-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_236

-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.107030_t
Valid prediction for GeneMark_model.107032_t
Valid prediction for GlimmerHMM_glimmerT_61550-T1
Valid prediction for GlimmerHMM_glimmerT_61551-T1
Couldn't classify 222, 239
Sorry, prediction GeneMark_model.107028_t fails validation.
(AAA)	 AG	222-239	GT	AGG
(GGA)	 AG	838-987	GT	GAG
(AGG)	 AG	1024-1059	GT	TGG
(GCT)	 AG	1971-2306	GT	AGG
(AGA)	 AG	2331-2366	GT	GAG
(AGA)	 AG	2399-2452	GT	GAG
(GGA)	 AG	2490-2607	AC	AAA
-recovered GeneMark_model.107028_t, terminal, 2490, 2607
-recovered GeneMark_model.107028_t, internal, 222, 239
-recovered GeneMark_model.107028_t, internal, 838, 987
-recovered GeneMark_model.107028_t, internal, 1024, 1059
-recovered GeneMark_model.107028_t, internal, 1971, 2306
-recovered GeneMark_model.107028_t, internal, 2331, 2366
-recovered GeneMark_model.107028_t, internal, 2399, 2452
Couldn't classify 1931, 2306
Couldn't classify 7998, 8023
Sorry, prediction snap_scaffold_236-snap.1-T1 fails validation.
(GAT)	 AG	1931-2306	GT	AGG
(ATG)	 AG	2376-2603	GT	AGG
(GAT)	 AG	7998-8023	GT	TTG
add_exon() Sorry, snap_scaffold_236-snap.1-T1 2376-2603-initial-1 is invalid.
-recovered snap_scaffold_236-snap.1-T1, initial, 2376, 2603
add_exon() Sorry, snap_scaffold_236-snap.1-T1 2376-2603-terminal-1 is invalid.
-recovered snap_scaffold_236-snap.1-T1, terminal, 2376, 2603
-recovered snap_scaffold_236-snap.1-T1, internal, 1931, 2306
-recovered snap_scaffold_236-snap.1-T1, internal, 2376, 2603
-recovered snap_scaffold_236-snap.1-T1, internal, 7998, 8023

-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 Augustus_model.g40930.t1
Valid prediction for GeneMark_model.107029_t
Couldn't classify 1130, 1166
Couldn't classify 7108, 7276
Sorry, prediction snap_scaffold_236-snap.2-T1 fails validation.
(CCC)	 AG	1130-1166	GT	TAG
(CTG)	 AG	5666-5751	GT	AGG
(GTC)	 AG	6047-6052	GT	CGG
(GAC)	 AG	7108-7276	GT	AGG
-recovered snap_scaffold_236-snap.2-T1, internal, 1130, 1166
-recovered snap_scaffold_236-snap.2-T1, internal, 5666, 5751
-recovered snap_scaffold_236-snap.2-T1, internal, 6047, 6052
-recovered snap_scaffold_236-snap.2-T1, internal, 7108, 7276
Valid prediction for GeneMark_model.107031_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8023, rend_intergenic: 1964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9239
-exon list size: 53


building trellis

1.8    
3.6    
5.5    
7.3    
9.1    
10.9    
12.7    
14.5    
16.4    
18.2    
20.0    
21.8    
23.6    
25.5    
27.3    
29.1    
30.9    
32.7    
34.5    
36.4    
38.2    
40.0    
41.8    
43.6    
45.5    
47.3    
49.1    
50.9    
52.7    
54.5    
56.4    
58.2    
60.0    
61.8    
63.6    
65.5    
67.3    
69.1    
70.9    
72.7    
74.5    
76.4    
78.2    
80.0    
81.8    
83.6    
85.5    
87.3    
89.1    
90.9    
92.7    
94.5    
96.4    
98.2    
-found 4 predictions from path traversal
Error with prediction: snap lend_intergenic: 8023, rend_intergenic: 1964  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