-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_11669929-11809523

-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 Augustus_model.g23225.t1
Valid prediction for GlimmerHMM_glimmerT_34735-T1
Valid prediction for HiQ_model.g23235.t1
Valid prediction for HiQ_model.g23227.t1
Valid prediction for GlimmerHMM_glimmerT_34729-T1
Valid prediction for snap_scaffold_14-snap.2392-T1
Valid prediction for snap_scaffold_14-snap.2378-T1
Valid prediction for snap_scaffold_14-snap.2391-T1
Valid prediction for snap_scaffold_14-snap.2376-T1
Couldn't classify 47268, 47573
Sorry, prediction pasa_asmbl_12401.p1 fails validation.
(CCG)	 AA	47268-47573	CG	GAC
Valid prediction for snap_scaffold_14-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_34727-T1
Valid prediction for CodingQuarry_transcript_15858-T1
Valid prediction for pasa_asmbl_12400.p1
Valid prediction for Augustus_model.g23230.t1
Valid prediction for GlimmerHMM_glimmerT_34741-T1
Valid prediction for GlimmerHMM_glimmerT_34726-T1
Valid prediction for Augustus_model.g23220.t1
Valid prediction for Augustus_model.g23217.t1
Valid prediction for GlimmerHMM_glimmerT_34722-T1
Valid prediction for GlimmerHMM_glimmerT_34732-T1
Valid prediction for snap_scaffold_14-snap.2371-T1
Valid prediction for Augustus_model.g23223.t1
Valid prediction for GlimmerHMM_glimmerT_34720-T1
Valid prediction for snap_scaffold_14-snap.2383-T1
Valid prediction for Augustus_model.g23222.t1
Valid prediction for snap_scaffold_14-snap.2377-T1
Valid prediction for CodingQuarry_transcript_15864-T1
Valid prediction for pasa_asmbl_12405.p1
Valid prediction for GlimmerHMM_glimmerT_34738-T1
Valid prediction for CodingQuarry_transcript_15861-T1
Valid prediction for snap_scaffold_14-snap.2389-T1
Valid prediction for snap_scaffold_14-snap.2381-T1
Valid prediction for Augustus_model.g23224.t1
Valid prediction for pasa_asmbl_12398.p1
Valid prediction for GlimmerHMM_glimmerT_34745-T1
Valid prediction for HiQ_model.g23232.t1
Valid prediction for HiQ_model.g23215.t1
Valid prediction for GlimmerHMM_glimmerT_34742-T1
Valid prediction for snap_scaffold_14-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_34733-T1
Valid prediction for Augustus_model.g23221.t1
Valid prediction for GlimmerHMM_glimmerT_34731-T1
Valid prediction for snap_scaffold_14-snap.2375-T1
Valid prediction for HiQ_model.g23218.t1
Valid prediction for Augustus_model.g23233.t1
Valid prediction for snap_scaffold_14-snap.2368-T1
Valid prediction for snap_scaffold_14-snap.2384-T1
Couldn't classify 85102, 85263
Sorry, prediction pasa_asmbl_12403.p1 fails validation.
(ATG)	 GA	83729-83777	GT	AGG
(CCC)	 AG	84112-84283	GT	GAG
(TGA)	 AG	84407-84569	GT	ACG
(AAA)	 AG	85102-85263	GC	CTG
-recovered pasa_asmbl_12403.p1, initial, 83729, 83777
-recovered pasa_asmbl_12403.p1, internal, 84112, 84283
-recovered pasa_asmbl_12403.p1, internal, 84407, 84569
-recovered pasa_asmbl_12403.p1, internal, 85102, 85263
Valid prediction for snap_scaffold_14-snap.2370-T1
Valid prediction for snap_scaffold_14-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_34723-T1
Valid prediction for snap_scaffold_14-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_34725-T1
Valid prediction for snap_scaffold_14-snap.2379-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 snap_scaffold_14-snap.2388-T1
Valid prediction for HiQ_model.g23231.t1
Valid prediction for GlimmerHMM_glimmerT_34728-T1
Valid prediction for HiQ_model.g23219.t1
Valid prediction for GlimmerHMM_glimmerT_34730-T1
Valid prediction for snap_scaffold_14-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_34743-T1
Valid prediction for snap_scaffold_14-snap.2395-T1
Valid prediction for HiQ_model.g23229.t1
Valid prediction for HiQ_model.g23228.t1
Valid prediction for pasa_asmbl_13523.p1
Valid prediction for Augustus_model.g23234.t1
Valid prediction for snap_scaffold_14-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_34737-T1
Valid prediction for Augustus_model.g23216.t1
Valid prediction for Augustus_model.g23226.t1
Couldn't classify 133026, 133027
Sorry, prediction CodingQuarry_transcript_15860-T1 fails validation.
(ATG)	 AC	129574-130230	GT	CGG
(TTG)	 AG	130396-130592	GT	AGG
(GAA)	 AG	130707-131017	GT	CAG
(TCC)	 AG	131144-131208	GT	AGG
(ATG)	 AG	131386-131453	GT	CGG
(ATG)	 AG	131985-132109	GT	TGG
(TGG)	 AG	132195-132267	GT	GAG
(ATG)	 AG	132603-132664	GC	ATG
(GAA)	 AG	133026-133027	AC	GAA
-recovered CodingQuarry_transcript_15860-T1, initial, 129574, 130230
-recovered CodingQuarry_transcript_15860-T1, initial, 131386, 131453
add_exon() Sorry, CodingQuarry_transcript_15860-T1 131985-132109-initial-1 is invalid.
-recovered CodingQuarry_transcript_15860-T1, initial, 131985, 132109
-recovered CodingQuarry_transcript_15860-T1, initial, 132603, 132664
-recovered CodingQuarry_transcript_15860-T1, internal, 130396, 130592
-recovered CodingQuarry_transcript_15860-T1, internal, 130707, 131017
-recovered CodingQuarry_transcript_15860-T1, internal, 131144, 131208
-recovered CodingQuarry_transcript_15860-T1, internal, 131386, 131453
-recovered CodingQuarry_transcript_15860-T1, internal, 131985, 132109
-recovered CodingQuarry_transcript_15860-T1, internal, 132195, 132267
-recovered CodingQuarry_transcript_15860-T1, internal, 132603, 132664
Valid prediction for snap_scaffold_14-snap.2387-T1
Valid prediction for snap_scaffold_14-snap.2396-T1
Valid prediction for snap_scaffold_14-snap.2385-T1
Valid prediction for CodingQuarry_transcript_15859-T1
Valid prediction for GlimmerHMM_glimmerT_34736-T1
Valid prediction for CodingQuarry_transcript_15865-T1
Valid prediction for CodingQuarry_transcript_15867-T1
Valid prediction for CodingQuarry_transcript_15862-T1
Valid prediction for GlimmerHMM_glimmerT_34721-T1
Valid prediction for CodingQuarry_transcript_15863-T1
Valid prediction for CodingQuarry_transcript_15869-T1
Valid prediction for pasa_asmbl_13531.p1
Valid prediction for CodingQuarry_transcript_15866-T1
Valid prediction for GlimmerHMM_glimmerT_34724-T1
Valid prediction for snap_scaffold_14-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_34734-T1
Valid prediction for pasa_asmbl_13518.p1
Valid prediction for snap_scaffold_14-snap.2382-T1
Valid prediction for pasa_asmbl_13536.p1
Valid prediction for GlimmerHMM_glimmerT_34739-T1
Valid prediction for GlimmerHMM_glimmerT_34740-T1
Valid prediction for pasa_asmbl_13530.p1
Couldn't classify 33532, 33729
Sorry, prediction pasa_asmbl_13534.p1 fails validation.
(CGT)	 TG	33532-33729	GT	AGG
(TGC)	 AG	34094-34218	GT	AAG
(GGA)	 AG	34316-34415	GT	TGG
(GAA)	 AG	34653-34706	GT	AGG
(ATT)	 AG	34791-34919	GT	ATG
(TAC)	 AG	35072-35142	GT	TGG
(GGG)	 AG	35252-35417	GA	GAG
-recovered pasa_asmbl_13534.p1, terminal, 35252, 35417
-recovered pasa_asmbl_13534.p1, internal, 34094, 34218
-recovered pasa_asmbl_13534.p1, internal, 34316, 34415
-recovered pasa_asmbl_13534.p1, internal, 34653, 34706
-recovered pasa_asmbl_13534.p1, internal, 34791, 34919
-recovered pasa_asmbl_13534.p1, internal, 35072, 35142
Valid prediction for snap_scaffold_14-snap.2380-T1
Valid prediction for snap_scaffold_14-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_34744-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 70478, rend_intergenic: 65980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123260, rend_intergenic: 122742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128201, rend_intergenic: 123631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139595
-exon list size: 289


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.2    
5.5    
5.8    
6.2    
6.5    
6.9    
7.2    
7.6    
7.9    
8.2    
8.6    
8.9    
9.3    
9.6    
10.0    
10.3    
10.7    
11.0    
11.3    
11.7    
12.0    
12.4    
12.7    
13.1    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.3    
21.6    
22.0    
22.3    
22.7    
23.0    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.2    
30.6    
30.9    
31.3    
31.6    
32.0    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.7    
36.1    
36.4    
36.8    
37.1    
37.5    
37.8    
38.1    
38.5    
38.8    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.6    
41.9    
42.3    
42.6    
43.0    
43.3    
43.6    
44.0    
44.3    
44.7    
45.0    
45.4    
45.7    
46.0    
46.4    
46.7    
47.1    
47.4    
47.8    
48.1    
48.5    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.5    
51.9    
52.2    
52.6    
52.9    
53.3    
53.6    
54.0    
54.3    
54.6    
55.0    
55.3    
55.7    
56.0    
56.4    
56.7    
57.0    
57.4    
57.7    
58.1    
58.4    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.2    
61.5    
61.9    
62.2    
62.5    
62.9    
63.2    
63.6    
63.9    
64.3    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.0    
68.4    
68.7    
69.1    
69.4    
69.8    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
77.0    
77.3    
77.7    
78.0    
78.4    
78.7    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
86.9    
87.3    
87.6    
88.0    
88.3    
88.7    
89.0    
89.3    
89.7    
90.0    
90.4    
90.7    
91.1    
91.4    
91.8    
92.1    
92.4    
92.8    
93.1    
93.5    
93.8    
94.2    
94.5    
94.8    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 70478, rend_intergenic: 65980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123260, rend_intergenic: 122742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128201, rend_intergenic: 123631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support