-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_3192682-3340121

-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.686-T1
Valid prediction for snap_scaffold_25-snap.690-T1
Valid prediction for GeneMark_model.96294_t
Valid prediction for snap_scaffold_25-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_55133-T1
Valid prediction for snap_scaffold_25-snap.681-T1
Couldn't classify 27060, 27156
Couldn't classify 29112, 29177
Sorry, prediction pasa_asmbl_33405.p1 fails validation.
(GAT)	 GT	27060-27156	GT	AGG
(TGT)	 AG	27262-27440	GT	TGG
(GCG)	 AG	29112-29177	AC	GCA
-recovered pasa_asmbl_33405.p1, internal, 27262, 27440
Valid prediction for GeneMark_model.96331_t
Valid prediction for GeneMark_model.96313_t
Couldn't classify 81465, 81705
Couldn't classify 84051, 84194
Sorry, prediction pasa_asmbl_33411.p1 fails validation.
(AAG)	 AT	81465-81705	GT	AGG
(ACG)	 AG	81812-82023	GT	AGG
(GTT)	 AG	82167-82305	GT	GGG
(GTA)	 AG	83674-83822	GT	TGG
(CCA)	 AG	84051-84194	AG	TCA
-recovered pasa_asmbl_33411.p1, internal, 81812, 82023
-recovered pasa_asmbl_33411.p1, internal, 82167, 82305
-recovered pasa_asmbl_33411.p1, internal, 83674, 83822
Valid prediction for snap_scaffold_25-snap.678-T1
Valid prediction for GlimmerHMM_glimmerT_55141-T1
Valid prediction for snap_scaffold_25-snap.692-T1
Valid prediction for GeneMark_model.96298_t
Valid prediction for snap_scaffold_25-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_55134-T1
Valid prediction for snap_scaffold_25-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_55137-T1
Valid prediction for GeneMark_model.96323_t
Valid prediction for snap_scaffold_25-snap.687-T1
Valid prediction for GeneMark_model.96329_t
Valid prediction for GeneMark_model.96316_t
Valid prediction for snap_scaffold_25-snap.695-T1
Valid prediction for Augustus_model.g36778.t1
Valid prediction for GeneMark_model.96320_t
Valid prediction for GeneMark_model.96307_t
Valid prediction for GeneMark_model.96308_t
Couldn't classify 77027, 77788
Couldn't classify 77867, 77983
Sorry, prediction pasa_asmbl_33409.p1 fails validation.
(CCC)	 GC	77027-77788	GT	AGG
(ATG)	 AG	77867-77983	AC	ACA
Valid prediction for snap_scaffold_25-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_55143-T1
Valid prediction for GlimmerHMM_glimmerT_55146-T1
Valid prediction for GeneMark_model.96290_t
Valid prediction for Augustus_model.g36784.t1
Valid prediction for GeneMark_model.96300_t
Valid prediction for GeneMark_model.96293_t
Valid prediction for GeneMark_model.96311_t
Valid prediction for GeneMark_model.96318_t
Valid prediction for snap_scaffold_25-snap.684-T1
Valid prediction for snap_scaffold_25-snap.663-T1
Valid prediction for GeneMark_model.96305_t
Valid prediction for GeneMark_model.96287_t
Couldn't classify 24162, 24232
Couldn't classify 25129, 25197
Sorry, prediction pasa_asmbl_33404.p1 fails validation.
(GAA)	 AT	24162-24232	GT	ATG
(CAT)	 AG	24379-24521	GT	CGG
(AGA)	 AG	24650-24705	GT	AGG
(CTA)	 AG	25129-25197	AA	ACA
-recovered pasa_asmbl_33404.p1, internal, 24379, 24521
-recovered pasa_asmbl_33404.p1, internal, 24650, 24705
Couldn't classify 76624, 76942
Sorry, prediction pasa_asmbl_33408.p1 fails validation.
(ATG)	 TT	76088-76177	GT	GGG
(ACT)	 AG	76265-76338	GT	AGG
(CCC)	 AG	76624-76942	AA	GCA
-recovered pasa_asmbl_33408.p1, initial, 76088, 76177
-recovered pasa_asmbl_33408.p1, internal, 76265, 76338
Valid prediction for GeneMark_model.96327_t
Valid prediction for GeneMark_model.96291_t
Valid prediction for GeneMark_model.96302_t
Couldn't classify 37048, 37054
Couldn't classify 40836, 40897
Sorry, prediction pasa_asmbl_33406.p1 fails validation.
(CTA)	 TG	37048-37054	GT	CGG
(CCC)	 AG	37297-37395	GT	CCG
(AGG)	 AG	37877-37962	GT	CTG
(GAG)	 AG	40496-40688	GT	AGG
(ACG)	 AG	40836-40897	GA	GAG
-recovered pasa_asmbl_33406.p1, internal, 37297, 37395
-recovered pasa_asmbl_33406.p1, internal, 37877, 37962
-recovered pasa_asmbl_33406.p1, internal, 40496, 40688
Valid prediction for snap_scaffold_25-snap.670-T1
Valid prediction for Augustus_model.g36785.t1
Valid prediction for CodingQuarry_transcript_38579-T1
Valid prediction for snap_scaffold_25-snap.673-T1
Valid prediction for GeneMark_model.96296_t
Valid prediction for snap_scaffold_25-snap.696-T1
Valid prediction for Augustus_model.g36777.t1
Valid prediction for GeneMark_model.96325_t
Valid prediction for Augustus_model.g36782.t1
Valid prediction for snap_scaffold_25-snap.689-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_55142-T1
Valid prediction for snap_scaffold_25-snap.667-T1
Valid prediction for snap_scaffold_25-snap.664-T1
Valid prediction for snap_scaffold_25-snap.676-T1
Valid prediction for HiQ_model.g36776.t1
Valid prediction for GeneMark_model.96310_t
Valid prediction for GeneMark_model.96297_t
Valid prediction for Augustus_model.g36781.t1
Valid prediction for GlimmerHMM_glimmerT_55135-T1
Valid prediction for snap_scaffold_25-snap.680-T1
Valid prediction for GeneMark_model.96328_t
Valid prediction for snap_scaffold_25-snap.672-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.96314_t
Valid prediction for snap_scaffold_25-snap.682-T1
Valid prediction for snap_scaffold_25-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_55136-T1
Valid prediction for snap_scaffold_25-snap.691-T1
Couldn't classify 47792, 48025
Sorry, prediction pasa_asmbl_34108.p1 fails validation.
(AAA)	 AA	47792-48025	GT	AGG
(AAG)	 AG	48314-48449	GT	CAG
(ACT)	 AG	48615-48839	GT	AGG
(GAG)	 AG	49155-49276	GT	TGG
(GGT)	 AG	49369-49495	GT	AGG
(GTG)	 AG	49606-49737	GT	CAG
(GGA)	 AG	50002-50175	GT	AGG
(GAA)	 AG	50381-50640	GA	GAG
-recovered pasa_asmbl_34108.p1, terminal, 50381, 50640
-recovered pasa_asmbl_34108.p1, internal, 48314, 48449
-recovered pasa_asmbl_34108.p1, internal, 48615, 48839
-recovered pasa_asmbl_34108.p1, internal, 49155, 49276
-recovered pasa_asmbl_34108.p1, internal, 49369, 49495
-recovered pasa_asmbl_34108.p1, internal, 49606, 49737
-recovered pasa_asmbl_34108.p1, internal, 50002, 50175
Couldn't classify 92824, 92899
Sorry, prediction pasa_asmbl_34104.p1 fails validation.
(CAG)	 AC	92824-92899	GT	AGG
(CCA)	 AG	93586-93773	GT	AGG
(GCG)	 AG	94882-95028	GT	AGG
(CTT)	 AG	95183-95293	GT	AGG
(CAA)	 AG	95985-96092	GT	CAG
(GAG)	 AG	96520-96631	GT	AGG
(TGG)	 AG	96784-98243	GA	AAG
-recovered pasa_asmbl_34104.p1, terminal, 96784, 98243
-recovered pasa_asmbl_34104.p1, internal, 93586, 93773
-recovered pasa_asmbl_34104.p1, internal, 94882, 95028
-recovered pasa_asmbl_34104.p1, internal, 95183, 95293
-recovered pasa_asmbl_34104.p1, internal, 95985, 96092
-recovered pasa_asmbl_34104.p1, internal, 96520, 96631
Valid prediction for GeneMark_model.96309_t
Valid prediction for GeneMark_model.96315_t
Valid prediction for snap_scaffold_25-snap.662-T1
Valid prediction for GeneMark_model.96299_t
Valid prediction for GeneMark_model.96326_t
Valid prediction for snap_scaffold_25-snap.697-T1
Valid prediction for GeneMark_model.96312_t
Valid prediction for GeneMark_model.96322_t
Valid prediction for GeneMark_model.96289_t
Valid prediction for pasa_asmbl_34106.p1
Couldn't classify 126082, 126532
Sorry, prediction pasa_asmbl_34581.p1 fails validation.
(TCA)	 TG	126082-126532	GT	GGG
(TCA)	 AG	128357-128529	GT	TGG
(GGA)	 AG	130444-130696	GT	ATG
(GTC)	 AG	130940-131196	CG	AGC
-recovered pasa_asmbl_34581.p1, terminal, 130940, 131196
-recovered pasa_asmbl_34581.p1, internal, 128357, 128529
-recovered pasa_asmbl_34581.p1, internal, 130444, 130696
Valid prediction for GlimmerHMM_glimmerT_55144-T1
Valid prediction for GeneMark_model.96330_t
Valid prediction for CodingQuarry_transcript_38580-T1
Valid prediction for snap_scaffold_25-snap.671-T1
Valid prediction for GeneMark_model.96288_t
Valid prediction for GlimmerHMM_glimmerT_55145-T1
Valid prediction for snap_scaffold_25-snap.693-T1
Valid prediction for snap_scaffold_25-snap.665-T1
Valid prediction for GeneMark_model.96286_t
Valid prediction for CodingQuarry_transcript_38581-T1
Valid prediction for GeneMark_model.96319_t
Valid prediction for GeneMark_model.96321_t
Valid prediction for GeneMark_model.96301_t
Valid prediction for GeneMark_model.96303_t
Valid prediction for GlimmerHMM_glimmerT_55140-T1
Valid prediction for Augustus_model.g36780.t1
Valid prediction for snap_scaffold_25-snap.685-T1
Valid prediction for snap_scaffold_25-snap.668-T1
Valid prediction for snap_scaffold_25-snap.675-T1
Valid prediction for Augustus_model.g36779.t1
Valid prediction for snap_scaffold_25-snap.683-T1
Valid prediction for GeneMark_model.96306_t
Valid prediction for GeneMark_model.96304_t
Valid prediction for snap_scaffold_25-snap.666-T1
Valid prediction for GeneMark_model.96292_t
Valid prediction for GlimmerHMM_glimmerT_55138-T1
Valid prediction for GlimmerHMM_glimmerT_55139-T1
Valid prediction for GeneMark_model.96285_t
Valid prediction for GeneMark_model.96324_t
Valid prediction for GeneMark_model.96295_t
Valid prediction for snap_scaffold_25-snap.679-T1
Valid prediction for HiQ_model.g36783.t1
Valid prediction for GeneMark_model.96317_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13584, rend_intergenic: 8780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38228, rend_intergenic: 34524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47249, rend_intergenic: 42726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64355, rend_intergenic: 50845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68266, rend_intergenic: 67623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70584, rend_intergenic: 68500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91821, rend_intergenic: 78148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105160, rend_intergenic: 97319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127658, rend_intergenic: 117026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137748, rend_intergenic: 128762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147440
-exon list size: 663


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
0.9    
1.1    
1.2    
1.4    
1.5    
1.7    
1.8    
2.0    
2.1    
2.3    
2.4    
2.6    
2.7    
2.9    
3.0    
3.2    
3.3    
3.5    
3.6    
3.8    
3.9    
4.1    
4.2    
4.4    
4.5    
4.7    
4.8    
5.0    
5.1    
5.3    
5.4    
5.6    
5.7    
5.9    
6.0    
6.2    
6.3    
6.5    
6.6    
6.8    
6.9    
7.1    
7.2    
7.4    
7.5    
7.7    
7.8    
8.0    
8.1    
8.3    
8.4    
8.6    
8.7    
8.9    
9.0    
9.2    
9.3    
9.5    
9.6    
9.8    
9.9    
10.1    
10.2    
10.4    
10.5    
10.7    
10.8    
11.0    
11.1    
11.3    
11.4    
11.6    
11.7    
11.9    
12.0    
12.2    
12.3    
12.5    
12.6    
12.8    
12.9    
13.1    
13.2    
13.4    
13.5    
13.7    
13.8    
14.0    
14.1    
14.3    
14.4    
14.6    
14.7    
14.9    
15.0    
15.2    
15.3    
15.5    
15.6    
15.8    
15.9    
16.1    
16.2    
16.4    
16.5    
16.7    
16.8    
17.0    
17.1    
17.3    
17.4    
17.6    
17.7    
17.9    
18.0    
18.2    
18.3    
18.5    
18.6    
18.8    
18.9    
19.1    
19.2    
19.4    
19.5    
19.7    
19.8    
20.0    
20.2    
20.3    
20.5    
20.6    
20.8    
20.9    
21.1    
21.2    
21.4    
21.5    
21.7    
21.8    
22.0    
22.1    
22.3    
22.4    
22.6    
22.7    
22.9    
23.0    
23.2    
23.3    
23.5    
23.6    
23.8    
23.9    
24.1    
24.2    
24.4    
24.5    
24.7    
24.8    
25.0    
25.1    
25.3    
25.4    
25.6    
25.7    
25.9    
26.0    
26.2    
26.3    
26.5    
26.6    
26.8    
26.9    
27.1    
27.2    
27.4    
27.5    
27.7    
27.8    
28.0    
28.1    
28.3    
28.4    
28.6    
28.7    
28.9    
29.0    
29.2    
29.3    
29.5    
29.6    
29.8    
29.9    
30.1    
30.2    
30.4    
30.5    
30.7    
30.8    
31.0    
31.1    
31.3    
31.4    
31.6    
31.7    
31.9    
32.0    
32.2    
32.3    
32.5    
32.6    
32.8    
32.9    
33.1    
33.2    
33.4    
33.5    
33.7    
33.8    
34.0    
34.1    
34.3    
34.4    
34.6    
34.7    
34.9    
35.0    
35.2    
35.3    
35.5    
35.6    
35.8    
35.9    
36.1    
36.2    
36.4    
36.5    
36.7    
36.8    
37.0    
37.1    
37.3    
37.4    
37.6    
37.7    
37.9    
38.0    
38.2    
38.3    
38.5    
38.6    
38.8    
38.9    
39.1    
39.2    
39.4    
39.5    
39.7    
39.8    
40.0    
40.2    
40.3    
40.5    
40.6    
40.8    
40.9    
41.1    
41.2    
41.4    
41.5    
41.7    
41.8    
42.0    
42.1    
42.3    
42.4    
42.6    
42.7    
42.9    
43.0    
43.2    
43.3    
43.5    
43.6    
43.8    
43.9    
44.1    
44.2    
44.4    
44.5    
44.7    
44.8    
45.0    
45.1    
45.3    
45.4    
45.6    
45.7    
45.9    
46.0    
46.2    
46.3    
46.5    
46.6    
46.8    
46.9    
47.1    
47.2    
47.4    
47.5    
47.7    
47.8    
48.0    
48.1    
48.3    
48.4    
48.6    
48.7    
48.9    
49.0    
49.2    
49.3    
49.5    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.5    
50.7    
50.8    
51.0    
51.1    
51.3    
51.4    
51.6    
51.7    
51.9    
52.0    
52.2    
52.3    
52.5    
52.6    
52.8    
52.9    
53.1    
53.2    
53.4    
53.5    
53.7    
53.8    
54.0    
54.1    
54.3    
54.4    
54.6    
54.7    
54.9    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.1    
57.3    
57.4    
57.6    
57.7    
57.9    
58.0    
58.2    
58.3    
58.5    
58.6    
58.8    
58.9    
59.1    
59.2    
59.4    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 13584, rend_intergenic: 8780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38228, rend_intergenic: 34524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47249, rend_intergenic: 42726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64355, rend_intergenic: 50845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68266, rend_intergenic: 67623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70584, rend_intergenic: 68500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91821, rend_intergenic: 78148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105160, rend_intergenic: 97319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127658, rend_intergenic: 117026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137748, rend_intergenic: 128762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support