-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_4769544-5036248

-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 GlimmerHMM_glimmerT_17767-T1
Valid prediction for snap_scaffold_7-snap.1101-T1
Valid prediction for Augustus_model.g11932.t1
Valid prediction for GeneMark_model.29868_t
Valid prediction for CodingQuarry_transcript_57343-T1
Valid prediction for snap_scaffold_7-snap.1096-T1
Valid prediction for snap_scaffold_7-snap.1080-T1
Valid prediction for snap_scaffold_7-snap.1086-T1
Valid prediction for snap_scaffold_7-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_17768-T1
Valid prediction for Augustus_model.g11923.t1
Valid prediction for GlimmerHMM_glimmerT_17780-T1
Valid prediction for Augustus_model.g11925.t1
Valid prediction for snap_scaffold_7-snap.1092-T1
Couldn't classify 139614, 139764
Sorry, prediction pasa_asmbl_50640.p1 fails validation.
(ATG)	 AC	131011-131051	GT	AGG
(GCT)	 AG	132806-138571	GT	AGG
(AGC)	 AG	139614-139764	TA	GGT
-recovered pasa_asmbl_50640.p1, initial, 131011, 131051
-recovered pasa_asmbl_50640.p1, internal, 132806, 138571
Valid prediction for snap_scaffold_7-snap.1097-T1
Valid prediction for pasa_asmbl_50636.p1
Valid prediction for snap_scaffold_7-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_17765-T1
Valid prediction for GeneMark_model.29871_t
Valid prediction for GeneMark_model.29872_t
Valid prediction for GeneMark_model.29884_t
Valid prediction for GlimmerHMM_glimmerT_17777-T1
Valid prediction for snap_scaffold_7-snap.1081-T1
Valid prediction for snap_scaffold_7-snap.1095-T1
Valid prediction for pasa_asmbl_50661.p1
Valid prediction for CodingQuarry_transcript_57342-T1
Valid prediction for snap_scaffold_7-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_17759-T1
Valid prediction for GeneMark_model.29875_t
Valid prediction for GlimmerHMM_glimmerT_17778-T1
Valid prediction for GlimmerHMM_glimmerT_17769-T1
Valid prediction for GeneMark_model.29867_t
Valid prediction for snap_scaffold_7-snap.1082-T1
Valid prediction for GeneMark_model.29876_t
Valid prediction for snap_scaffold_7-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_17772-T1
Valid prediction for GeneMark_model.29883_t
Valid prediction for GeneMark_model.29870_t
Valid prediction for GlimmerHMM_glimmerT_17773-T1
Valid prediction for snap_scaffold_7-snap.1070-T1
Valid prediction for pasa_asmbl_50631.p1
Valid prediction for GlimmerHMM_glimmerT_17761-T1
Valid prediction for Augustus_model.g11927.t1
Valid prediction for snap_scaffold_7-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_17774-T1
Valid prediction for snap_scaffold_7-snap.1088-T1
Valid prediction for GeneMark_model.29861_t
Valid prediction for GeneMark_model.29874_t
Valid prediction for snap_scaffold_7-snap.1069-T1
Valid prediction for CodingQuarry_transcript_57341-T1
Valid prediction for snap_scaffold_7-snap.1102-T1
Valid prediction for HiQ_model.g11922.t1
Valid prediction for GeneMark_model.29885_t
Valid prediction for snap_scaffold_7-snap.1089-T1
Valid prediction for CodingQuarry_transcript_57340-T1
Couldn't classify 145584, 146543
Sorry, prediction pasa_asmbl_50643.p1 fails validation.
(TGC)	 GG	145584-146543	TA	GGT
Valid prediction for GeneMark_model.29865_t
Valid prediction for snap_scaffold_7-snap.1099-T1
Valid prediction for snap_scaffold_7-snap.1093-T1
Valid prediction for snap_scaffold_7-snap.1076-T1
Valid prediction for GeneMark_model.29862_t
Valid prediction for GlimmerHMM_glimmerT_17771-T1
Valid prediction for snap_scaffold_7-snap.1078-T1
Valid prediction for GeneMark_model.29886_t
Valid prediction for GeneMark_model.29873_t
Valid prediction for Augustus_model.g11920.t1
Valid prediction for Augustus_model.g11926.t1
Valid prediction for GlimmerHMM_glimmerT_17762-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 HiQ_model.g11919.t1
Valid prediction for GeneMark_model.29880_t
Valid prediction for GeneMark_model.29878_t
Valid prediction for GeneMark_model.29866_t
Valid prediction for GeneMark_model.29882_t
Valid prediction for GlimmerHMM_glimmerT_17775-T1
Couldn't classify 37961, 38032
Sorry, prediction GeneMark_model.29881_t fails validation.
(CGC)	 AG	37961-38032	GT	AGG
(CTC)	 AG	38111-38183	GT	GAG
(TGG)	 AG	38207-38221	GT	GAG
(AGA)	 AG	38257-38275	GC	ACG
(ACG)	 AG	38885-38992	CA	AGC
-recovered GeneMark_model.29881_t, terminal, 38885, 38992
-recovered GeneMark_model.29881_t, internal, 37961, 38032
-recovered GeneMark_model.29881_t, internal, 38111, 38183
-recovered GeneMark_model.29881_t, internal, 38207, 38221
-recovered GeneMark_model.29881_t, internal, 38257, 38275
Valid prediction for snap_scaffold_7-snap.1087-T1
Valid prediction for snap_scaffold_7-snap.1072-T1
Valid prediction for GlimmerHMM_glimmerT_17758-T1
Valid prediction for snap_scaffold_7-snap.1068-T1
Valid prediction for Augustus_model.g11915.t1
Valid prediction for GlimmerHMM_glimmerT_17779-T1
Valid prediction for Augustus_model.g11929.t1
Valid prediction for GeneMark_model.29864_t
Valid prediction for CodingQuarry_transcript_57338-T1
Valid prediction for GlimmerHMM_glimmerT_17776-T1
Valid prediction for CodingQuarry_transcript_57339-T1
Valid prediction for Augustus_model.g11928.t1
Valid prediction for snap_scaffold_7-snap.1077-T1
Valid prediction for snap_scaffold_7-snap.1074-T1
Valid prediction for snap_scaffold_7-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_17760-T1
Valid prediction for Augustus_model.g11917.t1
Valid prediction for snap_scaffold_7-snap.1071-T1
Valid prediction for snap_scaffold_7-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_17766-T1
Valid prediction for GlimmerHMM_glimmerT_17764-T1
Valid prediction for snap_scaffold_7-snap.1090-T1
Valid prediction for GlimmerHMM_glimmerT_17781-T1
Valid prediction for snap_scaffold_7-snap.1100-T1
Valid prediction for snap_scaffold_7-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_17763-T1
Valid prediction for snap_scaffold_7-snap.1098-T1
Valid prediction for pasa_asmbl_49683.p1
Valid prediction for GlimmerHMM_glimmerT_17770-T1
Valid prediction for Augustus_model.g11918.t1
Valid prediction for Augustus_model.g11921.t1
Valid prediction for GeneMark_model.29859_t
Couldn't classify 121634, 121969
Sorry, prediction pasa_asmbl_50642.p1 fails validation.
(TTC)	 GT	121634-121969	TC	CCT
Valid prediction for pasa_asmbl_49682.p1
Valid prediction for Augustus_model.g11924.t1
Valid prediction for GeneMark_model.29863_t
Valid prediction for GeneMark_model.29877_t
Valid prediction for Augustus_model.g11931.t1
Valid prediction for GeneMark_model.29869_t
Valid prediction for GeneMark_model.29879_t
Valid prediction for Augustus_model.g11916.t1
Valid prediction for snap_scaffold_7-snap.1067-T1
Valid prediction for GeneMark_model.29860_t
Valid prediction for snap_scaffold_7-snap.1103-T1
Valid prediction for Augustus_model.g11930.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 154764, rend_intergenic: 154250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266705
-exon list size: 378


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 154764, rend_intergenic: 154250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 31384
-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 2265 - 31384
-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 2265 - 30715
-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

-building DP trellis

-building trellis in range 2265 - 21666
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 11114 - 21666

-building DP trellis

-building trellis in range 253084 - 266705
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-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 255422 - 266705
-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

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