-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_1-205165

-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_3-snap.18-T1
Valid prediction for snap_scaffold_3-snap.32-T1
Valid prediction for Augustus_model.g3923.t1
Valid prediction for snap_scaffold_3-snap.20-T1
Valid prediction for GlimmerHMM_glimmerT_5960-T1
Valid prediction for snap_scaffold_3-snap.42-T1
Valid prediction for snap_scaffold_3-snap.14-T1
Valid prediction for GeneMark_model.9680_t
Valid prediction for GlimmerHMM_glimmerT_5955-T1
Valid prediction for GeneMark_model.9687_t
Valid prediction for GlimmerHMM_glimmerT_5958-T1
Valid prediction for GeneMark_model.9745_t
Valid prediction for GlimmerHMM_glimmerT_5959-T1
Valid prediction for GlimmerHMM_glimmerT_5936-T1
Valid prediction for snap_scaffold_3-snap.12-T1
Valid prediction for HiQ_model.g3918.t1
Valid prediction for GeneMark_model.9703_t
Valid prediction for GeneMark_model.9722_t
Valid prediction for GlimmerHMM_glimmerT_5934-T1
Valid prediction for GeneMark_model.9717_t
Valid prediction for snap_scaffold_3-snap.15-T1
Valid prediction for GlimmerHMM_glimmerT_5940-T1
Valid prediction for snap_scaffold_3-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_5953-T1
Valid prediction for snap_scaffold_3-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_5935-T1
Valid prediction for GeneMark_model.9681_t
Valid prediction for GeneMark_model.9732_t
Valid prediction for snap_scaffold_3-snap.7-T1
Valid prediction for snap_scaffold_3-snap.22-T1
Valid prediction for snap_scaffold_3-snap.26-T1
Valid prediction for GeneMark_model.9707_t
Valid prediction for snap_scaffold_3-snap.36-T1
Valid prediction for GeneMark_model.9731_t
Valid prediction for GeneMark_model.9734_t
Valid prediction for GlimmerHMM_glimmerT_5937-T1
Valid prediction for GeneMark_model.9713_t
Valid prediction for GlimmerHMM_glimmerT_5949-T1
Valid prediction for GeneMark_model.9748_t
Valid prediction for GlimmerHMM_glimmerT_5946-T1
Valid prediction for snap_scaffold_3-snap.34-T1
Valid prediction for GeneMark_model.9725_t
Valid prediction for GeneMark_model.9698_t
Valid prediction for GeneMark_model.9744_t
Valid prediction for GeneMark_model.9700_t
Valid prediction for CodingQuarry_transcript_45948-T1
Valid prediction for snap_scaffold_3-snap.30-T1
Valid prediction for GeneMark_model.9740_t
Valid prediction for snap_scaffold_3-snap.40-T1
Valid prediction for GeneMark_model.9741_t
Valid prediction for Augustus_model.g3919.t1
Valid prediction for GeneMark_model.9730_t
Valid prediction for GeneMark_model.9696_t
Valid prediction for GlimmerHMM_glimmerT_5954-T1
Valid prediction for GeneMark_model.9716_t
Valid prediction for GeneMark_model.9709_t
Valid prediction for snap_scaffold_3-snap.6-T1
Valid prediction for GeneMark_model.9683_t
Valid prediction for snap_scaffold_3-snap.37-T1
Valid prediction for GeneMark_model.9691_t
Valid prediction for GlimmerHMM_glimmerT_5948-T1
Valid prediction for Augustus_model.g3922.t1
Valid prediction for snap_scaffold_3-snap.39-T1
Valid prediction for snap_scaffold_3-snap.4-T1
Valid prediction for pasa_asmbl_39760.p1
Valid prediction for GeneMark_model.9742_t
Valid prediction for GeneMark_model.9746_t
Valid prediction for GeneMark_model.9711_t
Valid prediction for GeneMark_model.9685_t
Valid prediction for GlimmerHMM_glimmerT_5945-T1
Valid prediction for snap_scaffold_3-snap.24-T1
Valid prediction for Augustus_model.g3920.t1
Valid prediction for GeneMark_model.9690_t
Valid prediction for GeneMark_model.9714_t
Valid prediction for GeneMark_model.9738_t
Valid prediction for GeneMark_model.9729_t
Valid prediction for Augustus_model.g3924.t1
Valid prediction for GeneMark_model.9694_t
Valid prediction for Augustus_model.g3915.t1
Valid prediction for GlimmerHMM_glimmerT_5942-T1
Valid prediction for GeneMark_model.9727_t
Valid prediction for snap_scaffold_3-snap.8-T1
Valid prediction for snap_scaffold_3-snap.9-T1
Valid prediction for GeneMark_model.9688_t
Valid prediction for GlimmerHMM_glimmerT_5933-T1
Valid prediction for GeneMark_model.9736_t
Valid prediction for GlimmerHMM_glimmerT_5944-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 snap_scaffold_3-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_5938-T1
Valid prediction for snap_scaffold_3-snap.25-T1
Valid prediction for GeneMark_model.9702_t
Valid prediction for snap_scaffold_3-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_5947-T1
Valid prediction for Augustus_model.g3916.t1
Valid prediction for snap_scaffold_3-snap.35-T1
Valid prediction for GeneMark_model.9695_t
Valid prediction for snap_scaffold_3-snap.16-T1
Valid prediction for GeneMark_model.9728_t
Valid prediction for snap_scaffold_3-snap.41-T1
Valid prediction for snap_scaffold_3-snap.3-T1
Valid prediction for GeneMark_model.9749_t
Valid prediction for GeneMark_model.9735_t
Valid prediction for GeneMark_model.9682_t
Valid prediction for GlimmerHMM_glimmerT_5939-T1
Valid prediction for GeneMark_model.9708_t
Couldn't classify 204078, 204197
Sorry, prediction GeneMark_model.9679_t fails validation.
(ATG)	 TG	203824-203828	GT	CTG
(AGG)	 AG	204002-204010	GT	AGG
(AGA)	 AG	204031-204054	GT	CAG
(TGA)	 AG	204078-204197	GT	CAG
-recovered GeneMark_model.9679_t, initial, 203824, 203828
-recovered GeneMark_model.9679_t, internal, 204002, 204010
-recovered GeneMark_model.9679_t, internal, 204031, 204054
-recovered GeneMark_model.9679_t, internal, 204078, 204197
Valid prediction for snap_scaffold_3-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_5956-T1
Valid prediction for snap_scaffold_3-snap.1-T1
Valid prediction for GeneMark_model.9693_t
Valid prediction for GeneMark_model.9723_t
Valid prediction for GeneMark_model.9720_t
Valid prediction for GeneMark_model.9726_t
Valid prediction for Augustus_model.g3917.t1
Valid prediction for snap_scaffold_3-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_5950-T1
Valid prediction for GeneMark_model.9699_t
Valid prediction for snap_scaffold_3-snap.2-T1
Valid prediction for GeneMark_model.9686_t
Valid prediction for GlimmerHMM_glimmerT_5941-T1
Valid prediction for GeneMark_model.9739_t
Valid prediction for GlimmerHMM_glimmerT_5951-T1
Valid prediction for snap_scaffold_3-snap.13-T1
Valid prediction for GeneMark_model.9705_t
Valid prediction for GeneMark_model.9684_t
Valid prediction for GeneMark_model.9689_t
Valid prediction for GeneMark_model.9697_t
Valid prediction for GeneMark_model.9721_t
Valid prediction for snap_scaffold_3-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_5943-T1
Valid prediction for GeneMark_model.9724_t
Valid prediction for GeneMark_model.9743_t
Valid prediction for GeneMark_model.9718_t
Valid prediction for snap_scaffold_3-snap.23-T1
Valid prediction for GeneMark_model.9733_t
Valid prediction for Augustus_model.g3921.t1
Valid prediction for snap_scaffold_3-snap.31-T1
Valid prediction for GeneMark_model.9737_t
Valid prediction for snap_scaffold_3-snap.5-T1
Valid prediction for GeneMark_model.9706_t
Valid prediction for snap_scaffold_3-snap.29-T1
Valid prediction for GeneMark_model.9747_t
Valid prediction for GlimmerHMM_glimmerT_5957-T1
Valid prediction for GlimmerHMM_glimmerT_5952-T1
Valid prediction for snap_scaffold_3-snap.28-T1
Valid prediction for snap_scaffold_3-snap.43-T1
Valid prediction for GeneMark_model.9692_t
Valid prediction for GeneMark_model.9710_t
Valid prediction for GeneMark_model.9715_t
Valid prediction for snap_scaffold_3-snap.17-T1
Valid prediction for GeneMark_model.9704_t
Valid prediction for GeneMark_model.9712_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22807, rend_intergenic: 18160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28932, rend_intergenic: 24060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36759, rend_intergenic: 30423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43595, rend_intergenic: 37294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50892, rend_intergenic: 47190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67830, rend_intergenic: 51812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100309, rend_intergenic: 91889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107518, rend_intergenic: 100342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132604, rend_intergenic: 121445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137388, rend_intergenic: 135783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142798, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151966, rend_intergenic: 142884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157127, rend_intergenic: 152108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160068, rend_intergenic: 158465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163478, rend_intergenic: 160973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172108, rend_intergenic: 164771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186716, rend_intergenic: 178887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198852, rend_intergenic: 197768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202157, rend_intergenic: 199405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205165
-exon list size: 850


building trellis

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81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 22807, rend_intergenic: 18160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28932, rend_intergenic: 24060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36759, rend_intergenic: 30423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43595, rend_intergenic: 37294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50892, rend_intergenic: 47190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67830, rend_intergenic: 51812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100309, rend_intergenic: 91889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107518, rend_intergenic: 100342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132604, rend_intergenic: 121445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137388, rend_intergenic: 135783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142798, rend_intergenic: 139510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151966, rend_intergenic: 142884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157127, rend_intergenic: 152108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160068, rend_intergenic: 158465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163478, rend_intergenic: 160973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172108, rend_intergenic: 164771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186716, rend_intergenic: 178887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198852, rend_intergenic: 197768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202157, rend_intergenic: 199405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18193
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support