-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_71

-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_71-snap.9-T1
Valid prediction for GeneMark_model.106398_t
Valid prediction for GeneMark_model.106389_t
Valid prediction for GlimmerHMM_glimmerT_61184-T1
Valid prediction for GeneMark_model.106393_t
Valid prediction for Augustus_model.g40699.t1
Valid prediction for GeneMark_model.106387_t
Valid prediction for snap_scaffold_71-snap.4-T1
Valid prediction for Augustus_model.g40701.t1
Valid prediction for snap_scaffold_71-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_61178-T1
Valid prediction for GeneMark_model.106386_t
Valid prediction for GlimmerHMM_glimmerT_61183-T1
Valid prediction for snap_scaffold_71-snap.2-T1
Valid prediction for GeneMark_model.106390_t
Valid prediction for GeneMark_model.106392_t
Valid prediction for GeneMark_model.106396_t
Valid prediction for GlimmerHMM_glimmerT_61177-T1
Valid prediction for Augustus_model.g40703.t1
Valid prediction for GlimmerHMM_glimmerT_61179-T1
Valid prediction for Augustus_model.g40702.t1
Couldn't classify 62, 184
Sorry, prediction GeneMark_model.106384_t fails validation.
(AGC)	 AG	62-184	GT	AAG
(CCT)	 AG	383-745	GT	GGG
(AGG)	 AG	912-968	GT	CTG
(AGA)	 AG	1003-1041	GT	GGG
(GGA)	 AG	1156-1240	AC	AAA
-recovered GeneMark_model.106384_t, terminal, 1156, 1240
-recovered GeneMark_model.106384_t, internal, 62, 184
-recovered GeneMark_model.106384_t, internal, 383, 745
-recovered GeneMark_model.106384_t, internal, 912, 968
-recovered GeneMark_model.106384_t, internal, 1003, 1041
Valid prediction for snap_scaffold_71-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_61176-T1
Valid prediction for GlimmerHMM_glimmerT_61180-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: -)Couldn't classify 1125, 1181
Sorry, prediction GeneMark_model.106399_t fails validation.
(GGA)	 AG	1125-1181	GT	TGG
(AGA)	 AG	1492-1610	GT	GTG
(ATT)	 AG	1705-1732	GT	GAG
-recovered GeneMark_model.106399_t, terminal, 1705, 1732
-recovered GeneMark_model.106399_t, internal, 1125, 1181
-recovered GeneMark_model.106399_t, internal, 1492, 1610
-recovered GeneMark_model.106399_t, internal, 1705, 1732
Valid prediction for snap_scaffold_71-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_61185-T1
Valid prediction for GeneMark_model.106385_t
Valid prediction for GeneMark_model.106394_t
Valid prediction for snap_scaffold_71-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_61182-T1
Valid prediction for snap_scaffold_71-snap.3-T1
Valid prediction for GeneMark_model.106395_t
Valid prediction for GeneMark_model.106391_t
Valid prediction for Augustus_model.g40700.t1
Valid prediction for GeneMark_model.106388_t
Valid prediction for snap_scaffold_71-snap.10-T1
Valid prediction for snap_scaffold_71-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_61186-T1
Valid prediction for GlimmerHMM_glimmerT_61181-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2512, rend_intergenic: 1777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 3642, rend_intergenic: 2722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9222, rend_intergenic: 5703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15671, rend_intergenic: 9304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16707, rend_intergenic: 15928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19549, rend_intergenic: 16816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 8646, rend_intergenic: 8643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 25000
-exon list size: 158


building trellis

0.6    
1.2    
1.9    
2.5    
3.1    
3.8    
4.4    
5.0    
5.6    
6.2    
6.9    
7.5    
8.1    
8.8    
9.4    
10.0    
10.6    
11.2    
11.9    
12.5    
13.1    
13.8    
14.4    
15.0    
15.6    
16.2    
16.9    
17.5    
18.1    
18.8    
19.4    
20.0    
20.6    
21.2    
21.9    
22.5    
23.1    
23.8    
24.4    
25.0    
25.6    
26.2    
26.9    
27.5    
28.1    
28.7    
29.4    
30.0    
30.6    
31.2    
31.9    
32.5    
33.1    
33.8    
34.4    
35.0    
35.6    
36.2    
36.9    
37.5    
38.1    
38.8    
39.4    
40.0    
40.6    
41.2    
41.9    
42.5    
43.1    
43.8    
44.4    
45.0    
45.6    
46.2    
46.9    
47.5    
48.1    
48.8    
49.4    
50.0    
50.6    
51.2    
51.9    
52.5    
53.1    
53.8    
54.4    
55.0    
55.6    
56.2    
56.9    
57.5    
58.1    
58.8    
59.4    
60.0    
60.6    
61.3    
61.9    
62.5    
63.1    
63.7    
64.4    
65.0    
65.6    
66.2    
66.9    
67.5    
68.1    
68.8    
69.4    
70.0    
70.6    
71.2    
71.9    
72.5    
73.1    
73.8    
74.4    
75.0    
75.6    
76.2    
76.9    
77.5    
78.1    
78.8    
79.4    
80.0    
80.6    
81.2    
81.9    
82.5    
83.1    
83.8    
84.4    
85.0    
85.6    
86.2    
86.9    
87.5    
88.1    
88.8    
89.4    
90.0    
90.6    
91.2    
91.9    
92.5    
93.1    
93.8    
94.4    
95.0    
95.6    
96.2    
96.9    
97.5    
98.1    
98.8    
99.4    
-found 12 predictions from path traversal
Error with prediction: snap lend_intergenic: 2512, rend_intergenic: 1777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 3642, rend_intergenic: 2722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9222, rend_intergenic: 5703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15671, rend_intergenic: 9304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16707, rend_intergenic: 15928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19549, rend_intergenic: 16816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 8646, rend_intergenic: 8643  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 9 predictions persist after filtering for low support