-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_9745115-9841960

-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_18-snap.2089-T1
Valid prediction for snap_scaffold_18-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_42953-T1
Valid prediction for GlimmerHMM_glimmerT_42950-T1
Couldn't classify 25661, 25948
Couldn't classify 26232, 26729
Sorry, prediction pasa_asmbl_20889.p1 fails validation.
(TTC)	 CC	25661-25948	GT	AGG
(GTG)	 AG	26232-26729	GG	AAG
Valid prediction for snap_scaffold_18-snap.2083-T1
Couldn't classify 46406, 46513
Sorry, prediction pasa_asmbl_20891.p1 fails validation.
(ATG)	 TC	44167-44232	GT	GGG
(GCT)	 AG	44915-45082	GT	AGG
(CTG)	 AG	45518-45634	GT	AGG
(CCT)	 AG	45956-46033	GT	AGG
(GCC)	 AG	46173-46295	GT	AGG
(ATT)	 AG	46406-46513	TC	GGT
-recovered pasa_asmbl_20891.p1, initial, 44167, 44232
-recovered pasa_asmbl_20891.p1, internal, 44915, 45082
-recovered pasa_asmbl_20891.p1, internal, 45518, 45634
-recovered pasa_asmbl_20891.p1, internal, 45956, 46033
-recovered pasa_asmbl_20891.p1, internal, 46173, 46295
Valid prediction for snap_scaffold_18-snap.2086-T1
Valid prediction for snap_scaffold_18-snap.2078-T1
Valid prediction for snap_scaffold_18-snap.2087-T1
Valid prediction for Augustus_model.g28634.t1
Valid prediction for Augustus_model.g28635.t1
Valid prediction for snap_scaffold_18-snap.2092-T1
Valid prediction for snap_scaffold_18-snap.2095-T1
Valid prediction for GlimmerHMM_glimmerT_42954-T1
Valid prediction for Augustus_model.g28632.t1
Valid prediction for HiQ_model.g28631.t1
Valid prediction for GlimmerHMM_glimmerT_42959-T1
Valid prediction for snap_scaffold_18-snap.2080-T1
Couldn't classify 30706, 30856
Sorry, prediction pasa_asmbl_20890.p1 fails validation.
(AAG)	 TT	30706-30856	GT	AGG
(CTG)	 AG	33640-34064	AC	AAA
-recovered pasa_asmbl_20890.p1, terminal, 33640, 34064
Valid prediction for snap_scaffold_18-snap.2091-T1
Valid prediction for GlimmerHMM_glimmerT_42949-T1
Valid prediction for snap_scaffold_18-snap.2082-T1
Valid prediction for snap_scaffold_18-snap.2090-T1
Valid prediction for snap_scaffold_18-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_42957-T1
Valid prediction for GlimmerHMM_glimmerT_42947-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 CodingQuarry_transcript_23879-T1
Valid prediction for snap_scaffold_18-snap.2088-T1
Valid prediction for Augustus_model.g28638.t1
Valid prediction for snap_scaffold_18-snap.2077-T1
Valid prediction for snap_scaffold_18-snap.2084-T1
Valid prediction for CodingQuarry_transcript_23882-T1
Couldn't classify 39736, 39852
Sorry, prediction pasa_asmbl_20089.p1 fails validation.
(CTG)	 AG	39736-39852	GT	AGG
(GCT)	 AG	39949-40026	GT	AGG
(GCC)	 AG	40160-40282	GT	AGG
(GTT)	 AG	40797-40903	GT	TGG
(GGC)	 AG	41715-41796	GT	AGG
(GTC)	 AG	42002-42085	GT	AGG
(GTG)	 AG	42225-42307	GT	TGG
(GGG)	 AG	42441-42483	AG	GAA
-recovered pasa_asmbl_20089.p1, terminal, 42441, 42483
-recovered pasa_asmbl_20089.p1, internal, 39736, 39852
-recovered pasa_asmbl_20089.p1, internal, 39949, 40026
-recovered pasa_asmbl_20089.p1, internal, 40160, 40282
-recovered pasa_asmbl_20089.p1, internal, 40797, 40903
-recovered pasa_asmbl_20089.p1, internal, 41715, 41796
-recovered pasa_asmbl_20089.p1, internal, 42002, 42085
-recovered pasa_asmbl_20089.p1, internal, 42225, 42307
Valid prediction for Augustus_model.g28637.t1
Valid prediction for Augustus_model.g28636.t1
Valid prediction for Augustus_model.g28640.t1
Couldn't classify 46466, 46543
Sorry, prediction pasa_asmbl_20088.p1 fails validation.
(ATG)	 CG	45100-45165	GT	AGG
(TCG)	 AG	45550-45717	GT	AGG
(CTG)	 AG	46066-46182	GT	AGG
(GCT)	 AG	46466-46543	GT	AGG
-recovered pasa_asmbl_20088.p1, initial, 45100, 45165
-recovered pasa_asmbl_20088.p1, internal, 45550, 45717
-recovered pasa_asmbl_20088.p1, internal, 46066, 46182
-recovered pasa_asmbl_20088.p1, internal, 46466, 46543
Valid prediction for GlimmerHMM_glimmerT_42956-T1
Valid prediction for GlimmerHMM_glimmerT_42960-T1
Valid prediction for snap_scaffold_18-snap.2085-T1
Valid prediction for GlimmerHMM_glimmerT_42955-T1
Valid prediction for GlimmerHMM_glimmerT_42948-T1
Valid prediction for Augustus_model.g28633.t1
Couldn't classify 32675, 32887
Sorry, prediction pasa_asmbl_20092.p1 fails validation.
(TGC)	 AG	32675-32887	GT	AGG
(GTA)	 AG	34066-34237	GT	CGG
(GCT)	 AG	35053-35239	GT	AAG
(GTT)	 AG	35438-35625	GT	AGG
(GTG)	 AG	35916-36109	GT	GGG
(TTC)	 AG	36460-36588	AC	GAA
-recovered pasa_asmbl_20092.p1, terminal, 36460, 36588
-recovered pasa_asmbl_20092.p1, internal, 32675, 32887
-recovered pasa_asmbl_20092.p1, internal, 34066, 34237
-recovered pasa_asmbl_20092.p1, internal, 35053, 35239
-recovered pasa_asmbl_20092.p1, internal, 35438, 35625
-recovered pasa_asmbl_20092.p1, internal, 35916, 36109
Valid prediction for Augustus_model.g28639.t1
Valid prediction for GlimmerHMM_glimmerT_42952-T1
Valid prediction for snap_scaffold_18-snap.2096-T1
Valid prediction for CodingQuarry_transcript_23881-T1
Valid prediction for GlimmerHMM_glimmerT_42946-T1
Valid prediction for snap_scaffold_18-snap.2079-T1
Valid prediction for snap_scaffold_18-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_42958-T1
Valid prediction for GlimmerHMM_glimmerT_42951-T1
Valid prediction for snap_scaffold_18-snap.2093-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27223, rend_intergenic: 18854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27618, rend_intergenic: 27285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34528, rend_intergenic: 28193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57126, rend_intergenic: 54546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61316, rend_intergenic: 60259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79608, rend_intergenic: 61560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86315, rend_intergenic: 85023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93819, rend_intergenic: 86360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 96846
-exon list size: 194


building trellis

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3.1    
3.6    
4.1    
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5.1    
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6.1    
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7.1    
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8.2    
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9.2    
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10.2    
10.7    
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11.7    
12.2    
12.8    
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13.8    
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14.8    
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18.4    
18.9    
19.4    
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20.4    
20.9    
21.4    
21.9    
22.4    
23.0    
23.5    
24.0    
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25.0    
25.5    
26.0    
26.5    
27.0    
27.6    
28.1    
28.6    
29.1    
29.6    
30.1    
30.6    
31.1    
31.6    
32.1    
32.7    
33.2    
33.7    
34.2    
34.7    
35.2    
35.7    
36.2    
36.7    
37.2    
37.8    
38.3    
38.8    
39.3    
39.8    
40.3    
40.8    
41.3    
41.8    
42.3    
42.9    
43.4    
43.9    
44.4    
44.9    
45.4    
45.9    
46.4    
46.9    
47.4    
48.0    
48.5    
49.0    
49.5    
50.0    
50.5    
51.0    
51.5    
52.0    
52.6    
53.1    
53.6    
54.1    
54.6    
55.1    
55.6    
56.1    
56.6    
57.1    
57.7    
58.2    
58.7    
59.2    
59.7    
60.2    
60.7    
61.2    
61.7    
62.2    
62.8    
63.3    
63.8    
64.3    
64.8    
65.3    
65.8    
66.3    
66.8    
67.3    
67.9    
68.4    
68.9    
69.4    
69.9    
70.4    
70.9    
71.4    
71.9    
72.4    
73.0    
73.5    
74.0    
74.5    
75.0    
75.5    
76.0    
76.5    
77.0    
77.6    
78.1    
78.6    
79.1    
79.6    
80.1    
80.6    
81.1    
81.6    
82.1    
82.7    
83.2    
83.7    
84.2    
84.7    
85.2    
85.7    
86.2    
86.7    
87.2    
87.8    
88.3    
88.8    
89.3    
89.8    
90.3    
90.8    
91.3    
91.8    
92.3    
92.9    
93.4    
93.9    
94.4    
94.9    
95.4    
95.9    
96.4    
96.9    
97.4    
98.0    
98.5    
99.0    
99.5    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 27223, rend_intergenic: 18854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27618, rend_intergenic: 27285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34528, rend_intergenic: 28193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57126, rend_intergenic: 54546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61316, rend_intergenic: 60259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79608, rend_intergenic: 61560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86315, rend_intergenic: 85023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93819, rend_intergenic: 86360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support