-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_17202790-17378549

-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_18855-T1
Valid prediction for snap_scaffold_7-snap.3289-T1
Valid prediction for snap_scaffold_7-snap.3287-T1
Valid prediction for snap_scaffold_7-snap.3284-T1
Valid prediction for snap_scaffold_7-snap.3268-T1
Valid prediction for snap_scaffold_7-snap.3296-T1
Valid prediction for snap_scaffold_7-snap.3269-T1
Valid prediction for Augustus_model.g12663.t1
Valid prediction for snap_scaffold_7-snap.3286-T1
Couldn't classify 32081, 33022
Sorry, prediction pasa_asmbl_50477.p1 fails validation.
(GAC)	 CA	32081-33022	TA	GAT
Valid prediction for Augustus_model.g12659.t1
Valid prediction for snap_scaffold_7-snap.3272-T1
Valid prediction for GlimmerHMM_glimmerT_18844-T1
Valid prediction for GlimmerHMM_glimmerT_18837-T1
Valid prediction for Augustus_model.g12658.t1
Valid prediction for snap_scaffold_7-snap.3298-T1
Valid prediction for snap_scaffold_7-snap.3300-T1
Valid prediction for snap_scaffold_7-snap.3299-T1
Valid prediction for snap_scaffold_7-snap.3265-T1
Valid prediction for GlimmerHMM_glimmerT_18842-T1
Valid prediction for GlimmerHMM_glimmerT_18838-T1
Valid prediction for GlimmerHMM_glimmerT_18840-T1
Valid prediction for snap_scaffold_7-snap.3290-T1
Valid prediction for snap_scaffold_7-snap.3263-T1
Valid prediction for snap_scaffold_7-snap.3280-T1
Valid prediction for snap_scaffold_7-snap.3281-T1
Valid prediction for snap_scaffold_7-snap.3277-T1
Valid prediction for snap_scaffold_7-snap.3267-T1
Valid prediction for GlimmerHMM_glimmerT_18850-T1
Valid prediction for snap_scaffold_7-snap.3274-T1
Valid prediction for snap_scaffold_7-snap.3266-T1
Valid prediction for GlimmerHMM_glimmerT_18853-T1
Valid prediction for Augustus_model.g12664.t1
Valid prediction for snap_scaffold_7-snap.3302-T1
Valid prediction for GlimmerHMM_glimmerT_18848-T1
Valid prediction for snap_scaffold_7-snap.3291-T1
Valid prediction for GlimmerHMM_glimmerT_18843-T1
Valid prediction for GlimmerHMM_glimmerT_18858-T1
Valid prediction for GlimmerHMM_glimmerT_18857-T1
Valid prediction for snap_scaffold_7-snap.3294-T1
Couldn't classify 116812, 116918
Sorry, prediction pasa_asmbl_50480.p1 fails validation.
(ATG)	 GG	111488-111623	GT	AGG
(GGG)	 AG	112104-112171	GT	GGG
(GCG)	 AG	112991-113059	GT	AGG
(GAC)	 AG	113218-113338	GT	TGG
(GAA)	 AG	113820-113904	GT	TGG
(CTT)	 AG	113995-114074	GT	CAG
(AGT)	 AG	116812-116918	GT	ACG
-recovered pasa_asmbl_50480.p1, initial, 111488, 111623
-recovered pasa_asmbl_50480.p1, internal, 112104, 112171
-recovered pasa_asmbl_50480.p1, internal, 112991, 113059
-recovered pasa_asmbl_50480.p1, internal, 113218, 113338
-recovered pasa_asmbl_50480.p1, internal, 113820, 113904
-recovered pasa_asmbl_50480.p1, internal, 113995, 114074
-recovered pasa_asmbl_50480.p1, internal, 116812, 116918

-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_7-snap.3292-T1
Valid prediction for snap_scaffold_7-snap.3275-T1
Valid prediction for GlimmerHMM_glimmerT_18849-T1
Valid prediction for snap_scaffold_7-snap.3264-T1
Valid prediction for snap_scaffold_7-snap.3278-T1
Valid prediction for snap_scaffold_7-snap.3301-T1
Valid prediction for Augustus_model.g12660.t1
Valid prediction for snap_scaffold_7-snap.3273-T1
Valid prediction for snap_scaffold_7-snap.3295-T1
Valid prediction for GlimmerHMM_glimmerT_18856-T1
Valid prediction for snap_scaffold_7-snap.3285-T1
Valid prediction for GlimmerHMM_glimmerT_18845-T1
Valid prediction for snap_scaffold_7-snap.3276-T1
Valid prediction for snap_scaffold_7-snap.3303-T1
Valid prediction for Augustus_model.g12666.t1
Valid prediction for snap_scaffold_7-snap.3279-T1
Valid prediction for GlimmerHMM_glimmerT_18839-T1
Valid prediction for GlimmerHMM_glimmerT_18846-T1
Valid prediction for Augustus_model.g12665.t1
Valid prediction for snap_scaffold_7-snap.3283-T1
Valid prediction for snap_scaffold_7-snap.3293-T1
Valid prediction for snap_scaffold_7-snap.3297-T1
Valid prediction for snap_scaffold_7-snap.3288-T1
Valid prediction for snap_scaffold_7-snap.3270-T1
Valid prediction for GlimmerHMM_glimmerT_18847-T1
Valid prediction for GlimmerHMM_glimmerT_18854-T1
Valid prediction for GlimmerHMM_glimmerT_18841-T1
Valid prediction for GlimmerHMM_glimmerT_18851-T1
Valid prediction for Augustus_model.g12661.t1
Valid prediction for snap_scaffold_7-snap.3271-T1
Valid prediction for snap_scaffold_7-snap.3282-T1
Valid prediction for Augustus_model.g12662.t1
Valid prediction for GlimmerHMM_glimmerT_18852-T1
Valid prediction for GlimmerHMM_glimmerT_18859-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22733, rend_intergenic: 9315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40531, rend_intergenic: 38113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48302, rend_intergenic: 44898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66410, rend_intergenic: 61152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70921, rend_intergenic: 69898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85081, rend_intergenic: 79555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95079, rend_intergenic: 90123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102086, rend_intergenic: 96102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137182, rend_intergenic: 123940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143405, rend_intergenic: 141298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145186, rend_intergenic: 143498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158134, rend_intergenic: 148987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168422, rend_intergenic: 166793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169745, rend_intergenic: 169149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172921, rend_intergenic: 170947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175760
-exon list size: 239


building trellis

0.4    
0.8    
1.2    
1.7    
2.1    
2.5    
2.9    
3.3    
3.7    
4.1    
4.6    
5.0    
5.4    
5.8    
6.2    
6.6    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.5    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.3    
18.7    
19.1    
19.5    
19.9    
20.3    
20.7    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
46.1    
46.5    
46.9    
47.3    
47.7    
48.1    
48.5    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.5    
51.9    
52.3    
52.7    
53.1    
53.5    
53.9    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.3    
79.7    
80.1    
80.5    
80.9    
81.3    
81.7    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.4    
93.8    
94.2    
94.6    
95.0    
95.4    
95.9    
96.3    
96.7    
97.1    
97.5    
97.9    
98.3    
98.8    
99.2    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 22733, rend_intergenic: 9315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40531, rend_intergenic: 38113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48302, rend_intergenic: 44898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66410, rend_intergenic: 61152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70921, rend_intergenic: 69898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85081, rend_intergenic: 79555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95079, rend_intergenic: 90123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102086, rend_intergenic: 96102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137182, rend_intergenic: 123940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143405, rend_intergenic: 141298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145186, rend_intergenic: 143498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158134, rend_intergenic: 148987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168422, rend_intergenic: 166793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169745, rend_intergenic: 169149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172921, rend_intergenic: 170947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 155999 - 175760
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support