-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_6485269-6721373

-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 Augustus_model.g2697.t1
Valid prediction for HiQ_model.g2693.t1
Valid prediction for GeneMark_model.6607_t
Valid prediction for GlimmerHMM_glimmerT_4056-T1
Valid prediction for pasa_asmbl_24514.p1
Valid prediction for GeneMark_model.6640_t
Valid prediction for snap_scaffold_2-snap.1445-T1
Valid prediction for GeneMark_model.6620_t
Valid prediction for GlimmerHMM_glimmerT_4073-T1
Valid prediction for GlimmerHMM_glimmerT_4055-T1
Valid prediction for GlimmerHMM_glimmerT_4048-T1
Valid prediction for snap_scaffold_2-snap.1479-T1
Valid prediction for GeneMark_model.6624_t
Valid prediction for snap_scaffold_2-snap.1466-T1
Valid prediction for snap_scaffold_2-snap.1456-T1
Valid prediction for CodingQuarry_transcript_28525-T1
Valid prediction for GlimmerHMM_glimmerT_4063-T1
Valid prediction for snap_scaffold_2-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_4069-T1
Valid prediction for Augustus_model.g2710.t1
Valid prediction for Augustus_model.g2696.t1
Valid prediction for GeneMark_model.6619_t
Valid prediction for snap_scaffold_2-snap.1446-T1
Valid prediction for HiQ_model.g2695.t1
Valid prediction for Augustus_model.g2708.t1
Valid prediction for GeneMark_model.6623_t
Valid prediction for snap_scaffold_2-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_4053-T1
Valid prediction for GlimmerHMM_glimmerT_4049-T1
Valid prediction for HiQ_model.g2704.t1
Valid prediction for GlimmerHMM_glimmerT_4065-T1
Valid prediction for pasa_asmbl_24504.p1
Valid prediction for GeneMark_model.6617_t
Valid prediction for Augustus_model.g2698.t1
Valid prediction for GlimmerHMM_glimmerT_4058-T1
Valid prediction for GeneMark_model.6637_t
Valid prediction for snap_scaffold_2-snap.1461-T1
Valid prediction for pasa_asmbl_24501.p1
Valid prediction for CodingQuarry_transcript_28530-T1
Valid prediction for Augustus_model.g2699.t1
Valid prediction for snap_scaffold_2-snap.1476-T1
Valid prediction for snap_scaffold_2-snap.1450-T1
Valid prediction for GeneMark_model.6609_t
Valid prediction for snap_scaffold_2-snap.1443-T1
Valid prediction for GeneMark_model.6631_t
Valid prediction for snap_scaffold_2-snap.1454-T1
Valid prediction for snap_scaffold_2-snap.1473-T1
Valid prediction for CodingQuarry_transcript_28531-T1
Valid prediction for GeneMark_model.6611_t
Valid prediction for CodingQuarry_transcript_28524-T1
Valid prediction for GlimmerHMM_glimmerT_4071-T1
Valid prediction for snap_scaffold_2-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_4052-T1
Valid prediction for snap_scaffold_2-snap.1471-T1
Valid prediction for GeneMark_model.6636_t
Valid prediction for GeneMark_model.6613_t
Valid prediction for GlimmerHMM_glimmerT_4054-T1
Valid prediction for snap_scaffold_2-snap.1452-T1
Valid prediction for Augustus_model.g2702.t1
Valid prediction for GeneMark_model.6638_t
Valid prediction for HiQ_model.g2694.t1
Couldn't classify 52329, 52546
Sorry, prediction pasa_asmbl_24507.p1 fails validation.
(ATG)	 CC	50153-50286	GT	ATG
(GGT)	 AG	51800-51981	GT	AGG
(GAA)	 AG	52329-52546	TC	GCT
-recovered pasa_asmbl_24507.p1, initial, 50153, 50286
add_exon() Sorry, pasa_asmbl_24507.p1 51800-51981-terminal-2 is invalid.
-recovered pasa_asmbl_24507.p1, terminal, 51800, 51981
-recovered pasa_asmbl_24507.p1, internal, 51800, 51981
Valid prediction for CodingQuarry_transcript_28526-T1
Valid prediction for GeneMark_model.6605_t
Valid prediction for GlimmerHMM_glimmerT_4046-T1
Valid prediction for GlimmerHMM_glimmerT_4057-T1
Valid prediction for GeneMark_model.6622_t
Valid prediction for GlimmerHMM_glimmerT_4050-T1
Valid prediction for GlimmerHMM_glimmerT_4062-T1
Couldn't classify 57667, 57781
Sorry, prediction pasa_asmbl_24510.p2 fails validation.
(ACG)	 GG	57667-57781	GT	CGG
(GGT)	 AG	57914-58027	GT	AGG
(GCT)	 AG	58338-58447	AC	AGA
-recovered pasa_asmbl_24510.p2, terminal, 58338, 58447
-recovered pasa_asmbl_24510.p2, internal, 57914, 58027
Valid prediction for GeneMark_model.6629_t
Valid prediction for GeneMark_model.6621_t
Valid prediction for GeneMark_model.6614_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 GlimmerHMM_glimmerT_4066-T1
Valid prediction for GlimmerHMM_glimmerT_4064-T1
Valid prediction for GeneMark_model.6618_t
Valid prediction for GeneMark_model.6639_t
Valid prediction for GeneMark_model.6626_t
Valid prediction for GeneMark_model.6616_t
Valid prediction for HiQ_model.g2707.t1
Valid prediction for snap_scaffold_2-snap.1462-T1
Valid prediction for snap_scaffold_2-snap.1447-T1
Valid prediction for Augustus_model.g2705.t1
Valid prediction for CodingQuarry_transcript_28529-T1
Valid prediction for Augustus_model.g2700.t1
Valid prediction for snap_scaffold_2-snap.1453-T1
Valid prediction for GeneMark_model.6612_t
Valid prediction for snap_scaffold_2-snap.1449-T1
Valid prediction for HiQ_model.g2703.t1
Valid prediction for snap_scaffold_2-snap.1475-T1
Valid prediction for HiQ_model.g2692.t1
Valid prediction for snap_scaffold_2-snap.1444-T1
Valid prediction for snap_scaffold_2-snap.1451-T1
Valid prediction for GlimmerHMM_glimmerT_4060-T1
Valid prediction for CodingQuarry_transcript_28528-T1
Valid prediction for CodingQuarry_transcript_28523-T1
Valid prediction for GlimmerHMM_glimmerT_4061-T1
Valid prediction for GeneMark_model.6604_t
Valid prediction for snap_scaffold_2-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_4067-T1
Valid prediction for Augustus_model.g2701.t1
Valid prediction for CodingQuarry_transcript_28522-T1
Valid prediction for snap_scaffold_2-snap.1472-T1
Valid prediction for GeneMark_model.6630_t
Valid prediction for GeneMark_model.6627_t
Valid prediction for CodingQuarry_transcript_28527-T1
Valid prediction for snap_scaffold_2-snap.1463-T1
Valid prediction for GeneMark_model.6608_t
Valid prediction for snap_scaffold_2-snap.1474-T1
Valid prediction for GlimmerHMM_glimmerT_4059-T1
Valid prediction for GlimmerHMM_glimmerT_4047-T1
Valid prediction for pasa_asmbl_23249.p1
Valid prediction for snap_scaffold_2-snap.1458-T1
Valid prediction for CodingQuarry_transcript_28521-T1
Valid prediction for GeneMark_model.6610_t
Valid prediction for CodingQuarry_transcript_28532-T1
Valid prediction for Augustus_model.g2691.t1
Valid prediction for snap_scaffold_2-snap.1467-T1
Valid prediction for snap_scaffold_2-snap.1464-T1
Valid prediction for snap_scaffold_2-snap.1465-T1
Valid prediction for pasa_asmbl_23240.p1
Valid prediction for snap_scaffold_2-snap.1455-T1
Valid prediction for GeneMark_model.6625_t
Valid prediction for Augustus_model.g2706.t1
Valid prediction for snap_scaffold_2-snap.1442-T1
Valid prediction for GeneMark_model.6634_t
Valid prediction for GeneMark_model.6633_t
Valid prediction for pasa_asmbl_23232.p1
Valid prediction for snap_scaffold_2-snap.1477-T1
Couldn't classify 88222, 88386
Sorry, prediction pasa_asmbl_23242.p1 fails validation.
(ATG)	 GC	87965-88114	GT	GGG
(CAG)	 AG	88222-88386	CG	CCC
-recovered pasa_asmbl_23242.p1, initial, 87965, 88114
Valid prediction for snap_scaffold_2-snap.1459-T1
Valid prediction for snap_scaffold_2-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_4070-T1
Valid prediction for GeneMark_model.6632_t
Valid prediction for GlimmerHMM_glimmerT_4051-T1
Valid prediction for GeneMark_model.6606_t
Valid prediction for GlimmerHMM_glimmerT_4068-T1
Valid prediction for snap_scaffold_2-snap.1468-T1
Valid prediction for Augustus_model.g2709.t1
Valid prediction for GeneMark_model.6615_t
Valid prediction for snap_scaffold_2-snap.1470-T1
Valid prediction for GeneMark_model.6635_t
Valid prediction for GlimmerHMM_glimmerT_4072-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54403, rend_intergenic: 50461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58447, rend_intergenic: 56156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65462, rend_intergenic: 64704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72016, rend_intergenic: 65997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76616, rend_intergenic: 76380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80316, rend_intergenic: 78623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108580, rend_intergenic: 80320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109237, rend_intergenic: 109227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143637, rend_intergenic: 136725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176698, rend_intergenic: 174820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184434, rend_intergenic: 178874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189088, rend_intergenic: 186635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236105
-exon list size: 566


building trellis

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20.8    
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21.3    
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22.9    
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23.9    
24.1    
24.3    
24.5    
24.6    
24.8    
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25.9    
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27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.3    
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28.9    
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29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
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36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.5    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
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50.7    
50.9    
51.1    
51.2    
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51.6    
51.8    
51.9    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
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63.0    
63.2    
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64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.1    
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66.0    
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66.9    
67.1    
67.3    
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67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
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70.1    
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71.0    
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75.0    
75.2    
75.4    
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76.1    
76.2    
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76.6    
76.8    
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77.1    
77.3    
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77.6    
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78.0    
78.2    
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78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
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81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
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84.7    
84.9    
85.0    
85.2    
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85.6    
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86.1    
86.3    
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86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
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88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
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89.6    
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90.0    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 54403, rend_intergenic: 50461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58447, rend_intergenic: 56156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65462, rend_intergenic: 64704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72016, rend_intergenic: 65997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76616, rend_intergenic: 76380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80316, rend_intergenic: 78623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108580, rend_intergenic: 80320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109237, rend_intergenic: 109227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143637, rend_intergenic: 136725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176698, rend_intergenic: 174820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184434, rend_intergenic: 178874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189088, rend_intergenic: 186635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21426
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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

-building DP trellis

-building trellis in range 1 - 21359
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 1 - 21321
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 20992
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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

-building DP trellis

-building trellis in range 1 - 20577
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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
	-no exons in range 1 - 15012