-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_4014277-4174983

-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_25-snap.856-T1
Valid prediction for GeneMark_model.96498_t
Valid prediction for GeneMark_model.96491_t
Valid prediction for snap_scaffold_25-snap.860-T1
Valid prediction for Augustus_model.g36860.t1
Valid prediction for snap_scaffold_25-snap.874-T1
Valid prediction for snap_scaffold_25-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_55264-T1
Valid prediction for GeneMark_model.96483_t
Valid prediction for Augustus_model.g36868.t1
Valid prediction for GeneMark_model.96492_t
Valid prediction for GlimmerHMM_glimmerT_55249-T1
Valid prediction for snap_scaffold_25-snap.879-T1
Valid prediction for GeneMark_model.96490_t
Valid prediction for GeneMark_model.96500_t
Valid prediction for GlimmerHMM_glimmerT_55255-T1
Valid prediction for Augustus_model.g36859.t1
Valid prediction for snap_scaffold_25-snap.878-T1
Valid prediction for HiQ_model.g36865.t1
Valid prediction for snap_scaffold_25-snap.881-T1
Valid prediction for Augustus_model.g36867.t1
Valid prediction for snap_scaffold_25-snap.870-T1
Couldn't classify 104916, 104966
Sorry, prediction pasa_asmbl_33474.p1 fails validation.
(ACC)	 GA	104916-104966	GT	AGG
(CTT)	 AG	105101-105190	GT	AGG
(GAG)	 AG	105320-105506	GT	CAG
(ATA)	 AG	106297-106370	GT	AGG
(AAA)	 AG	106577-106663	GT	AGG
(CAA)	 AG	106759-106818	TG	GAT
-recovered pasa_asmbl_33474.p1, terminal, 106759, 106818
-recovered pasa_asmbl_33474.p1, internal, 105101, 105190
-recovered pasa_asmbl_33474.p1, internal, 105320, 105506
-recovered pasa_asmbl_33474.p1, internal, 106297, 106370
-recovered pasa_asmbl_33474.p1, internal, 106577, 106663
Couldn't classify 104322, 104378
Sorry, prediction pasa_asmbl_33471.p1 fails validation.
(ATG)	 AC	103377-103457	GT	GAG
(GCT)	 AG	103548-103612	GT	TGG
(GGT)	 AG	103702-103846	GT	TTG
(GGT)	 AG	104077-104226	GT	AGG
(GTT)	 AG	104322-104378	TG	GTT
-recovered pasa_asmbl_33471.p1, initial, 103377, 103457
-recovered pasa_asmbl_33471.p1, internal, 103548, 103612
-recovered pasa_asmbl_33471.p1, internal, 103702, 103846
-recovered pasa_asmbl_33471.p1, internal, 104077, 104226
Valid prediction for GeneMark_model.96485_t
Valid prediction for GeneMark_model.96477_t
Valid prediction for Augustus_model.g36857.t1
Valid prediction for Augustus_model.g36869.t1
Valid prediction for snap_scaffold_25-snap.876-T1
Valid prediction for snap_scaffold_25-snap.875-T1
Valid prediction for GeneMark_model.96479_t
Valid prediction for snap_scaffold_25-snap.854-T1
Valid prediction for GeneMark_model.96510_t
Valid prediction for GeneMark_model.96488_t
Valid prediction for GeneMark_model.96496_t
Valid prediction for GeneMark_model.96502_t
Valid prediction for GlimmerHMM_glimmerT_55257-T1
Valid prediction for GeneMark_model.96507_t
Valid prediction for Augustus_model.g36861.t1
Valid prediction for snap_scaffold_25-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_55250-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 GlimmerHMM_glimmerT_55259-T1
Valid prediction for GlimmerHMM_glimmerT_55251-T1
Valid prediction for snap_scaffold_25-snap.873-T1
Valid prediction for GeneMark_model.96508_t
Valid prediction for GlimmerHMM_glimmerT_55258-T1
Valid prediction for Augustus_model.g36858.t1
Valid prediction for Augustus_model.g36866.t1
Valid prediction for GeneMark_model.96506_t
Valid prediction for GeneMark_model.96495_t
Valid prediction for snap_scaffold_25-snap.869-T1
Valid prediction for snap_scaffold_25-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_55261-T1
Valid prediction for Augustus_model.g36862.t1
Valid prediction for GeneMark_model.96476_t
Couldn't classify 76432, 77040
Sorry, prediction pasa_asmbl_34150.p1 fails validation.
(CTG)	 GT	76432-77040	AT	AGA
Couldn't classify 66368, 66625
Sorry, prediction pasa_asmbl_34602.p2 fails validation.
(ATG)	 CC	64868-65005	GT	AGG
(GTG)	 AG	66368-66625	GT	CGG
-recovered pasa_asmbl_34602.p2, initial, 64868, 65005
-recovered pasa_asmbl_34602.p2, internal, 66368, 66625
Valid prediction for snap_scaffold_25-snap.868-T1
Valid prediction for GeneMark_model.96499_t
Valid prediction for GlimmerHMM_glimmerT_55262-T1
Valid prediction for Augustus_model.g36856.t1
Valid prediction for GeneMark_model.96484_t
Valid prediction for Augustus_model.g36864.t1
Valid prediction for GlimmerHMM_glimmerT_55260-T1
Valid prediction for snap_scaffold_25-snap.872-T1
Valid prediction for snap_scaffold_25-snap.862-T1
Valid prediction for snap_scaffold_25-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_55253-T1
Valid prediction for GeneMark_model.96494_t
Valid prediction for snap_scaffold_25-snap.864-T1
Valid prediction for GeneMark_model.96486_t
Valid prediction for snap_scaffold_25-snap.871-T1
Valid prediction for GeneMark_model.96481_t
Valid prediction for GeneMark_model.96487_t
Valid prediction for GlimmerHMM_glimmerT_55252-T1
Valid prediction for GeneMark_model.96509_t
Valid prediction for GlimmerHMM_glimmerT_55263-T1
Valid prediction for snap_scaffold_25-snap.877-T1
Valid prediction for GeneMark_model.96482_t
Valid prediction for GeneMark_model.96505_t
Couldn't classify 50846, 50869
Sorry, prediction pasa_asmbl_34153.p1 fails validation.
(ATA)	 TT	50846-50869	GT	AGG
(TCC)	 AG	51093-51200	GT	GGG
(CTT)	 AG	51368-51448	GT	GAG
(CAC)	 AG	51554-51757	GC	GAG
-recovered pasa_asmbl_34153.p1, terminal, 51554, 51757
-recovered pasa_asmbl_34153.p1, internal, 51093, 51200
-recovered pasa_asmbl_34153.p1, internal, 51368, 51448
-recovered pasa_asmbl_34153.p1, internal, 51554, 51757
Valid prediction for snap_scaffold_25-snap.863-T1
Valid prediction for GeneMark_model.96504_t
Valid prediction for GeneMark_model.96478_t
Valid prediction for GlimmerHMM_glimmerT_55254-T1
Valid prediction for GeneMark_model.96497_t
Valid prediction for GeneMark_model.96475_t
Couldn't classify 67160, 68638
Sorry, prediction pasa_asmbl_34152.p1 fails validation.
(CAT)	 CT	67160-68638	TA	GAT
Valid prediction for Augustus_model.g36863.t1
Valid prediction for snap_scaffold_25-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_55256-T1
Valid prediction for snap_scaffold_25-snap.855-T1
Valid prediction for GeneMark_model.96511_t
Valid prediction for GeneMark_model.96480_t
Valid prediction for snap_scaffold_25-snap.882-T1
Valid prediction for snap_scaffold_25-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_55265-T1
Valid prediction for GeneMark_model.96503_t
Valid prediction for snap_scaffold_25-snap.857-T1
Valid prediction for snap_scaffold_25-snap.866-T1
Valid prediction for GeneMark_model.96501_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23488, rend_intergenic: 16968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153019, rend_intergenic: 149316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160707
-exon list size: 423


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.2    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23488, rend_intergenic: 16968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153019, rend_intergenic: 149316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 14922
-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

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

-building DP trellis

-building trellis in range 1 - 10905
-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

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

-building DP trellis

-building trellis in range 1 - 10566
-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