-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_10047414-10231679

-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_5-snap.1918-T1
Valid prediction for GeneMark_model.21634_t
Valid prediction for GlimmerHMM_glimmerT_12794-T1
Valid prediction for pasa_asmbl_44331.p1
Valid prediction for Augustus_model.g8489.t1
Valid prediction for snap_scaffold_5-snap.1928-T1
Valid prediction for GeneMark_model.21642_t
Valid prediction for snap_scaffold_5-snap.1927-T1
Valid prediction for GeneMark_model.21649_t
Valid prediction for GlimmerHMM_glimmerT_12797-T1
Valid prediction for GlimmerHMM_glimmerT_12792-T1
Valid prediction for CodingQuarry_transcript_52076-T1
Valid prediction for GlimmerHMM_glimmerT_12786-T1
Valid prediction for Augustus_model.g8492.t1
Valid prediction for GlimmerHMM_glimmerT_12789-T1
Valid prediction for Augustus_model.g8488.t1
Valid prediction for GeneMark_model.21655_t
Valid prediction for GeneMark_model.21654_t
Valid prediction for Augustus_model.g8498.t1
Valid prediction for CodingQuarry_transcript_52077-T1
Valid prediction for snap_scaffold_5-snap.1929-T1
Valid prediction for CodingQuarry_transcript_52074-T1
Valid prediction for Augustus_model.g8490.t1
Valid prediction for GeneMark_model.21643_t
Valid prediction for snap_scaffold_5-snap.1936-T1
Valid prediction for snap_scaffold_5-snap.1924-T1
Valid prediction for Augustus_model.g8505.t1
Valid prediction for CodingQuarry_transcript_52075-T1
Valid prediction for HiQ_model.g8499.t1
Valid prediction for snap_scaffold_5-snap.1912-T1
Valid prediction for pasa_asmbl_44333.p1
Valid prediction for pasa_asmbl_44329.p1
Valid prediction for snap_scaffold_5-snap.1937-T1
Valid prediction for Augustus_model.g8485.t1
Valid prediction for snap_scaffold_5-snap.1922-T1
Valid prediction for HiQ_model.g8491.t1
Valid prediction for GlimmerHMM_glimmerT_12783-T1
Valid prediction for GeneMark_model.21652_t
Valid prediction for GlimmerHMM_glimmerT_12804-T1
Valid prediction for snap_scaffold_5-snap.1915-T1
Valid prediction for GeneMark_model.21641_t
Valid prediction for Augustus_model.g8495.t1
Valid prediction for GlimmerHMM_glimmerT_12796-T1
Valid prediction for GeneMark_model.21660_t
Valid prediction for snap_scaffold_5-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_12784-T1
Valid prediction for GeneMark_model.21632_t
Valid prediction for pasa_asmbl_44322.p1
Valid prediction for GeneMark_model.21647_t
Valid prediction for GlimmerHMM_glimmerT_12791-T1
Valid prediction for GlimmerHMM_glimmerT_12777-T1
Valid prediction for snap_scaffold_5-snap.1925-T1
Valid prediction for Augustus_model.g8486.t1
Valid prediction for GlimmerHMM_glimmerT_12781-T1
Valid prediction for snap_scaffold_5-snap.1911-T1
Valid prediction for Augustus_model.g8496.t1
Valid prediction for GeneMark_model.21659_t
Valid prediction for GeneMark_model.21636_t
Valid prediction for GlimmerHMM_glimmerT_12776-T1
Valid prediction for GeneMark_model.21651_t
Valid prediction for GeneMark_model.21645_t
Valid prediction for GlimmerHMM_glimmerT_12795-T1
Valid prediction for GeneMark_model.21639_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_12785-T1
Valid prediction for GeneMark_model.21646_t
Valid prediction for GeneMark_model.21640_t
Valid prediction for snap_scaffold_5-snap.1920-T1
Valid prediction for pasa_asmbl_45710.p1
Valid prediction for GeneMark_model.21658_t
Valid prediction for snap_scaffold_5-snap.1908-T1
Valid prediction for GlimmerHMM_glimmerT_12799-T1
Valid prediction for snap_scaffold_5-snap.1935-T1
Valid prediction for Augustus_model.g8500.t1
Valid prediction for CodingQuarry_transcript_52078-T1
Valid prediction for GlimmerHMM_glimmerT_12802-T1
Valid prediction for GeneMark_model.21656_t
Valid prediction for GlimmerHMM_glimmerT_12800-T1
Valid prediction for snap_scaffold_5-snap.1914-T1
Valid prediction for GlimmerHMM_glimmerT_12801-T1
Valid prediction for snap_scaffold_5-snap.1931-T1
Valid prediction for snap_scaffold_5-snap.1934-T1
Valid prediction for HiQ_model.g8503.t1
Valid prediction for snap_scaffold_5-snap.1930-T1
Valid prediction for GeneMark_model.21657_t
Valid prediction for snap_scaffold_5-snap.1932-T1
Couldn't classify 47386, 47503
Sorry, prediction pasa_asmbl_45699.p1 fails validation.
(AGT)	 CC	47386-47503	GT	AGG
(CTT)	 AG	47704-47835	GT	AGG
(TAC)	 AG	47927-47996	GT	CGG
(GTC)	 AG	48417-48428	GT	AGG
(GAT)	 AG	48666-48701	GT	CGG
(AGA)	 AG	49297-49525	CT	AAC
-recovered pasa_asmbl_45699.p1, terminal, 49297, 49525
-recovered pasa_asmbl_45699.p1, internal, 47704, 47835
-recovered pasa_asmbl_45699.p1, internal, 47927, 47996
-recovered pasa_asmbl_45699.p1, internal, 48417, 48428
-recovered pasa_asmbl_45699.p1, internal, 48666, 48701
Valid prediction for GlimmerHMM_glimmerT_12787-T1
Valid prediction for GlimmerHMM_glimmerT_12788-T1
Valid prediction for GeneMark_model.21637_t
Valid prediction for snap_scaffold_5-snap.1919-T1
Valid prediction for Augustus_model.g8497.t1
Valid prediction for Augustus_model.g8493.t1
Valid prediction for Augustus_model.g8502.t1
Couldn't classify 93247, 93297
Couldn't classify 94035, 94103
Sorry, prediction pasa_asmbl_45691.p1 fails validation.
(GTC)	 TA	93247-93297	GT	AAG
(TGG)	 AG	93746-93943	GT	AGG
(GAA)	 AG	94035-94103	AA	GCA
-recovered pasa_asmbl_45691.p1, internal, 93746, 93943
Valid prediction for GlimmerHMM_glimmerT_12779-T1
Valid prediction for Augustus_model.g8494.t1
Valid prediction for snap_scaffold_5-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_12780-T1
Valid prediction for snap_scaffold_5-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_12790-T1
Valid prediction for GeneMark_model.21648_t
Valid prediction for GeneMark_model.21653_t
Valid prediction for snap_scaffold_5-snap.1917-T1
Valid prediction for Augustus_model.g8487.t1
Valid prediction for snap_scaffold_5-snap.1921-T1
Valid prediction for GeneMark_model.21638_t
Valid prediction for GlimmerHMM_glimmerT_12778-T1
Valid prediction for pasa_asmbl_45707.p1
Valid prediction for pasa_asmbl_45702.p1
Valid prediction for CodingQuarry_transcript_52080-T1
Valid prediction for GeneMark_model.21635_t
Couldn't classify 57044, 57123
Sorry, prediction pasa_asmbl_45698.p1 fails validation.
(CCC)	 AG	57044-57123	GT	AAG
(GCA)	 AG	57200-57323	GT	CAG
(GAT)	 AG	57421-57603	GT	AGG
(ATC)	 AG	57749-57865	GT	AGG
(GTT)	 AG	57980-58112	GT	TGG
(GAC)	 AG	58208-58662	AC	AAA
-recovered pasa_asmbl_45698.p1, terminal, 58208, 58662
-recovered pasa_asmbl_45698.p1, internal, 57044, 57123
-recovered pasa_asmbl_45698.p1, internal, 57200, 57323
-recovered pasa_asmbl_45698.p1, internal, 57421, 57603
-recovered pasa_asmbl_45698.p1, internal, 57749, 57865
-recovered pasa_asmbl_45698.p1, internal, 57980, 58112
Valid prediction for GeneMark_model.21644_t
Valid prediction for GeneMark_model.21650_t
Valid prediction for GlimmerHMM_glimmerT_12782-T1
Valid prediction for snap_scaffold_5-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_12793-T1
Valid prediction for HiQ_model.g8504.t1
Valid prediction for snap_scaffold_5-snap.1916-T1
Valid prediction for GlimmerHMM_glimmerT_12803-T1
Valid prediction for Augustus_model.g8501.t1
Valid prediction for snap_scaffold_5-snap.1926-T1
Valid prediction for GeneMark_model.21633_t
Valid prediction for GlimmerHMM_glimmerT_12798-T1
Valid prediction for GlimmerHMM_glimmerT_12775-T1
Valid prediction for Augustus_model.g8484.t1
Valid prediction for snap_scaffold_5-snap.1913-T1
Valid prediction for snap_scaffold_5-snap.1910-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9566, rend_intergenic: 5176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47414, rend_intergenic: 44261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184266
-exon list size: 453


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
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5.5    
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5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.2    
9.5    
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9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.7    
13.0    
13.2    
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13.6    
13.8    
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14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.8    
51.0    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 9566, rend_intergenic: 5176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47414, rend_intergenic: 44261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 157143 - 184266
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 157143 - 172114
-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

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

-building DP trellis

-building trellis in range 157143 - 169006
-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

-building DP trellis

-building trellis in range 172210 - 184266
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 172210 - 182282
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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