-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_10555578-10710095

-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_4-snap.2289-T1
Valid prediction for Augustus_model.g6762.t1
Valid prediction for GeneMark_model.16855_t
Valid prediction for Augustus_model.g6765.t1
Valid prediction for snap_scaffold_4-snap.2268-T1
Valid prediction for snap_scaffold_4-snap.2287-T1
Valid prediction for GeneMark_model.16859_t
Valid prediction for Augustus_model.g6766.t1
Valid prediction for snap_scaffold_4-snap.2282-T1
Valid prediction for snap_scaffold_4-snap.2256-T1
Valid prediction for GlimmerHMM_glimmerT_10321-T1
Valid prediction for GeneMark_model.16852_t
Valid prediction for GeneMark_model.16841_t
Valid prediction for snap_scaffold_4-snap.2281-T1
Valid prediction for GlimmerHMM_glimmerT_10332-T1
Valid prediction for snap_scaffold_4-snap.2283-T1
Valid prediction for Augustus_model.g6771.t1
Valid prediction for Augustus_model.g6772.t1
Valid prediction for snap_scaffold_4-snap.2276-T1
Valid prediction for GlimmerHMM_glimmerT_10333-T1
Valid prediction for GeneMark_model.16866_t
Valid prediction for GeneMark_model.16844_t
Valid prediction for Augustus_model.g6760.t1
Valid prediction for snap_scaffold_4-snap.2274-T1
Valid prediction for snap_scaffold_4-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_10327-T1
Valid prediction for GlimmerHMM_glimmerT_10328-T1
Valid prediction for snap_scaffold_4-snap.2261-T1
Valid prediction for GlimmerHMM_glimmerT_10334-T1
Valid prediction for GlimmerHMM_glimmerT_10338-T1
Valid prediction for snap_scaffold_4-snap.2278-T1
Valid prediction for snap_scaffold_4-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_10323-T1
Valid prediction for snap_scaffold_4-snap.2257-T1
Valid prediction for GeneMark_model.16868_t
Valid prediction for snap_scaffold_4-snap.2271-T1
Valid prediction for GeneMark_model.16860_t
Valid prediction for snap_scaffold_4-snap.2259-T1
Valid prediction for snap_scaffold_4-snap.2275-T1
Valid prediction for Augustus_model.g6773.t1
Valid prediction for GlimmerHMM_glimmerT_10337-T1
Valid prediction for snap_scaffold_4-snap.2277-T1
Valid prediction for snap_scaffold_4-snap.2270-T1
Valid prediction for GeneMark_model.16863_t
Valid prediction for Augustus_model.g6759.t1
Valid prediction for GeneMark_model.16869_t
Valid prediction for GeneMark_model.16842_t
Valid prediction for snap_scaffold_4-snap.2286-T1
Valid prediction for GlimmerHMM_glimmerT_10322-T1
Valid prediction for Augustus_model.g6761.t1
Valid prediction for GlimmerHMM_glimmerT_10335-T1
Valid prediction for snap_scaffold_4-snap.2290-T1
Valid prediction for GeneMark_model.16847_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 snap_scaffold_4-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_10330-T1
Valid prediction for snap_scaffold_4-snap.2260-T1
Valid prediction for snap_scaffold_4-snap.2267-T1
Valid prediction for snap_scaffold_4-snap.2272-T1
Valid prediction for GeneMark_model.16843_t
Valid prediction for snap_scaffold_4-snap.2264-T1
Valid prediction for GeneMark_model.16864_t
Valid prediction for GlimmerHMM_glimmerT_10329-T1
Valid prediction for GlimmerHMM_glimmerT_10331-T1
Valid prediction for GeneMark_model.16856_t
Valid prediction for GlimmerHMM_glimmerT_10325-T1
Valid prediction for Augustus_model.g6775.t1
Valid prediction for GeneMark_model.16845_t
Valid prediction for GeneMark_model.16867_t
Valid prediction for Augustus_model.g6767.t1
Valid prediction for Augustus_model.g6768.t1
Valid prediction for snap_scaffold_4-snap.2285-T1
Valid prediction for Augustus_model.g6764.t1
Valid prediction for Augustus_model.g6763.t1
Valid prediction for GlimmerHMM_glimmerT_10324-T1
Valid prediction for GeneMark_model.16865_t
Valid prediction for snap_scaffold_4-snap.2273-T1
Valid prediction for Augustus_model.g6770.t1
Valid prediction for Augustus_model.g6774.t1
Valid prediction for snap_scaffold_4-snap.2265-T1
Valid prediction for GeneMark_model.16851_t
Valid prediction for GeneMark_model.16858_t
Valid prediction for GeneMark_model.16870_t
Valid prediction for Augustus_model.g6769.t1
Valid prediction for snap_scaffold_4-snap.2262-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.16853_t
Valid prediction for GlimmerHMM_glimmerT_10326-T1
Valid prediction for GeneMark_model.16850_t
Valid prediction for GlimmerHMM_glimmerT_10336-T1
Couldn't classify 116889, 117032
Sorry, prediction pasa_asmbl_41601.p1 fails validation.
(ATG)	 AA	112572-112823	GT	AGG
(GCG)	 AG	113365-113523	GT	CGG
(GTC)	 AG	113749-113928	GT	AAG
(GGG)	 AG	115408-115597	GT	AGG
(GAA)	 AG	115883-116039	GT	AAG
(CGA)	 AG	116290-116431	GT	TGG
(CAT)	 AG	116889-117032	TG	GGT
-recovered pasa_asmbl_41601.p1, initial, 112572, 112823
-recovered pasa_asmbl_41601.p1, internal, 113365, 113523
-recovered pasa_asmbl_41601.p1, internal, 113749, 113928
-recovered pasa_asmbl_41601.p1, internal, 115408, 115597
-recovered pasa_asmbl_41601.p1, internal, 115883, 116039
-recovered pasa_asmbl_41601.p1, internal, 116290, 116431
Valid prediction for snap_scaffold_4-snap.2266-T1
Valid prediction for GeneMark_model.16846_t
Valid prediction for snap_scaffold_4-snap.2288-T1
Valid prediction for GeneMark_model.16861_t
Valid prediction for GeneMark_model.16857_t
Valid prediction for GeneMark_model.16862_t
Valid prediction for snap_scaffold_4-snap.2284-T1
Valid prediction for GeneMark_model.16848_t
Valid prediction for GeneMark_model.16854_t
Valid prediction for snap_scaffold_4-snap.2279-T1
Valid prediction for snap_scaffold_4-snap.2269-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16225, rend_intergenic: 10461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19034, rend_intergenic: 17433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23164, rend_intergenic: 22212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51162, rend_intergenic: 47599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127190, rend_intergenic: 126264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132430, rend_intergenic: 129260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154518
-exon list size: 390


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 16225, rend_intergenic: 10461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19034, rend_intergenic: 17433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23164, rend_intergenic: 22212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51162, rend_intergenic: 47599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127190, rend_intergenic: 126264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132430, rend_intergenic: 129260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support