-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_10524301-10639857

-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_19-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_45803-T1
Valid prediction for snap_scaffold_19-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_45808-T1
Valid prediction for snap_scaffold_19-snap.2014-T1
Valid prediction for Augustus_model.g30556.t1
Valid prediction for GeneMark_model.79896_t
Valid prediction for Augustus_model.g30551.t1
Valid prediction for GeneMark_model.79903_t
Valid prediction for GlimmerHMM_glimmerT_45809-T1
Valid prediction for snap_scaffold_19-snap.2035-T1
Valid prediction for snap_scaffold_19-snap.2032-T1
Valid prediction for snap_scaffold_19-snap.2025-T1
Valid prediction for snap_scaffold_19-snap.2022-T1
Valid prediction for snap_scaffold_19-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_45806-T1
Valid prediction for snap_scaffold_19-snap.2030-T1
Valid prediction for snap_scaffold_19-snap.2019-T1
Valid prediction for GeneMark_model.79906_t
Valid prediction for GlimmerHMM_glimmerT_45815-T1
Valid prediction for Augustus_model.g30553.t1
Valid prediction for GeneMark_model.79894_t
Valid prediction for GlimmerHMM_glimmerT_45816-T1
Valid prediction for GlimmerHMM_glimmerT_45804-T1
Valid prediction for pasa_asmbl_22452.p1
Valid prediction for GeneMark_model.79911_t
Valid prediction for Augustus_model.g30549.t1
Valid prediction for snap_scaffold_19-snap.2029-T1
Valid prediction for GeneMark_model.79893_t
Valid prediction for GlimmerHMM_glimmerT_45807-T1
Valid prediction for GeneMark_model.79900_t
Valid prediction for CodingQuarry_transcript_25733-T1
Valid prediction for GeneMark_model.79913_t
Valid prediction for snap_scaffold_19-snap.2027-T1
Valid prediction for GlimmerHMM_glimmerT_45812-T1
Valid prediction for Augustus_model.g30559.t1
Valid prediction for snap_scaffold_19-snap.2039-T1
Valid prediction for snap_scaffold_19-snap.2023-T1
Valid prediction for snap_scaffold_19-snap.2021-T1
Valid prediction for snap_scaffold_19-snap.2033-T1
Valid prediction for GeneMark_model.79905_t
Valid prediction for snap_scaffold_19-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_45817-T1
Valid prediction for Augustus_model.g30552.t1
Valid prediction for Augustus_model.g30554.t1
Valid prediction for GlimmerHMM_glimmerT_45818-T1
Valid prediction for snap_scaffold_19-snap.2041-T1
Valid prediction for snap_scaffold_19-snap.2026-T1
Valid prediction for snap_scaffold_19-snap.2042-T1
Valid prediction for snap_scaffold_19-snap.2024-T1
Valid prediction for GeneMark_model.79891_t
Valid prediction for GeneMark_model.79898_t
Valid prediction for Augustus_model.g30555.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.79895_t
Valid prediction for GlimmerHMM_glimmerT_45805-T1
Valid prediction for GeneMark_model.79897_t
Valid prediction for Augustus_model.g30558.t1
Valid prediction for GeneMark_model.79910_t
Couldn't classify 2386, 2430
Sorry, prediction pasa_asmbl_21558.p1 fails validation.
(TCC)	 CC	2386-2430	GT	TGG
(GTG)	 AG	2535-2618	GT	AGG
(GTT)	 AG	2717-2858	GT	AGG
(ACG)	 AG	2959-3062	CC	GAC
-recovered pasa_asmbl_21558.p1, terminal, 2959, 3062
-recovered pasa_asmbl_21558.p1, internal, 2535, 2618
-recovered pasa_asmbl_21558.p1, internal, 2717, 2858
Valid prediction for snap_scaffold_19-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_45813-T1
Valid prediction for snap_scaffold_19-snap.2020-T1
Valid prediction for GeneMark_model.79904_t
Valid prediction for GeneMark_model.79909_t
Valid prediction for CodingQuarry_transcript_25734-T1
Valid prediction for snap_scaffold_19-snap.2036-T1
Valid prediction for snap_scaffold_19-snap.2017-T1
Valid prediction for snap_scaffold_19-snap.2028-T1
Valid prediction for snap_scaffold_19-snap.2031-T1
Valid prediction for snap_scaffold_19-snap.2040-T1
Valid prediction for GeneMark_model.79912_t
Valid prediction for GlimmerHMM_glimmerT_45802-T1
Valid prediction for GeneMark_model.79907_t
Valid prediction for GeneMark_model.79899_t
Valid prediction for GlimmerHMM_glimmerT_45810-T1
Valid prediction for GeneMark_model.79902_t
Valid prediction for GeneMark_model.79908_t
Valid prediction for GeneMark_model.79892_t
Valid prediction for Augustus_model.g30550.t1
Valid prediction for snap_scaffold_19-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_45811-T1
Valid prediction for Augustus_model.g30557.t1
Valid prediction for GeneMark_model.79914_t
Valid prediction for GeneMark_model.79901_t
Valid prediction for GlimmerHMM_glimmerT_45819-T1
Valid prediction for Augustus_model.g30560.t1
Valid prediction for snap_scaffold_19-snap.2015-T1
Valid prediction for snap_scaffold_19-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_45814-T1
Valid prediction for Augustus_model.g30548.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17115, rend_intergenic: 13573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22074, rend_intergenic: 18054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51261, rend_intergenic: 46976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85585, rend_intergenic: 83009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111620, rend_intergenic: 105453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 115557
-exon list size: 424


building trellis

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37.3    
37.6    
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39.9    
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40.6    
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41.5    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
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43.7    
43.9    
44.1    
44.4    
44.6    
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45.5    
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87.6    
87.8    
88.0    
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89.9    
90.1    
90.4    
90.6    
90.8    
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91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
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93.9    
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94.4    
94.6    
94.8    
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95.3    
95.5    
95.8    
96.0    
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96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 17115, rend_intergenic: 13573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22074, rend_intergenic: 18054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51261, rend_intergenic: 46976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85585, rend_intergenic: 83009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111620, rend_intergenic: 105453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support