend_intergenic: 1728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18533, rend_intergenic: 2969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 18685
-exon list size: 80


building trellis

1.2    
2.4    
3.7    
4.9    
6.1    
7.3    
8.5    
9.8    
11.0    
12.2    
13.4    
14.6    
15.9    
17.1    
18.3    
19.5    
20.7    
22.0    
23.2    
24.4    
25.6    
26.8    
28.0    
29.3    
30.5    
31.7    
32.9    
34.1    
35.4    
36.6    
37.8    
39.0    
40.2    
41.5    
42.7    
43.9    
45.1    
46.3    
47.6    
48.8    
50.0    
51.2    
52.4    
53.7    
54.9    
56.1    
57.3    
58.5    
59.8    
61.0    
62.2    
63.4    
64.6    
65.9    
67.1    
68.3    
69.5    
70.7    
72.0    
73.2    
74.4    
75.6    
76.8    
78.0    
79.3    
80.5    
81.7    
82.9    
84.1    
85.4    
86.6    
87.8    
89.0    
90.2    
91.5    
92.7    
93.9    
95.1    
96.3    
97.6    
98.8    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 2091, rend_intergenic: 1728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18533, rend_intergenic: 2969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support