-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_9877506-10035089

-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.g38497.t1
Valid prediction for GlimmerHMM_glimmerT_57790-T1
Valid prediction for GeneMark_model.100664_t
Valid prediction for snap_scaffold_26-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_57775-T1
Valid prediction for snap_scaffold_26-snap.2219-T1
Valid prediction for GeneMark_model.100654_t
Valid prediction for GlimmerHMM_glimmerT_57792-T1
Couldn't classify 146172, 147989
Sorry, prediction pasa_asmbl_35821.p1 fails validation.
(ATG)	 CG	146172-147989	CA	CCC
Valid prediction for GlimmerHMM_glimmerT_57780-T1
Valid prediction for GeneMark_model.100661_t
Valid prediction for snap_scaffold_26-snap.2214-T1
Valid prediction for GeneMark_model.100669_t
Valid prediction for snap_scaffold_26-snap.2215-T1
Valid prediction for GeneMark_model.100656_t
Valid prediction for GlimmerHMM_glimmerT_57776-T1
Valid prediction for Augustus_model.g38498.t1
Valid prediction for snap_scaffold_26-snap.2229-T1
Valid prediction for Augustus_model.g38501.t1
Valid prediction for snap_scaffold_26-snap.2212-T1
Valid prediction for Augustus_model.g38496.t1
Valid prediction for Augustus_model.g38505.t1
Valid prediction for Augustus_model.g38506.t1
Valid prediction for GlimmerHMM_glimmerT_57777-T1
Valid prediction for GeneMark_model.100655_t
Valid prediction for GlimmerHMM_glimmerT_57789-T1
Valid prediction for snap_scaffold_26-snap.2228-T1
Valid prediction for Augustus_model.g38509.t1
Valid prediction for GeneMark_model.100670_t
Valid prediction for GlimmerHMM_glimmerT_57794-T1
Valid prediction for GeneMark_model.100662_t
Valid prediction for snap_scaffold_26-snap.2237-T1
Valid prediction for GeneMark_model.100652_t
Couldn't classify 23209, 24093
Sorry, prediction pasa_asmbl_35819.p1 fails validation.
(ACC)	 CA	23209-24093	GT	AAG
Valid prediction for GlimmerHMM_glimmerT_57787-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_26-snap.2224-T1
Valid prediction for snap_scaffold_26-snap.2232-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.2227-T1
Valid prediction for GeneMark_model.100666_t
Valid prediction for Augustus_model.g38503.t1
Valid prediction for GeneMark_model.100653_t
Valid prediction for snap_scaffold_26-snap.2216-T1
Valid prediction for snap_scaffold_26-snap.2233-T1
Valid prediction for snap_scaffold_26-snap.2220-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.2225-T1
Valid prediction for snap_scaffold_26-snap.2236-T1
Valid prediction for GeneMark_model.100660_t
Couldn't classify 112673, 112723
Sorry, prediction pasa_asmbl_35073.p1 fails validation.
(AGG)	 GT	112673-112723	GT	AGG
(TAC)	 AG	112850-112999	GT	AGG
(AAC)	 AG	115713-115886	GT	AGG
(GTT)	 AG	116015-116098	GT	AGG
(GAT)	 AG	116384-116470	GT	TGG
(ATG)	 AG	116654-116758	TC	GAT
-recovered pasa_asmbl_35073.p1, terminal, 116654, 116758
-recovered pasa_asmbl_35073.p1, internal, 112850, 112999
-recovered pasa_asmbl_35073.p1, internal, 115713, 115886
-recovered pasa_asmbl_35073.p1, internal, 116015, 116098
-recovered pasa_asmbl_35073.p1, internal, 116384, 116470
Valid prediction for snap_scaffold_26-snap.2221-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.2218-T1
Valid prediction for CodingQuarry_transcript_40363-T1
Valid prediction for snap_scaffold_26-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_57785-T1
Valid prediction for GlimmerHMM_glimmerT_57786-T1
Valid prediction for snap_scaffold_26-snap.2222-T1
Valid prediction for GlimmerHMM_glimmerT_57781-T1
Valid prediction for GeneMark_model.100659_t
Valid prediction for GlimmerHMM_glimmerT_57779-T1
Valid prediction for snap_scaffold_26-snap.2217-T1
Valid prediction for snap_scaffold_26-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_57783-T1
Couldn't classify 87446, 87599
Sorry, prediction pasa_asmbl_35076.p1 fails validation.
(TCA)	 TG	87446-87599	GT	AGG
(GAA)	 AG	87945-88088	GT	AGG
(CTC)	 AG	88292-88411	GT	TGG
(TGG)	 AG	88888-89031	GT	TGG
(ATG)	 AG	89150-89280	GT	GGG
(GAG)	 AG	89718-89850	GT	CAG
(TTG)	 AG	90005-90156	GT	TAG
(GTT)	 AG	90278-90374	GT	TGG
(GTC)	 AG	90571-90732	GT	TGG
(GCG)	 AG	90888-91051	GT	AGG
(GGT)	 AG	91200-91310	AC	GAA
add_exon() Sorry, pasa_asmbl_35076.p1 89150-89280-initial-1 is invalid.
-recovered pasa_asmbl_35076.p1, initial, 89150, 89280
-recovered pasa_asmbl_35076.p1, terminal, 91200, 91310
-recovered pasa_asmbl_35076.p1, internal, 87945, 88088
-recovered pasa_asmbl_35076.p1, internal, 88292, 88411
-recovered pasa_asmbl_35076.p1, internal, 88888, 89031
-recovered pasa_asmbl_35076.p1, internal, 89150, 89280
-recovered pasa_asmbl_35076.p1, internal, 89718, 89850
-recovered pasa_asmbl_35076.p1, internal, 90005, 90156
-recovered pasa_asmbl_35076.p1, internal, 90278, 90374
-recovered pasa_asmbl_35076.p1, internal, 90571, 90732
-recovered pasa_asmbl_35076.p1, internal, 90888, 91051
Valid prediction for GeneMark_model.100667_t
Valid prediction for snap_scaffold_26-snap.2226-T1
Valid prediction for GeneMark_model.100658_t
Valid prediction for snap_scaffold_26-snap.2231-T1
Valid prediction for Augustus_model.g38504.t1
Valid prediction for GlimmerHMM_glimmerT_57793-T1
Valid prediction for CodingQuarry_transcript_40362-T1
Valid prediction for GlimmerHMM_glimmerT_57778-T1
Valid prediction for GeneMark_model.100668_t
Valid prediction for Augustus_model.g38508.t1
Couldn't classify 73740, 73992
Couldn't classify 79952, 80181
Sorry, prediction pasa_asmbl_35078.p1 fails validation.
(CGT)	 AT	73740-73992	GT	GGG
(TCT)	 AG	74491-74754	GT	ACG
(ATC)	 AG	75045-75160	GT	CCG
(AAA)	 AG	75679-75832	GT	AAG
(TGA)	 AG	77642-77911	GT	AGG
(ACC)	 AG	78304-78489	GT	AGG
(GTC)	 AG	79668-79757	GT	GGG
(CGC)	 AG	79952-80181	CA	GAC
-recovered pasa_asmbl_35078.p1, internal, 74491, 74754
-recovered pasa_asmbl_35078.p1, internal, 75045, 75160
-recovered pasa_asmbl_35078.p1, internal, 75679, 75832
-recovered pasa_asmbl_35078.p1, internal, 77642, 77911
-recovered pasa_asmbl_35078.p1, internal, 78304, 78489
-recovered pasa_asmbl_35078.p1, internal, 79668, 79757
Valid prediction for Augustus_model.g38502.t1
Valid prediction for GlimmerHMM_glimmerT_57784-T1
Valid prediction for GeneMark_model.100657_t
Valid prediction for GlimmerHMM_glimmerT_57782-T1
Valid prediction for Augustus_model.g38500.t1
Valid prediction for GlimmerHMM_glimmerT_57791-T1
Valid prediction for snap_scaffold_26-snap.2234-T1
Valid prediction for GlimmerHMM_glimmerT_57788-T1
Valid prediction for Augustus_model.g38507.t1
Valid prediction for HiQ_model.g38499.t1
Valid prediction for snap_scaffold_26-snap.2223-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19800, rend_intergenic: 17867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157584
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 19800, rend_intergenic: 17867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11333
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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