-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_34

-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_34-snap.2-T1
Valid prediction for pasa_asmbl_40958.p1
Valid prediction for CodingQuarry_transcript_46429-T1
Valid prediction for Augustus_model.g40558.t1
Valid prediction for snap_scaffold_34-snap.6-T1
Valid prediction for HiQ_model.g40557.t1
Valid prediction for snap_scaffold_34-snap.1-T1
Valid prediction for GeneMark_model.106167_t
Valid prediction for GlimmerHMM_glimmerT_60971-T1
Couldn't classify 38387, 38468
Sorry, prediction GlimmerHMM_glimmerT_60972-T1 fails validation.
(ATG)	 AA	30759-30785	GT	AGG
(TTG)	 AG	34564-34637	GT	AGG
(ATT)	 AG	34893-35026	GT	TGG
(ACG)	 AG	38387-38468	GT	ATG
-recovered GlimmerHMM_glimmerT_60972-T1, initial, 30759, 30785
-recovered GlimmerHMM_glimmerT_60972-T1, internal, 34564, 34637
-recovered GlimmerHMM_glimmerT_60972-T1, internal, 34893, 35026
-recovered GlimmerHMM_glimmerT_60972-T1, internal, 38387, 38468
Valid prediction for GlimmerHMM_glimmerT_60970-T1
Valid prediction for pasa_asmbl_40959.p1
Valid prediction for GeneMark_model.106166_t
Valid prediction for GeneMark_model.106164_t
Valid prediction for GlimmerHMM_glimmerT_60968-T1
Valid prediction for snap_scaffold_34-snap.4-T1
Valid prediction for CodingQuarry_transcript_46428-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_34-snap.3-T1
Couldn't classify 40424, 40496
Sorry, prediction GeneMark_model.106163_t fails validation.
(ATG)	 CC	34358-34365	GT	TTG
(GGG)	 AG	35117-35236	GT	GGG
(AGA)	 AG	37514-37528	GT	GGG
(AGA)	 AG	37550-37684	GT	GGG
(AGA)	 AG	37809-37832	GT	GGG
(AGT)	 AG	37862-37876	GT	GGG
(AGA)	 AG	37988-37999	GT	AGG
(AGA)	 AG	38087-38098	GT	AGG
(GTT)	 AG	38226-38231	GT	GGG
(GCG)	 AG	38261-38269	GT	GGG
(AGA)	 AG	38453-38464	GT	AGG
(GGG)	 AG	38500-38508	GT	GGG
(AGA)	 AG	40424-40496	GC	AGG
-recovered GeneMark_model.106163_t, initial, 34358, 34365
-recovered GeneMark_model.106163_t, terminal, 37988, 37999
-recovered GeneMark_model.106163_t, terminal, 38087, 38098
-recovered GeneMark_model.106163_t, terminal, 38453, 38464
-recovered GeneMark_model.106163_t, internal, 35117, 35236
-recovered GeneMark_model.106163_t, internal, 37514, 37528
-recovered GeneMark_model.106163_t, internal, 37550, 37684
-recovered GeneMark_model.106163_t, internal, 37809, 37832
-recovered GeneMark_model.106163_t, internal, 37862, 37876
-recovered GeneMark_model.106163_t, internal, 37988, 37999
-recovered GeneMark_model.106163_t, internal, 38087, 38098
-recovered GeneMark_model.106163_t, internal, 38226, 38231
-recovered GeneMark_model.106163_t, internal, 38261, 38269
-recovered GeneMark_model.106163_t, internal, 38453, 38464
-recovered GeneMark_model.106163_t, internal, 38500, 38508
-recovered GeneMark_model.106163_t, internal, 40424, 40496
Valid prediction for GlimmerHMM_glimmerT_60969-T1
Valid prediction for snap_scaffold_34-snap.8-T1
Valid prediction for snap_scaffold_34-snap.5-T1
Valid prediction for snap_scaffold_34-snap.7-T1
Valid prediction for GeneMark_model.106165_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21828, rend_intergenic: 21302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26560, rend_intergenic: 21830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 40508
-exon list size: 105


building trellis

0.9    
1.9    
2.8    
3.7    
4.7    
5.6    
6.5    
7.5    
8.4    
9.3    
10.3    
11.2    
12.1    
13.1    
14.0    
15.0    
15.9    
16.8    
17.8    
18.7    
19.6    
20.6    
21.5    
22.4    
23.4    
24.3    
25.2    
26.2    
27.1    
28.0    
29.0    
29.9    
30.8    
31.8    
32.7    
33.6    
34.6    
35.5    
36.4    
37.4    
38.3    
39.3    
40.2    
41.1    
42.1    
43.0    
43.9    
44.9    
45.8    
46.7    
47.7    
48.6    
49.5    
50.5    
51.4    
52.3    
53.3    
54.2    
55.1    
56.1    
57.0    
57.9    
58.9    
59.8    
60.7    
61.7    
62.6    
63.6    
64.5    
65.4    
66.4    
67.3    
68.2    
69.2    
70.1    
71.0    
72.0    
72.9    
73.8    
74.8    
75.7    
76.6    
77.6    
78.5    
79.4    
80.4    
81.3    
82.2    
83.2    
84.1    
85.0    
86.0    
86.9    
87.9    
88.8    
89.7    
90.7    
91.6    
92.5    
93.5    
94.4    
95.3    
96.3    
97.2    
98.1    
99.1    
-found 5 predictions from path traversal
Error with prediction: snap lend_intergenic: 21828, rend_intergenic: 21302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26560, rend_intergenic: 21830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15541
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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 2284 - 15541
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

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