-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_3170397-3355295

-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 snap_scaffold_15-snap.715-T1
Valid prediction for GeneMark_model.63026_t
Valid prediction for GeneMark_model.63040_t
Couldn't classify 8655, 8713
Sorry, prediction pasa_asmbl_14856.p1 fails validation.
(AAC)	 GT	8655-8713	GT	AGG
(GTT)	 AG	8949-8967	GT	AGG
(GAG)	 AG	9406-10303	GT	AGG
(GAA)	 AG	10452-10628	GT	GTG
(TGG)	 AG	10750-11150	GG	AGG
-recovered pasa_asmbl_14856.p1, terminal, 10750, 11150
-recovered pasa_asmbl_14856.p1, internal, 8949, 8967
-recovered pasa_asmbl_14856.p1, internal, 9406, 10303
-recovered pasa_asmbl_14856.p1, internal, 10452, 10628
Valid prediction for GlimmerHMM_glimmerT_36607-T1
Valid prediction for GeneMark_model.63024_t
Valid prediction for Augustus_model.g24588.t1
Valid prediction for GeneMark_model.63038_t
Valid prediction for snap_scaffold_15-snap.701-T1
Valid prediction for snap_scaffold_15-snap.709-T1
Valid prediction for snap_scaffold_15-snap.697-T1
Valid prediction for GlimmerHMM_glimmerT_36623-T1
Valid prediction for GeneMark_model.63036_t
Valid prediction for GlimmerHMM_glimmerT_36609-T1
Valid prediction for snap_scaffold_15-snap.712-T1
Valid prediction for GeneMark_model.63016_t
Couldn't classify 20774, 20883
Couldn't classify 22136, 22232
Sorry, prediction pasa_asmbl_14036.p1 fails validation.
(GCA)	 AG	20774-20883	GT	AGG
(GAA)	 AG	21769-21894	GT	AAG
(GTA)	 AG	22136-22232	AC	ACA
-recovered pasa_asmbl_14036.p1, internal, 20774, 20883
-recovered pasa_asmbl_14036.p1, internal, 21769, 21894
Valid prediction for snap_scaffold_15-snap.717-T1
Valid prediction for GeneMark_model.63005_t
Valid prediction for GeneMark_model.63011_t
Valid prediction for snap_scaffold_15-snap.711-T1
Valid prediction for Augustus_model.g24594.t1
Valid prediction for Augustus_model.g24593.t1
Valid prediction for snap_scaffold_15-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_36611-T1
Valid prediction for snap_scaffold_15-snap.716-T1
Valid prediction for Augustus_model.g24592.t1
Valid prediction for GeneMark_model.63021_t
Valid prediction for GeneMark_model.63001_t
Valid prediction for GeneMark_model.63003_t
Valid prediction for snap_scaffold_15-snap.695-T1
Valid prediction for snap_scaffold_15-snap.694-T1
Valid prediction for GeneMark_model.63031_t
Valid prediction for snap_scaffold_15-snap.704-T1
Valid prediction for GeneMark_model.63018_t
Valid prediction for Augustus_model.g24584.t1
Valid prediction for snap_scaffold_15-snap.706-T1
Valid prediction for Augustus_model.g24586.t1
Valid prediction for snap_scaffold_15-snap.720-T1
Valid prediction for snap_scaffold_15-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_36608-T1
Valid prediction for GeneMark_model.63009_t
Valid prediction for GeneMark_model.63012_t
Valid prediction for GeneMark_model.63008_t
Valid prediction for GlimmerHMM_glimmerT_36614-T1
Valid prediction for GlimmerHMM_glimmerT_36622-T1
Valid prediction for GlimmerHMM_glimmerT_36616-T1
Valid prediction for GeneMark_model.63034_t
Valid prediction for GeneMark_model.63030_t
Valid prediction for Augustus_model.g24585.t1
Valid prediction for snap_scaffold_15-snap.702-T1
Valid prediction for snap_scaffold_15-snap.705-T1

-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 GeneMark_model.63025_t
Valid prediction for snap_scaffold_15-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_36618-T1
Valid prediction for snap_scaffold_15-snap.718-T1
Valid prediction for GeneMark_model.63007_t
Valid prediction for snap_scaffold_15-snap.698-T1
Valid prediction for GeneMark_model.63014_t
Valid prediction for GeneMark_model.63004_t
Valid prediction for GeneMark_model.63022_t
Valid prediction for GeneMark_model.63037_t
Valid prediction for Augustus_model.g24589.t1
Valid prediction for CodingQuarry_transcript_17910-T1
Valid prediction for GeneMark_model.63023_t
Valid prediction for GlimmerHMM_glimmerT_36615-T1
Valid prediction for snap_scaffold_15-snap.707-T1
Valid prediction for snap_scaffold_15-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_36617-T1
Valid prediction for GlimmerHMM_glimmerT_36613-T1
Valid prediction for snap_scaffold_15-snap.713-T1
Valid prediction for GeneMark_model.63041_t
Valid prediction for GeneMark_model.63035_t
Valid prediction for GeneMark_model.63027_t
Valid prediction for GeneMark_model.63029_t
Valid prediction for GlimmerHMM_glimmerT_36620-T1
Valid prediction for GeneMark_model.63033_t
Valid prediction for snap_scaffold_15-snap.703-T1
Valid prediction for snap_scaffold_15-snap.699-T1
Couldn't classify 543, 659
Sorry, prediction pasa_asmbl_15943.p2 fails validation.
(GGT)	 CA	543-659	GT	ACG
(GTA)	 AG	2790-2905	GT	AGG
(GTG)	 AG	3059-3190	GT	CGG
(GGT)	 AG	3589-3736	GT	AGG
(ACT)	 AG	5728-5895	GT	AGG
(GAC)	 AG	8544-8672	AC	AGA
-recovered pasa_asmbl_15943.p2, terminal, 8544, 8672
-recovered pasa_asmbl_15943.p2, internal, 2790, 2905
-recovered pasa_asmbl_15943.p2, internal, 3059, 3190
-recovered pasa_asmbl_15943.p2, internal, 3589, 3736
-recovered pasa_asmbl_15943.p2, internal, 5728, 5895
Valid prediction for GlimmerHMM_glimmerT_36612-T1
Valid prediction for GeneMark_model.63019_t
Valid prediction for Augustus_model.g24591.t1
Valid prediction for GeneMark_model.63020_t
Valid prediction for GeneMark_model.63006_t
Valid prediction for snap_scaffold_15-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_36621-T1
Valid prediction for GlimmerHMM_glimmerT_36619-T1
Valid prediction for snap_scaffold_15-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_36610-T1
Valid prediction for GlimmerHMM_glimmerT_36606-T1
Valid prediction for Augustus_model.g24587.t1
Valid prediction for snap_scaffold_15-snap.692-T1
Valid prediction for Augustus_model.g24583.t1
Valid prediction for GeneMark_model.63028_t
Valid prediction for Augustus_model.g24590.t1
Valid prediction for snap_scaffold_15-snap.721-T1
Valid prediction for GeneMark_model.63039_t
Valid prediction for GeneMark_model.63017_t
Valid prediction for GeneMark_model.63002_t
Valid prediction for GeneMark_model.63010_t
Valid prediction for GeneMark_model.63013_t
Valid prediction for snap_scaffold_15-snap.700-T1
Valid prediction for GeneMark_model.63015_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51865, rend_intergenic: 37801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158979, rend_intergenic: 155494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184899
-exon list size: 491


building trellis

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27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
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29.0    
29.2    
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29.6    
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30.4    
30.6    
30.8    
31.0    
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31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
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41.8    
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42.2    
42.4    
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43.6    
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44.0    
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44.4    
44.6    
44.8    
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46.0    
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47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
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49.9    
50.1    
50.3    
50.5    
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50.9    
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51.3    
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51.9    
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52.3    
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54.0    
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54.4    
54.6    
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55.0    
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56.0    
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56.6    
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57.2    
57.4    
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58.4    
58.6    
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59.0    
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60.2    
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60.9    
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61.3    
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61.9    
62.1    
62.3    
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62.9    
63.1    
63.3    
63.5    
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63.9    
64.1    
64.3    
64.5    
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64.9    
65.1    
65.3    
65.5    
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65.9    
66.1    
66.3    
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66.7    
66.9    
67.1    
67.3    
67.5    
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68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
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69.6    
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73.6    
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74.2    
74.4    
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74.8    
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75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
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77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 51865, rend_intergenic: 37801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158979, rend_intergenic: 155494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support