-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_3632783-3791537

-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_22-snap.658-T1
Valid prediction for GlimmerHMM_glimmerT_49210-T1
Valid prediction for snap_scaffold_22-snap.655-T1
Valid prediction for snap_scaffold_22-snap.668-T1
Valid prediction for Augustus_model.g32841.t1
Valid prediction for snap_scaffold_22-snap.680-T1
Valid prediction for Augustus_model.g32842.t1
Valid prediction for GlimmerHMM_glimmerT_49220-T1
Valid prediction for snap_scaffold_22-snap.672-T1
Valid prediction for snap_scaffold_22-snap.651-T1
Valid prediction for snap_scaffold_22-snap.670-T1
Valid prediction for GlimmerHMM_glimmerT_49218-T1
Couldn't classify 78264, 78638
Sorry, prediction pasa_asmbl_29955.p1 fails validation.
(GAT)	 GT	78264-78638	CA	CCC
Valid prediction for snap_scaffold_22-snap.677-T1
Valid prediction for snap_scaffold_22-snap.673-T1
Valid prediction for snap_scaffold_22-snap.661-T1
Valid prediction for snap_scaffold_22-snap.666-T1
Valid prediction for snap_scaffold_22-snap.665-T1
Couldn't classify 74794, 74881
Couldn't classify 76056, 76151
Sorry, prediction pasa_asmbl_29954.p1 fails validation.
(TTC)	 GC	74794-74881	GT	CGG
(AGC)	 AG	75432-75544	GT	AGG
(ATC)	 AG	75762-75884	GT	AGG
(CGT)	 AG	76056-76151	GC	ACG
-recovered pasa_asmbl_29954.p1, internal, 75432, 75544
-recovered pasa_asmbl_29954.p1, internal, 75762, 75884
-recovered pasa_asmbl_29954.p1, internal, 76056, 76151
Valid prediction for snap_scaffold_22-snap.679-T1
Valid prediction for snap_scaffold_22-snap.653-T1
Valid prediction for snap_scaffold_22-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_49216-T1
Valid prediction for snap_scaffold_22-snap.648-T1
Valid prediction for snap_scaffold_22-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_49211-T1
Valid prediction for snap_scaffold_22-snap.676-T1
Valid prediction for snap_scaffold_22-snap.682-T1
Valid prediction for snap_scaffold_22-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_49207-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 Augustus_model.g32845.t1
Valid prediction for GlimmerHMM_glimmerT_49219-T1
Valid prediction for Augustus_model.g32840.t1
Valid prediction for GlimmerHMM_glimmerT_49212-T1
Valid prediction for snap_scaffold_22-snap.675-T1
Valid prediction for snap_scaffold_22-snap.667-T1
Valid prediction for GlimmerHMM_glimmerT_49209-T1
Valid prediction for snap_scaffold_22-snap.674-T1
Couldn't classify 5411, 5513
Sorry, prediction pasa_asmbl_29183.p2 fails validation.
(AGT)	 GT	5411-5513	GT	AGG
(CTT)	 AG	8447-8484	GT	AGG
(ACG)	 AG	8717-8822	GT	CAG
(ATT)	 AG	8955-9013	GT	AGG
(GCT)	 AG	10974-11034	GT	AGG
(AAT)	 AG	11994-12001	GT	AGG
(ATC)	 AG	12137-12217	GT	AGG
(AGA)	 AG	15022-15135	AG	AAA
-recovered pasa_asmbl_29183.p2, terminal, 15022, 15135
-recovered pasa_asmbl_29183.p2, internal, 8447, 8484
-recovered pasa_asmbl_29183.p2, internal, 8717, 8822
-recovered pasa_asmbl_29183.p2, internal, 8955, 9013
-recovered pasa_asmbl_29183.p2, internal, 10974, 11034
-recovered pasa_asmbl_29183.p2, internal, 11994, 12001
-recovered pasa_asmbl_29183.p2, internal, 12137, 12217
Couldn't classify 15177, 15485
Sorry, prediction pasa_asmbl_29180.p2 fails validation.
(GGG)	 GG	15177-15485	CA	AGC
Valid prediction for snap_scaffold_22-snap.649-T1
Valid prediction for Augustus_model.g32843.t1
Couldn't classify 70100, 70157
Sorry, prediction pasa_asmbl_29178.p1 fails validation.
(AAG)	 GG	70100-70157	GT	TGG
(GCT)	 AG	70396-70607	GT	AGG
(GCA)	 AG	70747-70892	GT	TGG
(CTT)	 AG	71425-71539	GT	CGG
(CTG)	 AG	73891-74011	GT	CAG
(GTG)	 AG	75430-75594	GT	TGG
(GCA)	 AG	75684-75874	GT	AGG
(TCC)	 AG	76258-76422	GT	AGG
(GAA)	 AG	76558-76584	AC	AGA
-recovered pasa_asmbl_29178.p1, terminal, 76558, 76584
-recovered pasa_asmbl_29178.p1, internal, 70396, 70607
-recovered pasa_asmbl_29178.p1, internal, 70747, 70892
-recovered pasa_asmbl_29178.p1, internal, 71425, 71539
-recovered pasa_asmbl_29178.p1, internal, 73891, 74011
-recovered pasa_asmbl_29178.p1, internal, 75430, 75594
-recovered pasa_asmbl_29178.p1, internal, 75684, 75874
-recovered pasa_asmbl_29178.p1, internal, 76258, 76422
Valid prediction for GlimmerHMM_glimmerT_49213-T1
Valid prediction for snap_scaffold_22-snap.660-T1
Valid prediction for GlimmerHMM_glimmerT_49208-T1
Valid prediction for GlimmerHMM_glimmerT_49221-T1
Valid prediction for snap_scaffold_22-snap.659-T1
Valid prediction for Augustus_model.g32844.t1
Valid prediction for Augustus_model.g32839.t1
Valid prediction for GlimmerHMM_glimmerT_49223-T1
Valid prediction for GlimmerHMM_glimmerT_49222-T1
Valid prediction for snap_scaffold_22-snap.664-T1
Valid prediction for snap_scaffold_22-snap.654-T1
Valid prediction for snap_scaffold_22-snap.656-T1
Valid prediction for snap_scaffold_22-snap.647-T1
Valid prediction for snap_scaffold_22-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_49214-T1
Valid prediction for snap_scaffold_22-snap.678-T1
Valid prediction for snap_scaffold_22-snap.657-T1
Valid prediction for GlimmerHMM_glimmerT_49217-T1
Valid prediction for GlimmerHMM_glimmerT_49215-T1
Valid prediction for snap_scaffold_22-snap.683-T1
Valid prediction for snap_scaffold_22-snap.650-T1
Valid prediction for snap_scaffold_22-snap.652-T1
Valid prediction for snap_scaffold_22-snap.662-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 61733, rend_intergenic: 61730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12518, rend_intergenic: 6196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15291, rend_intergenic: 13017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26616, rend_intergenic: 20977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28199, rend_intergenic: 28112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31096, rend_intergenic: 28894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38227, rend_intergenic: 32088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50996, rend_intergenic: 46563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66209, rend_intergenic: 54946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 67309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90180, rend_intergenic: 82667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93447, rend_intergenic: 91215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100266, rend_intergenic: 93603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107689, rend_intergenic: 100628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115174, rend_intergenic: 108269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120756, rend_intergenic: 116938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128267, rend_intergenic: 120913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149152, rend_intergenic: 144291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158755
-exon list size: 292


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    
4.8    
5.1    
5.4    
5.8    
6.1    
6.5    
6.8    
7.1    
7.5    
7.8    
8.2    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.5    
10.9    
11.2    
11.6    
11.9    
12.2    
12.6    
12.9    
13.3    
13.6    
13.9    
14.3    
14.6    
15.0    
15.3    
15.6    
16.0    
16.3    
16.7    
17.0    
17.3    
17.7    
18.0    
18.4    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.8    
22.1    
22.4    
22.8    
23.1    
23.5    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.5    
26.9    
27.2    
27.6    
27.9    
28.2    
28.6    
28.9    
29.3    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.6    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.0    
35.4    
35.7    
36.1    
36.4    
36.7    
37.1    
37.4    
37.8    
38.1    
38.4    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.8    
42.2    
42.5    
42.9    
43.2    
43.5    
43.9    
44.2    
44.6    
44.9    
45.2    
45.6    
45.9    
46.3    
46.6    
46.9    
47.3    
47.6    
48.0    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.0    
52.4    
52.7    
53.1    
53.4    
53.7    
54.1    
54.4    
54.8    
55.1    
55.4    
55.8    
56.1    
56.5    
56.8    
57.1    
57.5    
57.8    
58.2    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.6    
61.9    
62.2    
62.6    
62.9    
63.3    
63.6    
63.9    
64.3    
64.6    
65.0    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.4    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.7    
71.1    
71.4    
71.8    
72.1    
72.4    
72.8    
73.1    
73.5    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.5    
76.9    
77.2    
77.6    
77.9    
78.2    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.6    
82.0    
82.3    
82.7    
83.0    
83.3    
83.7    
84.0    
84.4    
84.7    
85.0    
85.4    
85.7    
86.1    
86.4    
86.7    
87.1    
87.4    
87.8    
88.1    
88.4    
88.8    
89.1    
89.5    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.8    
92.2    
92.5    
92.9    
93.2    
93.5    
93.9    
94.2    
94.6    
94.9    
95.2    
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 15 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 61733, rend_intergenic: 61730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12518, rend_intergenic: 6196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15291, rend_intergenic: 13017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26616, rend_intergenic: 20977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28199, rend_intergenic: 28112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31096, rend_intergenic: 28894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38227, rend_intergenic: 32088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50996, rend_intergenic: 46563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66209, rend_intergenic: 54946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 67309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90180, rend_intergenic: 82667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93447, rend_intergenic: 91215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100266, rend_intergenic: 93603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107689, rend_intergenic: 100628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115174, rend_intergenic: 108269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120756, rend_intergenic: 116938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128267, rend_intergenic: 120913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149152, rend_intergenic: 144291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18612
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-found 4 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

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