-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_178

-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.106837_t
Valid prediction for GeneMark_model.106839_t
Couldn't classify 112, 188
Sorry, prediction snap_scaffold_178-snap.1-T1 fails validation.
(ATC)	 AG	112-188	GT	AGG
(ACA)	 AG	1739-1755	GT	CTG
(ATG)	 AG	1899-2112	GT	TCG
(AGG)	 AG	2229-2307	GT	TGG
(GAG)	 AG	2321-2467	GT	CAG
(CGC)	 AG	2916-2977	GT	TGG
(TTG)	 AG	3216-3386	GT	GGG
(TCA)	 AG	4659-4803	GT	CAG
(AAA)	 AG	4907-5424	GT	CGG
(GAC)	 AG	5611-5793	CC	AGC
add_exon() Sorry, snap_scaffold_178-snap.1-T1 1899-2112-initial-1 is invalid.
-recovered snap_scaffold_178-snap.1-T1, initial, 1899, 2112
-recovered snap_scaffold_178-snap.1-T1, terminal, 5611, 5793
-recovered snap_scaffold_178-snap.1-T1, internal, 112, 188
-recovered snap_scaffold_178-snap.1-T1, internal, 1739, 1755
-recovered snap_scaffold_178-snap.1-T1, internal, 1899, 2112
-recovered snap_scaffold_178-snap.1-T1, internal, 2229, 2307
-recovered snap_scaffold_178-snap.1-T1, internal, 2321, 2467
-recovered snap_scaffold_178-snap.1-T1, internal, 2916, 2977
-recovered snap_scaffold_178-snap.1-T1, internal, 3216, 3386
-recovered snap_scaffold_178-snap.1-T1, internal, 4659, 4803
-recovered snap_scaffold_178-snap.1-T1, internal, 4907, 5424

-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 10389, 10567
Sorry, prediction Augustus_model.g40872.t1 fails validation.
(ATG)	 AG	3429-3897	GT	AGG
(AAC)	 AG	4155-4277	GT	GGG
(ATC)	 AG	4492-5138	GT	AGG
(GTG)	 AG	6458-6595	GT	AAG
(CGC)	 AG	7177-7319	GT	CGG
(GTC)	 AG	7497-7664	GT	GGG
(GGA)	 AG	8240-8348	GT	AGG
(TGT)	 AG	8438-9952	GT	AAG
(GTA)	 AG	10389-10567		AG
-recovered Augustus_model.g40872.t1, initial, 3429, 3897
-recovered Augustus_model.g40872.t1, internal, 3429, 3897
-recovered Augustus_model.g40872.t1, internal, 4155, 4277
-recovered Augustus_model.g40872.t1, internal, 4492, 5138
-recovered Augustus_model.g40872.t1, internal, 6458, 6595
-recovered Augustus_model.g40872.t1, internal, 7177, 7319
-recovered Augustus_model.g40872.t1, internal, 7497, 7664
-recovered Augustus_model.g40872.t1, internal, 8240, 8348
-recovered Augustus_model.g40872.t1, internal, 8438, 9952
Valid prediction for GeneMark_model.106838_t
Couldn't classify 7585, 7664
Couldn't classify 8438, 9277
Sorry, prediction pasa_asmbl_19595.p1 fails validation.
(GCT)	 AC	7585-7664	GT	GGG
(GGA)	 AG	8240-8348	GT	AGG
(TGT)	 AG	8438-9277	AG	GGA
-recovered pasa_asmbl_19595.p1, internal, 8240, 8348
Valid prediction for snap_scaffold_178-snap.4-T1
add_exon() Sorry, snap_scaffold_178-snap.4-T1 1521-2064-terminal-1 is invalid.
Valid prediction for GeneMark_model.106840_t
Valid prediction for snap_scaffold_178-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61456-T1
Valid prediction for pasa_asmbl_19594.p1
Couldn't classify 10455, 10551
Sorry, prediction GeneMark_model.106836_t fails validation.
(ATG)	 GG	8394-8408	GT	CGG
(TGT)	 AG	8438-9952	GT	AAG
(ATC)	 AG	10455-10551	GC	CTG
-recovered GeneMark_model.106836_t, initial, 8394, 8408
-recovered GeneMark_model.106836_t, internal, 8438, 9952
-recovered GeneMark_model.106836_t, internal, 10455, 10551
Couldn't classify 8438, 9952
Sorry, prediction snap_scaffold_178-snap.2-T1 fails validation.
(ATG)	 TG	5860-5934	GT	CAG
(GTG)	 AG	6458-6595	GT	AAG
(CCT)	 AG	7132-7319	GT	CGG
(GTC)	 AG	7497-7664	GT	GGG
(GGA)	 AG	8240-8348	GT	AGG
(TGT)	 AG	8438-9952	GT	AAG
-recovered snap_scaffold_178-snap.2-T1, initial, 5860, 5934
-recovered snap_scaffold_178-snap.2-T1, internal, 6458, 6595
-recovered snap_scaffold_178-snap.2-T1, internal, 7132, 7319
-recovered snap_scaffold_178-snap.2-T1, internal, 7497, 7664
-recovered snap_scaffold_178-snap.2-T1, internal, 8240, 8348
-recovered snap_scaffold_178-snap.2-T1, internal, 8438, 9952

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5793, rend_intergenic: 616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 10567
-exon list size: 56


building trellis

1.7    
3.4    
5.2    
6.9    
8.6    
10.3    
12.1    
13.8    
15.5    
17.2    
19.0    
20.7    
22.4    
24.1    
25.9    
27.6    
29.3    
31.0    
32.8    
34.5    
36.2    
37.9    
39.7    
41.4    
43.1    
44.8    
46.6    
48.3    
50.0    
51.7    
53.4    
55.2    
56.9    
58.6    
60.3    
62.1    
63.8    
65.5    
67.2    
69.0    
70.7    
72.4    
74.1    
75.9    
77.6    
79.3    
81.0    
82.8    
84.5    
86.2    
87.9    
89.7    
91.4    
93.1    
94.8    
96.6    
98.3    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5793, rend_intergenic: 616  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