-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_10098531-10331693

-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.2186-T1
Couldn't classify 190241, 190573
Sorry, prediction pasa_asmbl_33851.p1 fails validation.
(CTG)	 AT	190241-190573	TC	TCT
Valid prediction for snap_scaffold_25-snap.2191-T1
Valid prediction for snap_scaffold_25-snap.2177-T1
Valid prediction for GeneMark_model.97876_t
Valid prediction for GlimmerHMM_glimmerT_56244-T1
Valid prediction for GlimmerHMM_glimmerT_56217-T1
Valid prediction for snap_scaffold_25-snap.2184-T1
Valid prediction for GeneMark_model.97872_t
Valid prediction for GlimmerHMM_glimmerT_56218-T1
Valid prediction for GeneMark_model.97859_t
Valid prediction for snap_scaffold_25-snap.2180-T1
Valid prediction for snap_scaffold_25-snap.2169-T1
Valid prediction for GeneMark_model.97875_t
Valid prediction for GeneMark_model.97868_t
Valid prediction for snap_scaffold_25-snap.2170-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56230-T1
Valid prediction for GeneMark_model.97866_t
Valid prediction for GlimmerHMM_glimmerT_56243-T1
Valid prediction for GlimmerHMM_glimmerT_56214-T1
Valid prediction for GeneMark_model.97856_t
Valid prediction for GlimmerHMM_glimmerT_56226-T1
Valid prediction for GlimmerHMM_glimmerT_56238-T1
Valid prediction for snap_scaffold_25-snap.2171-T1
Valid prediction for GlimmerHMM_glimmerT_56225-T1
Valid prediction for GlimmerHMM_glimmerT_56216-T1
Valid prediction for GeneMark_model.97863_t
Valid prediction for snap_scaffold_25-snap.2174-T1
Valid prediction for snap_scaffold_25-snap.2192-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56224-T1
Valid prediction for GlimmerHMM_glimmerT_56219-T1
Valid prediction for snap_scaffold_25-snap.2172-T1
Valid prediction for GeneMark_model.97862_t
Valid prediction for GeneMark_model.97864_t
Valid prediction for GeneMark_model.97858_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 GeneMark_model.97873_t
Valid prediction for GeneMark_model.97874_t
Valid prediction for snap_scaffold_25-snap.2175-T1
Valid prediction for snap_scaffold_25-snap.2173-T1
Valid prediction for snap_scaffold_25-snap.2176-T1
Valid prediction for GlimmerHMM_glimmerT_56234-T1
Valid prediction for GlimmerHMM_glimmerT_56221-T1
Valid prediction for GeneMark_model.97870_t
Valid prediction for snap_scaffold_25-snap.2178-T1
Valid prediction for GeneMark_model.97865_t
Valid prediction for snap_scaffold_25-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_56241-T1
Valid prediction for snap_scaffold_25-snap.2168-T1
Valid prediction for GlimmerHMM_glimmerT_56228-T1
Valid prediction for GlimmerHMM_glimmerT_56231-T1
Valid prediction for GlimmerHMM_glimmerT_56229-T1
Valid prediction for snap_scaffold_25-snap.2166-T1
Valid prediction for GlimmerHMM_glimmerT_56220-T1
Valid prediction for GeneMark_model.97869_t
Valid prediction for snap_scaffold_25-snap.2181-T1
Valid prediction for snap_scaffold_25-snap.2164-T1
Valid prediction for GeneMark_model.97867_t
Valid prediction for snap_scaffold_25-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_56240-T1
Valid prediction for snap_scaffold_25-snap.2161-T1
Valid prediction for GeneMark_model.97860_t
Valid prediction for GeneMark_model.97857_t
Valid prediction for GlimmerHMM_glimmerT_56235-T1
Valid prediction for snap_scaffold_25-snap.2182-T1
Valid prediction for snap_scaffold_25-snap.2183-T1
Valid prediction for snap_scaffold_25-snap.2162-T1
Valid prediction for GlimmerHMM_glimmerT_56227-T1
Valid prediction for snap_scaffold_25-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_56237-T1
Valid prediction for snap_scaffold_25-snap.2167-T1
Valid prediction for snap_scaffold_25-snap.2188-T1
Valid prediction for CodingQuarry_transcript_38755-T1
Valid prediction for GlimmerHMM_glimmerT_56215-T1
Valid prediction for snap_scaffold_25-snap.2185-T1
Valid prediction for GeneMark_model.97871_t
Valid prediction for GlimmerHMM_glimmerT_56222-T1
Valid prediction for GlimmerHMM_glimmerT_56233-T1
Valid prediction for GlimmerHMM_glimmerT_56223-T1
Valid prediction for snap_scaffold_25-snap.2187-T1
Valid prediction for snap_scaffold_25-snap.2189-T1
Valid prediction for snap_scaffold_25-snap.2163-T1
Valid prediction for GeneMark_model.97861_t
Valid prediction for snap_scaffold_25-snap.2165-T1
Couldn't classify 105099, 105269
Sorry, prediction pasa_asmbl_34507.p1 fails validation.
(ATA)	 AA	105099-105269	GT	AGG
(GCA)	 AG	105377-105454	GT	AGG
(GCA)	 AG	106106-106297	GT	CTG
(ATT)	 AG	106962-107033	GT	AGG
(ATC)	 AG	108339-108506	AC	AAA
-recovered pasa_asmbl_34507.p1, terminal, 108339, 108506
-recovered pasa_asmbl_34507.p1, internal, 105377, 105454
-recovered pasa_asmbl_34507.p1, internal, 106106, 106297
-recovered pasa_asmbl_34507.p1, internal, 106962, 107033
Valid prediction for GlimmerHMM_glimmerT_56232-T1
Valid prediction for GlimmerHMM_glimmerT_56239-T1
Valid prediction for GlimmerHMM_glimmerT_56242-T1
Valid prediction for GlimmerHMM_glimmerT_56236-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 75384, rend_intergenic: 70310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231722, rend_intergenic: 229942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233163
-exon list size: 293


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.1    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.8    
6.1    
6.4    
6.8    
7.1    
7.5    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.2    
11.5    
11.9    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
15.9    
16.3    
16.6    
16.9    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.4    
21.7    
22.0    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.2    
31.5    
31.9    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.6    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.4    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.4    
46.8    
47.1    
47.5    
47.8    
48.1    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.9    
52.2    
52.5    
52.9    
53.2    
53.6    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.6    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.4    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.1    
68.5    
68.8    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
78.0    
78.3    
78.6    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.1    
83.4    
83.7    
84.1    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.1    
88.5    
88.8    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.5    
92.9    
93.2    
93.6    
93.9    
94.2    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
96.9    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 75384, rend_intergenic: 70310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231722, rend_intergenic: 229942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12972
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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