-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_3228790-3357613

-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: +)Couldn't classify 109189, 109211
Sorry, prediction pasa_asmbl_43881.p1 fails validation.
(CCC)	 AC	109189-109211	GT	GGG
(GTC)	 AG	109565-109648	GT	TTG
(TTT)	 AG	109852-110101	AG	GAA
-recovered pasa_asmbl_43881.p1, terminal, 109852, 110101
-recovered pasa_asmbl_43881.p1, internal, 109565, 109648
Valid prediction for Augustus_model.g7836.t1
Valid prediction for snap_scaffold_5-snap.651-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11925-T1
Valid prediction for GlimmerHMM_glimmerT_11919-T1
Valid prediction for GeneMark_model.20093_t
Couldn't classify 48623, 48952
Sorry, prediction pasa_asmbl_43879.p1 fails validation.
(GTG)	 TC	48623-48952	AA	AGA
Valid prediction for GeneMark_model.20102_t
Valid prediction for GlimmerHMM_glimmerT_11929-T1
Valid prediction for GlimmerHMM_glimmerT_11923-T1
Valid prediction for GeneMark_model.20086_t
Valid prediction for GlimmerHMM_glimmerT_11914-T1
Valid prediction for snap_scaffold_5-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_11928-T1
Valid prediction for snap_scaffold_5-snap.658-T1
Valid prediction for GeneMark_model.20100_t
Valid prediction for GeneMark_model.20074_t
Valid prediction for GlimmerHMM_glimmerT_11920-T1
Valid prediction for snap_scaffold_5-snap.649-T1
Valid prediction for GeneMark_model.20081_t
Valid prediction for GlimmerHMM_glimmerT_11912-T1
Valid prediction for GeneMark_model.20084_t
Valid prediction for GeneMark_model.20078_t
Valid prediction for GeneMark_model.20079_t
Valid prediction for snap_scaffold_5-snap.643-T1
Valid prediction for snap_scaffold_5-snap.647-T1
Valid prediction for snap_scaffold_5-snap.654-T1
Valid prediction for snap_scaffold_5-snap.637-T1
Valid prediction for pasa_asmbl_43878.p1
Valid prediction for GeneMark_model.20083_t
Valid prediction for Augustus_model.g7839.t1
Couldn't classify 107544, 107561
Couldn't classify 109046, 109116
Sorry, prediction pasa_asmbl_43880.p1 fails validation.
(GTC)	 AC	107544-107561	GT	AGG
(GGG)	 AG	107827-107986	GT	AGG
(GCG)	 AG	108327-108527	GT	CAG
(GCT)	 AG	109046-109116	CC	CCC
-recovered pasa_asmbl_43880.p1, internal, 107827, 107986
-recovered pasa_asmbl_43880.p1, internal, 108327, 108527
Valid prediction for snap_scaffold_5-snap.639-T1
Valid prediction for GeneMark_model.20095_t
Valid prediction for snap_scaffold_5-snap.640-T1
Valid prediction for GeneMark_model.20088_t
Valid prediction for Augustus_model.g7838.t1
Valid prediction for GeneMark_model.20076_t
Valid prediction for snap_scaffold_5-snap.638-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.20104_t
Valid prediction for snap_scaffold_5-snap.657-T1
Valid prediction for GeneMark_model.20098_t
Valid prediction for GlimmerHMM_glimmerT_11918-T1
Valid prediction for GlimmerHMM_glimmerT_11916-T1
Valid prediction for GeneMark_model.20077_t
Valid prediction for GeneMark_model.20096_t
Valid prediction for Augustus_model.g7843.t1
Valid prediction for snap_scaffold_5-snap.642-T1
Valid prediction for GlimmerHMM_glimmerT_11924-T1
Valid prediction for Augustus_model.g7835.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 Augustus_model.g7842.t1
Valid prediction for GlimmerHMM_glimmerT_11930-T1
Valid prediction for GlimmerHMM_glimmerT_11913-T1
Valid prediction for GeneMark_model.20092_t
Valid prediction for GeneMark_model.20075_t
Valid prediction for GeneMark_model.20103_t
Valid prediction for GeneMark_model.20097_t
Valid prediction for GlimmerHMM_glimmerT_11927-T1
Valid prediction for snap_scaffold_5-snap.652-T1
Valid prediction for GlimmerHMM_glimmerT_11915-T1
Valid prediction for snap_scaffold_5-snap.644-T1
Valid prediction for GeneMark_model.20105_t
Valid prediction for snap_scaffold_5-snap.645-T1
Valid prediction for GeneMark_model.20090_t
Valid prediction for Augustus_model.g7833.t1
Valid prediction for pasa_asmbl_45297.p1
Couldn't classify 83739, 84320
Sorry, prediction pasa_asmbl_45295.p1 fails validation.
(TAC)	 CC	83739-84320	AC	AAA
Valid prediction for GeneMark_model.20089_t
Couldn't classify 14914, 15031
Sorry, prediction pasa_asmbl_45298.p1 fails validation.
(CGA)	 CC	14914-15031	GT	AGG
(TGA)	 AG	15409-15552	GT	TAG
(GGA)	 AG	15772-15909	GT	AGG
(TGA)	 AG	16126-16259	TT	GAT
-recovered pasa_asmbl_45298.p1, terminal, 16126, 16259
-recovered pasa_asmbl_45298.p1, internal, 15409, 15552
-recovered pasa_asmbl_45298.p1, internal, 15772, 15909
Valid prediction for CodingQuarry_transcript_51881-T1
Valid prediction for Augustus_model.g7844.t1
Valid prediction for snap_scaffold_5-snap.636-T1
Valid prediction for Augustus_model.g7837.t1
Valid prediction for GeneMark_model.20099_t
Valid prediction for GeneMark_model.20082_t
Valid prediction for GlimmerHMM_glimmerT_11917-T1
Valid prediction for GlimmerHMM_glimmerT_11921-T1
Valid prediction for GeneMark_model.20091_t
Valid prediction for snap_scaffold_5-snap.641-T1
Valid prediction for GeneMark_model.20094_t
Valid prediction for CodingQuarry_transcript_51880-T1
Valid prediction for GeneMark_model.20101_t
Valid prediction for GlimmerHMM_glimmerT_11922-T1
Valid prediction for GlimmerHMM_glimmerT_11926-T1
Valid prediction for snap_scaffold_5-snap.646-T1
Valid prediction for GeneMark_model.20087_t
Valid prediction for Augustus_model.g7834.t1
Valid prediction for snap_scaffold_5-snap.648-T1
Valid prediction for GeneMark_model.20080_t
Valid prediction for HiQ_model.g7840.t1
Valid prediction for Augustus_model.g7841.t1
Valid prediction for snap_scaffold_5-snap.656-T1
Couldn't classify 82841, 83051
Sorry, prediction pasa_asmbl_45296.p1 fails validation.
(ATG)	 TC	82210-82319	GT	AGG
(TTC)	 AG	82426-82525	GT	AGG
(ACC)	 AG	82673-82737	GT	AGG
(CCC)	 AG	82841-83051	AT	ACA
-recovered pasa_asmbl_45296.p1, initial, 82210, 82319
-recovered pasa_asmbl_45296.p1, internal, 82426, 82525
-recovered pasa_asmbl_45296.p1, internal, 82673, 82737
Valid prediction for snap_scaffold_5-snap.655-T1
Valid prediction for snap_scaffold_5-snap.650-T1
Valid prediction for GeneMark_model.20085_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 70876, rend_intergenic: 52301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73929, rend_intergenic: 72424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88211, rend_intergenic: 79410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98797, rend_intergenic: 92610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110101, rend_intergenic: 104956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128824
-exon list size: 428


building trellis

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31.9    
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32.3    
32.6    
32.8    
33.0    
33.3    
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35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
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37.9    
38.1    
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38.8    
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41.6    
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42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
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47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
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51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
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55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
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58.1    
58.4    
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65.6    
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66.0    
66.3    
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75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
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77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
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80.0    
80.2    
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80.9    
81.2    
81.4    
81.6    
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82.6    
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83.0    
83.3    
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85.3    
85.6    
85.8    
86.0    
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88.1    
88.4    
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89.3    
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90.0    
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90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
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94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
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 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 70876, rend_intergenic: 52301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73929, rend_intergenic: 72424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88211, rend_intergenic: 79410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98797, rend_intergenic: 92610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110101, rend_intergenic: 104956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 113815 - 128824
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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