-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_151138-464494

-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_19137-T1
Valid prediction for GlimmerHMM_glimmerT_19109-T1
Valid prediction for Augustus_model.g12795.t1
Couldn't classify 183937, 184097
Sorry, prediction pasa_asmbl_52651.p1 fails validation.
(GAT)	 GA	183937-184097	GT	AGG
(GAT)	 AG	184533-184722	GT	TGG
(GTA)	 AG	185091-185198	GT	CAG
(GAG)	 AG	185385-185522	GT	AGG
(GGT)	 AG	185853-185914	GT	GCG
(TGT)	 AG	186573-186789	GG	GAG
-recovered pasa_asmbl_52651.p1, terminal, 186573, 186789
-recovered pasa_asmbl_52651.p1, internal, 184533, 184722
-recovered pasa_asmbl_52651.p1, internal, 185091, 185198
-recovered pasa_asmbl_52651.p1, internal, 185385, 185522
-recovered pasa_asmbl_52651.p1, internal, 185853, 185914
Valid prediction for GlimmerHMM_glimmerT_19128-T1
Valid prediction for GlimmerHMM_glimmerT_19115-T1
Valid prediction for GlimmerHMM_glimmerT_19118-T1
Valid prediction for snap_scaffold_8-snap.78-T1
Valid prediction for Augustus_model.g12797.t1
Valid prediction for GlimmerHMM_glimmerT_19134-T1
Valid prediction for Augustus_model.g12798.t1
Valid prediction for snap_scaffold_8-snap.75-T1
Valid prediction for snap_scaffold_8-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_19127-T1
Valid prediction for GlimmerHMM_glimmerT_19111-T1
Valid prediction for snap_scaffold_8-snap.70-T1
Valid prediction for snap_scaffold_8-snap.45-T1
Valid prediction for snap_scaffold_8-snap.39-T1
Valid prediction for snap_scaffold_8-snap.44-T1
Valid prediction for snap_scaffold_8-snap.81-T1
Valid prediction for snap_scaffold_8-snap.74-T1
Valid prediction for Augustus_model.g12796.t1
Valid prediction for GlimmerHMM_glimmerT_19121-T1
Valid prediction for snap_scaffold_8-snap.54-T1
Valid prediction for snap_scaffold_8-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_19122-T1
Valid prediction for snap_scaffold_8-snap.58-T1
Valid prediction for Augustus_model.g12791.t1
Valid prediction for GlimmerHMM_glimmerT_19116-T1
Valid prediction for GlimmerHMM_glimmerT_19139-T1
Couldn't classify 187622, 187643
Couldn't classify 193799, 193921
Sorry, prediction pasa_asmbl_52654.p1 fails validation.
(GCA)	 AC	187622-187643	GT	AGG
(ATC)	 AG	187862-187985	GT	AGG
(GTC)	 AG	188071-188153	GT	CAG
(GTC)	 AG	188289-188338	GT	CGG
(AGG)	 AG	188663-188768	GT	TGG
(ACC)	 AG	189140-189281	GT	AAG
(GCT)	 AG	190203-190347	GT	AGG
(GAC)	 AG	191973-192038	GT	AGG
(GTG)	 AG	193799-193921	TG	GGT
-recovered pasa_asmbl_52654.p1, internal, 187862, 187985
-recovered pasa_asmbl_52654.p1, internal, 188071, 188153
-recovered pasa_asmbl_52654.p1, internal, 188289, 188338
-recovered pasa_asmbl_52654.p1, internal, 188663, 188768
-recovered pasa_asmbl_52654.p1, internal, 189140, 189281
-recovered pasa_asmbl_52654.p1, internal, 190203, 190347
-recovered pasa_asmbl_52654.p1, internal, 191973, 192038
Valid prediction for GlimmerHMM_glimmerT_19119-T1
Valid prediction for snap_scaffold_8-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_19136-T1
Valid prediction for GlimmerHMM_glimmerT_19123-T1
Valid prediction for Augustus_model.g12789.t1
Valid prediction for snap_scaffold_8-snap.36-T1
Valid prediction for GlimmerHMM_glimmerT_19130-T1
Valid prediction for snap_scaffold_8-snap.60-T1
Valid prediction for Augustus_model.g12794.t1
Valid prediction for snap_scaffold_8-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_19126-T1
Valid prediction for GlimmerHMM_glimmerT_19117-T1
Valid prediction for snap_scaffold_8-snap.77-T1
Valid prediction for snap_scaffold_8-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_19133-T1
Valid prediction for HiQ_model.g12793.t1
Valid prediction for Augustus_model.g12790.t1
Valid prediction for GlimmerHMM_glimmerT_19140-T1
Valid prediction for snap_scaffold_8-snap.56-T1
Valid prediction for snap_scaffold_8-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_19132-T1
Couldn't classify 140540, 140557
Sorry, prediction pasa_asmbl_52649.p2 fails validation.
(GTC)	 CT	140540-140557	GT	AGG
(CTG)	 AG	140981-141181	GT	TGG
(ATG)	 AG	141826-141948	GG	GAG
-recovered pasa_asmbl_52649.p2, terminal, 141826, 141948
-recovered pasa_asmbl_52649.p2, internal, 140981, 141181
Valid prediction for snap_scaffold_8-snap.51-T1
Valid prediction for snap_scaffold_8-snap.50-T1
Valid prediction for snap_scaffold_8-snap.72-T1
Valid prediction for snap_scaffold_8-snap.57-T1
Valid prediction for snap_scaffold_8-snap.63-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 GlimmerHMM_glimmerT_19125-T1
Valid prediction for GlimmerHMM_glimmerT_19131-T1
Valid prediction for snap_scaffold_8-snap.40-T1
Valid prediction for snap_scaffold_8-snap.65-T1
Valid prediction for snap_scaffold_8-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_19129-T1
Valid prediction for snap_scaffold_8-snap.48-T1
Valid prediction for snap_scaffold_8-snap.73-T1
Valid prediction for snap_scaffold_8-snap.43-T1
Valid prediction for snap_scaffold_8-snap.55-T1
Valid prediction for snap_scaffold_8-snap.79-T1
Valid prediction for snap_scaffold_8-snap.47-T1
Couldn't classify 166430, 166574
Couldn't classify 168371, 168531
Sorry, prediction pasa_asmbl_51696.p1 fails validation.
(GAG)	 GA	166430-166574	GT	CGG
(TGT)	 AG	166749-166847	GT	AGG
(CGT)	 AG	168371-168531	AG	ACA
-recovered pasa_asmbl_51696.p1, internal, 166749, 166847
Valid prediction for snap_scaffold_8-snap.62-T1
Valid prediction for Augustus_model.g12792.t1
Valid prediction for GlimmerHMM_glimmerT_19110-T1
Valid prediction for GlimmerHMM_glimmerT_19108-T1
Valid prediction for GlimmerHMM_glimmerT_19113-T1
Valid prediction for snap_scaffold_8-snap.67-T1
Valid prediction for snap_scaffold_8-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_19141-T1
Valid prediction for GlimmerHMM_glimmerT_19112-T1
Valid prediction for GlimmerHMM_glimmerT_19138-T1
Valid prediction for snap_scaffold_8-snap.69-T1
Valid prediction for GlimmerHMM_glimmerT_19124-T1
Valid prediction for GlimmerHMM_glimmerT_19114-T1
Valid prediction for snap_scaffold_8-snap.85-T1
Valid prediction for snap_scaffold_8-snap.42-T1
Valid prediction for Augustus_model.g12788.t1
Valid prediction for Augustus_model.g12799.t1
Valid prediction for snap_scaffold_8-snap.38-T1
Valid prediction for snap_scaffold_8-snap.52-T1
Valid prediction for snap_scaffold_8-snap.53-T1
Valid prediction for snap_scaffold_8-snap.76-T1
Valid prediction for snap_scaffold_8-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_19135-T1
Valid prediction for snap_scaffold_8-snap.64-T1
Valid prediction for snap_scaffold_8-snap.68-T1
Valid prediction for snap_scaffold_8-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_19120-T1
Valid prediction for snap_scaffold_8-snap.35-T1
Valid prediction for snap_scaffold_8-snap.41-T1
Valid prediction for snap_scaffold_8-snap.61-T1
Valid prediction for snap_scaffold_8-snap.86-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7563, rend_intergenic: 3164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19272, rend_intergenic: 8609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22865, rend_intergenic: 19426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33846, rend_intergenic: 23039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69567, rend_intergenic: 51585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96523, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143585, rend_intergenic: 115394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153782, rend_intergenic: 150991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167387, rend_intergenic: 153789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197533, rend_intergenic: 188642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200022, rend_intergenic: 198476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207919, rend_intergenic: 200359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223735, rend_intergenic: 209961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226535, rend_intergenic: 223784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238437, rend_intergenic: 232048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260794, rend_intergenic: 250012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289503, rend_intergenic: 283455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 302062, rend_intergenic: 289925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 313357
-exon list size: 443


building trellis

0.2    
0.4    
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0.9    
1.1    
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1.6    
1.8    
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3.1    
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3.8    
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7.0    
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8.1    
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8.8    
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9.4    
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10.1    
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10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
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12.6    
12.8    
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13.9    
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14.8    
15.1    
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15.5    
15.7    
16.0    
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16.6    
16.9    
17.1    
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17.5    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
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20.4    
20.7    
20.9    
21.1    
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21.6    
21.8    
22.0    
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22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 7563, rend_intergenic: 3164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19272, rend_intergenic: 8609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22865, rend_intergenic: 19426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33846, rend_intergenic: 23039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69567, rend_intergenic: 51585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96523, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143585, rend_intergenic: 115394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153782, rend_intergenic: 150991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167387, rend_intergenic: 153789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197533, rend_intergenic: 188642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200022, rend_intergenic: 198476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207919, rend_intergenic: 200359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223735, rend_intergenic: 209961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226535, rend_intergenic: 223784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238437, rend_intergenic: 232048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260794, rend_intergenic: 250012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289503, rend_intergenic: 283455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 302062, rend_intergenic: 289925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 298891 - 313357
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 298891 - 311154
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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