-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_65

-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_65-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_61150-T1
Valid prediction for GeneMark_model.106352_t
Valid prediction for GlimmerHMM_glimmerT_61148-T1
Valid prediction for GeneMark_model.106350_t
Valid prediction for snap_scaffold_65-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61151-T1
Valid prediction for Augustus_model.g40680.t1
Valid prediction for GlimmerHMM_glimmerT_61152-T1
Valid prediction for GeneMark_model.106354_t
Valid prediction for snap_scaffold_65-snap.8-T1
Valid prediction for snap_scaffold_65-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_61149-T1
Valid prediction for GeneMark_model.106348_t
Valid prediction for snap_scaffold_65-snap.5-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 GeneMark_model.106353_t
Valid prediction for GlimmerHMM_glimmerT_61147-T1
Valid prediction for snap_scaffold_65-snap.1-T1
Valid prediction for GeneMark_model.106351_t
Valid prediction for GeneMark_model.106349_t
Valid prediction for snap_scaffold_65-snap.7-T1
Valid prediction for Augustus_model.g40679.t1
Couldn't classify 36, 143
Sorry, prediction GeneMark_model.106355_t fails validation.
(GCG)	 AG	36-143	GT	AGG
(AGG)	 AG	205-216	GT	GGG
(GAA)	 AG	240-287	GT	ATG
(AGG)	 AG	329-343	GT	GGG
(GAG)	 AG	367-381	GT	ATG
(GGT)	 AG	667-682	GT	AAG
(TTC)	 AG	712-764	GT	GCG
(CTG)	 AG	1441-1537	AC	AGA
-recovered GeneMark_model.106355_t, terminal, 1441, 1537
-recovered GeneMark_model.106355_t, internal, 36, 143
-recovered GeneMark_model.106355_t, internal, 205, 216
-recovered GeneMark_model.106355_t, internal, 240, 287
-recovered GeneMark_model.106355_t, internal, 329, 343
-recovered GeneMark_model.106355_t, internal, 367, 381
-recovered GeneMark_model.106355_t, internal, 667, 682
-recovered GeneMark_model.106355_t, internal, 712, 764
Valid prediction for Augustus_model.g40678.t1
Couldn't classify 24870, 24899
Sorry, prediction GeneMark_model.106347_t fails validation.
(ATG)	 CC	24502-24668	GC	TCG
(GGC)	 AG	24752-24763	GT	AGG
(GCA)	 AG	24788-24802	GT	AGG
(GCA)	 AG	24827-24847	GT	AGG
(AAG)	 AG	24870-24899	GT	GGG
-recovered GeneMark_model.106347_t, initial, 24502, 24668
-recovered GeneMark_model.106347_t, internal, 24752, 24763
-recovered GeneMark_model.106347_t, internal, 24788, 24802
-recovered GeneMark_model.106347_t, internal, 24827, 24847
-recovered GeneMark_model.106347_t, internal, 24870, 24899
Valid prediction for snap_scaffold_65-snap.2-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10329, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23635, rend_intergenic: 21529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24946, rend_intergenic: 23983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 25000
-exon list size: 119


building trellis

0.8    
1.7    
2.5    
3.3    
4.1    
5.0    
5.8    
6.6    
7.4    
8.3    
9.1    
9.9    
10.7    
11.6    
12.4    
13.2    
14.0    
14.9    
15.7    
16.5    
17.4    
18.2    
19.0    
19.8    
20.7    
21.5    
22.3    
23.1    
24.0    
24.8    
25.6    
26.4    
27.3    
28.1    
28.9    
29.8    
30.6    
31.4    
32.2    
33.1    
33.9    
34.7    
35.5    
36.4    
37.2    
38.0    
38.8    
39.7    
40.5    
41.3    
42.1    
43.0    
43.8    
44.6    
45.5    
46.3    
47.1    
47.9    
48.8    
49.6    
50.4    
51.2    
52.1    
52.9    
53.7    
54.5    
55.4    
56.2    
57.0    
57.9    
58.7    
59.5    
60.3    
61.2    
62.0    
62.8    
63.6    
64.5    
65.3    
66.1    
66.9    
67.8    
68.6    
69.4    
70.2    
71.1    
71.9    
72.7    
73.6    
74.4    
75.2    
76.0    
76.9    
77.7    
78.5    
79.3    
80.2    
81.0    
81.8    
82.6    
83.5    
84.3    
85.1    
86.0    
86.8    
87.6    
88.4    
89.3    
90.1    
90.9    
91.7    
92.6    
93.4    
94.2    
95.0    
95.9    
96.7    
97.5    
98.3    
99.2    
-found 6 predictions from path traversal
Error with prediction: snap lend_intergenic: 10329, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23635, rend_intergenic: 21529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24946, rend_intergenic: 23983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support