-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_41

-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_61017-T1
Couldn't classify 2559, 2634
Sorry, prediction Augustus_model.g40590.t1 fails validation.
(AGG)	 AG	2559-2634	GT	TGG
(GAT)	 AG	3239-3341	GT	GGG
(GGC)	 AG	3783-3876	GT	ATG
(GTC)	 AG	4987-5098	GT	GGG
(AGA)	 AG	6220-6326	GT	AGG
(ACT)	 AG	6425-6466	GT	ATG
(TGT)	 AG	6635-6709	GT	CGG
(GCG)	 AG	7718-7791	GT	GGG
(GTC)	 AG	10107-10119	GT	AGG
(GGA)	 AG	10217-10311	GT	GAG
(TTC)	 AG	12397-12473	GT	AGG
(AGA)	 AG	13203-13346	GT	AGG
(ATG)	 AG	15965-16057	GT	CGG
(ACC)	 AG	18017-18226	GT	TGG
(ATT)	 AG	18492-18566	GT	AGG
(CCG)	 AG	20032-20108	GT	GGG
(AGC)	 AG	21484-21531	TG	AAT
-recovered Augustus_model.g40590.t1, initial, 15965, 16057
-recovered Augustus_model.g40590.t1, terminal, 21484, 21531
-recovered Augustus_model.g40590.t1, internal, 2559, 2634
-recovered Augustus_model.g40590.t1, internal, 3239, 3341
-recovered Augustus_model.g40590.t1, internal, 3783, 3876
-recovered Augustus_model.g40590.t1, internal, 4987, 5098
-recovered Augustus_model.g40590.t1, internal, 6220, 6326
-recovered Augustus_model.g40590.t1, internal, 6425, 6466
-recovered Augustus_model.g40590.t1, internal, 6635, 6709
-recovered Augustus_model.g40590.t1, internal, 7718, 7791
-recovered Augustus_model.g40590.t1, internal, 10107, 10119
-recovered Augustus_model.g40590.t1, internal, 10217, 10311
-recovered Augustus_model.g40590.t1, internal, 12397, 12473
-recovered Augustus_model.g40590.t1, internal, 13203, 13346
-recovered Augustus_model.g40590.t1, internal, 15965, 16057
-recovered Augustus_model.g40590.t1, internal, 18017, 18226
-recovered Augustus_model.g40590.t1, internal, 18492, 18566
-recovered Augustus_model.g40590.t1, internal, 20032, 20108
Valid prediction for GlimmerHMM_glimmerT_61020-T1
Valid prediction for GlimmerHMM_glimmerT_61016-T1
Couldn't classify 2559, 2634
Sorry, prediction GeneMark_model.106217_t fails validation.
(AGG)	 AG	2559-2634	GT	TGG
(GAT)	 AG	3239-3341	GT	GGG
(GGC)	 AG	3783-3876	GT	ATG
(GTC)	 AG	4987-5098	GT	GGG
(AGA)	 AG	6220-6326	GT	AGG
(TGT)	 AG	6635-6709	GT	CGG
(GCG)	 AG	7718-7791	GT	GGG
(GTC)	 AG	10107-10119	GT	AGG
(GGA)	 AG	10217-10315	GT	GAG
-recovered GeneMark_model.106217_t, terminal, 10217, 10315
-recovered GeneMark_model.106217_t, internal, 2559, 2634
-recovered GeneMark_model.106217_t, internal, 3239, 3341
-recovered GeneMark_model.106217_t, internal, 3783, 3876
-recovered GeneMark_model.106217_t, internal, 4987, 5098
-recovered GeneMark_model.106217_t, internal, 6220, 6326
-recovered GeneMark_model.106217_t, internal, 6635, 6709
-recovered GeneMark_model.106217_t, internal, 7718, 7791
-recovered GeneMark_model.106217_t, internal, 10107, 10119
-recovered GeneMark_model.106217_t, internal, 10217, 10315
Couldn't classify 2559, 2634
Sorry, prediction snap_scaffold_41-snap.1-T1 fails validation.
(AGG)	 AG	2559-2634	GT	TGG
(GAT)	 AG	3239-3341	GT	GGG
(GGC)	 AG	3783-3876	GT	ATG
(GTT)	 AG	4424-4432	GA	GAG
-recovered snap_scaffold_41-snap.1-T1, terminal, 4424, 4432
-recovered snap_scaffold_41-snap.1-T1, internal, 2559, 2634
-recovered snap_scaffold_41-snap.1-T1, internal, 3239, 3341
-recovered snap_scaffold_41-snap.1-T1, internal, 3783, 3876
Valid prediction for snap_scaffold_41-snap.8-T1
Valid prediction for Augustus_model.g40591.t1
Valid prediction for GeneMark_model.106219_t
Valid prediction for snap_scaffold_41-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61018-T1
Valid prediction for snap_scaffold_41-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_61019-T1
Valid prediction for snap_scaffold_41-snap.6-T1
Valid prediction for snap_scaffold_41-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 snap_scaffold_41-snap.7-T1
Valid prediction for GeneMark_model.106221_t
Valid prediction for GeneMark_model.106218_t
Valid prediction for GeneMark_model.106220_t
Valid prediction for GeneMark_model.106222_t
Valid prediction for snap_scaffold_41-snap.4-T1
Valid prediction for snap_scaffold_41-snap.9-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17609, rend_intergenic: 13205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21531, rend_intergenic: 17741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29580, rend_intergenic: 24647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 32582
-exon list size: 113


building trellis

0.9    
1.7    
2.6    
3.5    
4.3    
5.2    
6.1    
7.0    
7.8    
8.7    
9.6    
10.4    
11.3    
12.2    
13.0    
13.9    
14.8    
15.7    
16.5    
17.4    
18.3    
19.1    
20.0    
20.9    
21.7    
22.6    
23.5    
24.3    
25.2    
26.1    
27.0    
27.8    
28.7    
29.6    
30.4    
31.3    
32.2    
33.0    
33.9    
34.8    
35.7    
36.5    
37.4    
38.3    
39.1    
40.0    
40.9    
41.7    
42.6    
43.5    
44.3    
45.2    
46.1    
47.0    
47.8    
48.7    
49.6    
50.4    
51.3    
52.2    
53.0    
53.9    
54.8    
55.7    
56.5    
57.4    
58.3    
59.1    
60.0    
60.9    
61.7    
62.6    
63.5    
64.3    
65.2    
66.1    
67.0    
67.8    
68.7    
69.6    
70.4    
71.3    
72.2    
73.0    
73.9    
74.8    
75.7    
76.5    
77.4    
78.3    
79.1    
80.0    
80.9    
81.7    
82.6    
83.5    
84.3    
85.2    
86.1    
87.0    
87.8    
88.7    
89.6    
90.4    
91.3    
92.2    
93.0    
93.9    
94.8    
95.7    
96.5    
97.4    
98.3    
99.1    
-found 6 predictions from path traversal
Error with prediction: snap lend_intergenic: 17609, rend_intergenic: 13205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21531, rend_intergenic: 17741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29580, rend_intergenic: 24647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support