-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_2629616-2853621

-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_50300-T1
Valid prediction for GlimmerHMM_glimmerT_50296-T1
Valid prediction for snap_scaffold_22-snap.447-T1
Valid prediction for snap_scaffold_22-snap.475-T1
Couldn't classify 199139, 199390
Couldn't classify 203846, 203890
Sorry, prediction pasa_asmbl_29240.p1 fails validation.
(ATC)	 TG	199139-199390	GT	AGG
(CGC)	 AG	200677-200855	GT	AGG
(GCA)	 AG	200985-201111	GT	GGG
(GAA)	 AG	201210-201335	GT	GGG
(GAC)	 AG	202240-202394	GT	AGG
(TGC)	 AG	203060-203195	GT	AGG
(GAT)	 AG	203846-203890	AG	GAA
add_exon() Sorry, pasa_asmbl_29240.p1 202240-202394-terminal-2 is invalid.
-recovered pasa_asmbl_29240.p1, terminal, 202240, 202394
-recovered pasa_asmbl_29240.p1, internal, 200677, 200855
-recovered pasa_asmbl_29240.p1, internal, 200985, 201111
-recovered pasa_asmbl_29240.p1, internal, 201210, 201335
-recovered pasa_asmbl_29240.p1, internal, 202240, 202394
-recovered pasa_asmbl_29240.p1, internal, 203060, 203195
Valid prediction for GeneMark_model.87058_t
Valid prediction for snap_scaffold_22-snap.463-T1
Valid prediction for Augustus_model.g33739.t1
Valid prediction for GeneMark_model.87032_t
Valid prediction for GeneMark_model.87027_t
Valid prediction for GeneMark_model.87030_t
Valid prediction for snap_scaffold_22-snap.483-T1
Valid prediction for snap_scaffold_22-snap.474-T1
Valid prediction for snap_scaffold_22-snap.452-T1
Couldn't classify 172779, 173019
Couldn't classify 173453, 173523
Sorry, prediction pasa_asmbl_29829.p1 fails validation.
(TGG)	 GC	172779-173019	GT	AGG
(TGT)	 AG	173453-173523	AA	ACA
Valid prediction for snap_scaffold_22-snap.460-T1
Valid prediction for GeneMark_model.87046_t
Valid prediction for snap_scaffold_22-snap.476-T1
Valid prediction for Augustus_model.g33733.t1
Valid prediction for GeneMark_model.87051_t
Valid prediction for GeneMark_model.87023_t
Valid prediction for snap_scaffold_22-snap.466-T1
Valid prediction for Augustus_model.g33734.t1
Couldn't classify 188645, 188768
Couldn't classify 193676, 193780
Sorry, prediction pasa_asmbl_29239.p1 fails validation.
(TCC)	 AG	188645-188768	GT	TGG
(GTA)	 AG	191418-191593	GT	GGG
(GTG)	 AG	193423-193542	GT	AAG
(AAT)	 AG	193676-193780	GT	GGG
-recovered pasa_asmbl_29239.p1, internal, 188645, 188768
-recovered pasa_asmbl_29239.p1, internal, 191418, 191593
-recovered pasa_asmbl_29239.p1, internal, 193423, 193542
-recovered pasa_asmbl_29239.p1, internal, 193676, 193780
Valid prediction for GeneMark_model.87044_t
Valid prediction for GeneMark_model.87040_t
Valid prediction for GeneMark_model.87029_t
Valid prediction for GlimmerHMM_glimmerT_50293-T1
Valid prediction for GeneMark_model.87052_t
Valid prediction for GeneMark_model.87025_t
Valid prediction for snap_scaffold_22-snap.468-T1
Valid prediction for GlimmerHMM_glimmerT_50297-T1
Valid prediction for GeneMark_model.87038_t
Valid prediction for GeneMark_model.87048_t
Valid prediction for snap_scaffold_22-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_50303-T1
Valid prediction for GlimmerHMM_glimmerT_50287-T1
Valid prediction for snap_scaffold_22-snap.485-T1
Valid prediction for GeneMark_model.87055_t
Valid prediction for Augustus_model.g33738.t1
Valid prediction for snap_scaffold_22-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_50304-T1
Valid prediction for snap_scaffold_22-snap.484-T1
Valid prediction for GeneMark_model.87034_t
Valid prediction for snap_scaffold_22-snap.451-T1
Valid prediction for GeneMark_model.87056_t
Valid prediction for Augustus_model.g33736.t1
Valid prediction for GeneMark_model.87024_t
Valid prediction for snap_scaffold_22-snap.465-T1
Valid prediction for snap_scaffold_22-snap.482-T1
Valid prediction for snap_scaffold_22-snap.480-T1
Valid prediction for snap_scaffold_22-snap.477-T1
Valid prediction for snap_scaffold_22-snap.486-T1
Valid prediction for snap_scaffold_22-snap.464-T1
Valid prediction for GeneMark_model.87042_t
Valid prediction for snap_scaffold_22-snap.487-T1
Valid prediction for Augustus_model.g33737.t1
Valid prediction for snap_scaffold_22-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_50301-T1
Valid prediction for GlimmerHMM_glimmerT_50291-T1
Valid prediction for GlimmerHMM_glimmerT_50299-T1
Valid prediction for GeneMark_model.87057_t
Valid prediction for snap_scaffold_22-snap.462-T1
Valid prediction for snap_scaffold_22-snap.454-T1
Valid prediction for GeneMark_model.87035_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.87054_t
Valid prediction for GeneMark_model.87043_t
Valid prediction for GlimmerHMM_glimmerT_50289-T1
Valid prediction for GeneMark_model.87037_t
Valid prediction for snap_scaffold_22-snap.467-T1
Valid prediction for GlimmerHMM_glimmerT_50290-T1
Valid prediction for GeneMark_model.87047_t
Valid prediction for Augustus_model.g33729.t1
Valid prediction for Augustus_model.g33732.t1
Valid prediction for snap_scaffold_22-snap.461-T1
Valid prediction for snap_scaffold_22-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_50305-T1
Valid prediction for snap_scaffold_22-snap.470-T1
Valid prediction for Augustus_model.g33735.t1
Valid prediction for Augustus_model.g33731.t1
Valid prediction for GeneMark_model.87041_t
Valid prediction for GeneMark_model.87026_t
Valid prediction for snap_scaffold_22-snap.472-T1
Valid prediction for GeneMark_model.87050_t
Valid prediction for GlimmerHMM_glimmerT_50298-T1
Valid prediction for snap_scaffold_22-snap.458-T1
Valid prediction for snap_scaffold_22-snap.456-T1
Valid prediction for snap_scaffold_22-snap.459-T1
Valid prediction for GlimmerHMM_glimmerT_50294-T1
Valid prediction for GeneMark_model.87059_t
Valid prediction for GeneMark_model.87033_t
Valid prediction for snap_scaffold_22-snap.471-T1
Valid prediction for GeneMark_model.87045_t
Valid prediction for snap_scaffold_22-snap.453-T1
Valid prediction for snap_scaffold_22-snap.448-T1
Valid prediction for snap_scaffold_22-snap.457-T1
Valid prediction for GlimmerHMM_glimmerT_50295-T1
Valid prediction for GlimmerHMM_glimmerT_50292-T1
Valid prediction for snap_scaffold_22-snap.469-T1
Valid prediction for GeneMark_model.87049_t
Valid prediction for GeneMark_model.87031_t
Valid prediction for Augustus_model.g33730.t1
Valid prediction for GeneMark_model.87053_t
Valid prediction for GlimmerHMM_glimmerT_50288-T1
Valid prediction for GeneMark_model.87039_t
Valid prediction for GeneMark_model.87036_t
Valid prediction for snap_scaffold_22-snap.449-T1
Valid prediction for snap_scaffold_22-snap.478-T1
Valid prediction for GlimmerHMM_glimmerT_50302-T1
Valid prediction for GeneMark_model.87028_t
Valid prediction for snap_scaffold_22-snap.450-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36725, rend_intergenic: 34498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83330, rend_intergenic: 81961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92289, rend_intergenic: 89209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98265, rend_intergenic: 94692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119563, rend_intergenic: 113924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224006
-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 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 36725, rend_intergenic: 34498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83330, rend_intergenic: 81961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92289, rend_intergenic: 89209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98265, rend_intergenic: 94692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119563, rend_intergenic: 113924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13823
-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