-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_194

-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 GlimmerHMM_glimmerT_61483-T1
Couldn't classify 9585, 9714
Sorry, prediction GeneMark_model.106897_t fails validation.
(ATG)	 TG	9076-9084	GT	ATG
(GAG)	 AG	9133-9244	GT	AGG
(GGT)	 AG	9285-9300	GT	GTG
(GTC)	 AG	9585-9714	GT	AGG
-recovered GeneMark_model.106897_t, initial, 9076, 9084
-recovered GeneMark_model.106897_t, internal, 9133, 9244
-recovered GeneMark_model.106897_t, internal, 9285, 9300
-recovered GeneMark_model.106897_t, internal, 9585, 9714
Valid prediction for GlimmerHMM_glimmerT_61481-T1
Valid prediction for pasa_asmbl_22786.p2
Valid prediction for snap_scaffold_194-snap.3-T1
Couldn't classify 9617, 9714
Sorry, prediction Augustus_model.g40891.t1 fails validation.
(ATG)	 CC	8503-8659	GT	AGG
(GAA)	 AG	9116-9244	GT	AGG
(GCC)	 AG	9617-9714	GT	AGG
-recovered Augustus_model.g40891.t1, initial, 8503, 8659
-recovered Augustus_model.g40891.t1, internal, 9116, 9244
-recovered Augustus_model.g40891.t1, internal, 9617, 9714
Valid prediction for CodingQuarry_transcript_25862-T1
Couldn't classify 9617, 9714
Sorry, prediction snap_scaffold_194-snap.5-T1 fails validation.
(ATG)	 CC	8503-8659	GT	AGG
(GAA)	 AG	9116-9244	GT	AGG
(GCC)	 AG	9617-9714	GT	AGG
-recovered snap_scaffold_194-snap.5-T1, initial, 8503, 8659
-recovered snap_scaffold_194-snap.5-T1, internal, 9116, 9244
-recovered snap_scaffold_194-snap.5-T1, internal, 9617, 9714
Valid prediction for Augustus_model.g40888.t1
Couldn't classify 83, 211
Sorry, prediction snap_scaffold_194-snap.2-T1 fails validation.
(GAA)	 AG	83-211	GT	AGG
(GCC)	 AG	906-1003	GT	AGG
(ATT)	 AG	1349-1475	GT	ACG
(TGG)	 AG	1829-1923	GT	AGG
(AAC)	 AG	2000-2180	GT	AGG
(GAG)	 AG	2347-2459	CA	GAC
-recovered snap_scaffold_194-snap.2-T1, terminal, 2347, 2459
-recovered snap_scaffold_194-snap.2-T1, internal, 83, 211
-recovered snap_scaffold_194-snap.2-T1, internal, 906, 1003
-recovered snap_scaffold_194-snap.2-T1, internal, 1349, 1475
-recovered snap_scaffold_194-snap.2-T1, internal, 1829, 1923
-recovered snap_scaffold_194-snap.2-T1, internal, 2000, 2180
Couldn't classify 83, 211
Sorry, prediction GeneMark_model.106892_t fails validation.
(GAA)	 AG	83-211	GT	AGG
(GCC)	 AG	906-1003	GT	AGG
(ATT)	 AG	1349-1475	GT	ACG
(TGG)	 AG	1829-1923	GT	AGG
(AAC)	 AG	2000-2180	GT	AGG
(GAG)	 AG	2347-2459	CA	GAC
-recovered GeneMark_model.106892_t, terminal, 2347, 2459
-recovered GeneMark_model.106892_t, internal, 83, 211
-recovered GeneMark_model.106892_t, internal, 906, 1003
-recovered GeneMark_model.106892_t, internal, 1349, 1475
-recovered GeneMark_model.106892_t, internal, 1829, 1923
-recovered GeneMark_model.106892_t, internal, 2000, 2180
Couldn't classify 83, 211
Sorry, prediction Augustus_model.g40887.t1 fails validation.
(GAA)	 AG	83-211	GT	AGG
(GCC)	 AG	906-1003	GT	AGG
(ATT)	 AG	1349-1475	GT	ACG
(TGG)	 AG	1829-1923	GT	AGG
(AAC)	 AG	2000-2180	GT	AGG
(GAG)	 AG	2347-2459	CA	GAC
-recovered Augustus_model.g40887.t1, terminal, 2347, 2459
-recovered Augustus_model.g40887.t1, internal, 83, 211
-recovered Augustus_model.g40887.t1, internal, 906, 1003
-recovered Augustus_model.g40887.t1, internal, 1349, 1475
-recovered Augustus_model.g40887.t1, internal, 1829, 1923
-recovered Augustus_model.g40887.t1, internal, 2000, 2180

-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 snap_scaffold_194-snap.4-T1
Valid prediction for snap_scaffold_194-snap.1-T1
Valid prediction for GeneMark_model.106893_t
Valid prediction for GeneMark_model.106895_t
Valid prediction for Augustus_model.g40889.t1
Valid prediction for GlimmerHMM_glimmerT_61484-T1
Valid prediction for GlimmerHMM_glimmerT_61482-T1
Valid prediction for GlimmerHMM_glimmerT_61485-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g40890.t1
Couldn't classify 248, 348
Sorry, prediction GlimmerHMM_glimmerT_61486-T1 fails validation.
(AAT)	 AG	248-348	GT	CAG
(GTG)	 AG	1457-1786	AC	GAA
-recovered GlimmerHMM_glimmerT_61486-T1, terminal, 1457, 1786
-recovered GlimmerHMM_glimmerT_61486-T1, internal, 248, 348

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3417, rend_intergenic: 83  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9942
-exon list size: 57


building trellis

1.7    
3.4    
5.1    
6.8    
8.5    
10.2    
11.9    
13.6    
15.3    
16.9    
18.6    
20.3    
22.0    
23.7    
25.4    
27.1    
28.8    
30.5    
32.2    
33.9    
35.6    
37.3    
39.0    
40.7    
42.4    
44.1    
45.8    
47.5    
49.2    
50.8    
52.5    
54.2    
55.9    
57.6    
59.3    
61.0    
62.7    
64.4    
66.1    
67.8    
69.5    
71.2    
72.9    
74.6    
76.3    
78.0    
79.7    
81.4    
83.1    
84.7    
86.4    
88.1    
89.8    
91.5    
93.2    
94.9    
96.6    
98.3    
-found 8 predictions from path traversal
Error with prediction: snap lend_intergenic: 3417, rend_intergenic: 83  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support