-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_8941148-9166669

-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.30662_t
Valid prediction for Augustus_model.g12304.t1
Valid prediction for GeneMark_model.30646_t
Valid prediction for GeneMark_model.30656_t
Valid prediction for snap_scaffold_7-snap.1811-T1
Valid prediction for snap_scaffold_7-snap.1789-T1
Valid prediction for snap_scaffold_7-snap.1800-T1
Valid prediction for snap_scaffold_7-snap.1802-T1
Valid prediction for snap_scaffold_7-snap.1810-T1
Valid prediction for snap_scaffold_7-snap.1801-T1
Valid prediction for snap_scaffold_7-snap.1799-T1
Valid prediction for Augustus_model.g12311.t1
Valid prediction for GlimmerHMM_glimmerT_18284-T1
Valid prediction for snap_scaffold_7-snap.1783-T1
Valid prediction for snap_scaffold_7-snap.1780-T1
Valid prediction for Augustus_model.g12306.t1
Valid prediction for GeneMark_model.30654_t
Valid prediction for snap_scaffold_7-snap.1787-T1
Valid prediction for GeneMark_model.30641_t
Valid prediction for GeneMark_model.30638_t
Valid prediction for GlimmerHMM_glimmerT_18277-T1
Valid prediction for snap_scaffold_7-snap.1785-T1
Valid prediction for snap_scaffold_7-snap.1798-T1
Valid prediction for GeneMark_model.30652_t
Valid prediction for snap_scaffold_7-snap.1792-T1
Valid prediction for Augustus_model.g12310.t1
Valid prediction for GeneMark_model.30645_t
Valid prediction for GeneMark_model.30665_t
Couldn't classify 215730, 215883
Couldn't classify 219649, 219774
Sorry, prediction pasa_asmbl_51499.p1 fails validation.
(CCC)	 GT	215730-215883	GT	AGG
(GCT)	 AG	216957-217018	GT	CGG
(AAC)	 AG	219649-219774	TA	CCT
-recovered pasa_asmbl_51499.p1, internal, 216957, 217018
Valid prediction for GeneMark_model.30664_t
Valid prediction for GlimmerHMM_glimmerT_18288-T1
Valid prediction for GlimmerHMM_glimmerT_18287-T1
Valid prediction for snap_scaffold_7-snap.1805-T1
Valid prediction for snap_scaffold_7-snap.1784-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.1777-T1
Valid prediction for GeneMark_model.30659_t
Valid prediction for snap_scaffold_7-snap.1809-T1
Valid prediction for GeneMark_model.30637_t
Valid prediction for snap_scaffold_7-snap.1782-T1
Valid prediction for GeneMark_model.30651_t
Valid prediction for snap_scaffold_7-snap.1807-T1
Valid prediction for GeneMark_model.30635_t
Valid prediction for snap_scaffold_7-snap.1776-T1
Valid prediction for GeneMark_model.30636_t
Valid prediction for GeneMark_model.30648_t
Valid prediction for GeneMark_model.30633_t
Valid prediction for GeneMark_model.30668_t
Valid prediction for GeneMark_model.30640_t
Valid prediction for GeneMark_model.30650_t

-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_7-snap.1781-T1
Valid prediction for Augustus_model.g12305.t1
Valid prediction for GlimmerHMM_glimmerT_18275-T1
Valid prediction for snap_scaffold_7-snap.1790-T1
Valid prediction for GeneMark_model.30666_t
Valid prediction for GeneMark_model.30639_t
Valid prediction for GeneMark_model.30661_t
Valid prediction for GeneMark_model.30653_t
Valid prediction for snap_scaffold_7-snap.1779-T1
Valid prediction for Augustus_model.g12307.t1
Valid prediction for Augustus_model.g12308.t1
Valid prediction for GeneMark_model.30647_t
Valid prediction for GlimmerHMM_glimmerT_18282-T1
Valid prediction for pasa_asmbl_49853.p1
Valid prediction for GeneMark_model.30631_t
Valid prediction for snap_scaffold_7-snap.1808-T1
Valid prediction for snap_scaffold_7-snap.1788-T1
Valid prediction for snap_scaffold_7-snap.1796-T1
Valid prediction for GeneMark_model.30657_t
Valid prediction for GeneMark_model.30667_t
Valid prediction for GlimmerHMM_glimmerT_18279-T1
Valid prediction for GeneMark_model.30642_t
Valid prediction for GlimmerHMM_glimmerT_18285-T1
Valid prediction for GlimmerHMM_glimmerT_18286-T1
Valid prediction for GeneMark_model.30658_t
Valid prediction for GeneMark_model.30643_t
Valid prediction for Augustus_model.g12309.t1
Valid prediction for GlimmerHMM_glimmerT_18278-T1
Valid prediction for GlimmerHMM_glimmerT_18276-T1
Valid prediction for snap_scaffold_7-snap.1804-T1
Valid prediction for GeneMark_model.30660_t
Valid prediction for snap_scaffold_7-snap.1806-T1
Valid prediction for snap_scaffold_7-snap.1791-T1
Valid prediction for snap_scaffold_7-snap.1778-T1
Valid prediction for CodingQuarry_transcript_57434-T1
Valid prediction for GlimmerHMM_glimmerT_18281-T1
Valid prediction for GeneMark_model.30655_t
Valid prediction for snap_scaffold_7-snap.1803-T1
Valid prediction for snap_scaffold_7-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_18280-T1
Valid prediction for GlimmerHMM_glimmerT_18283-T1
Valid prediction for GeneMark_model.30634_t
Valid prediction for snap_scaffold_7-snap.1793-T1
Valid prediction for snap_scaffold_7-snap.1786-T1
Valid prediction for GeneMark_model.30663_t
Valid prediction for snap_scaffold_7-snap.1795-T1
Valid prediction for GeneMark_model.30644_t
Valid prediction for GeneMark_model.30632_t
Valid prediction for snap_scaffold_7-snap.1794-T1
Valid prediction for GeneMark_model.30649_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14742, rend_intergenic: 13728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32808, rend_intergenic: 29577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69444, rend_intergenic: 65208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81305, rend_intergenic: 69742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101077, rend_intergenic: 95476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150820, rend_intergenic: 141902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181276, rend_intergenic: 178295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190545, rend_intergenic: 189159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225522
-exon list size: 456


building trellis

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30.6    
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32.8    
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34.7    
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88.0    
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92.8    
93.0    
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97.2    
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97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 14742, rend_intergenic: 13728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32808, rend_intergenic: 29577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69444, rend_intergenic: 65208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81305, rend_intergenic: 69742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101077, rend_intergenic: 95476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150820, rend_intergenic: 141902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181276, rend_intergenic: 178295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190545, rend_intergenic: 189159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13632
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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