-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_4650884-4990316

-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 GeneMark_model.90557_t
Valid prediction for snap_scaffold_23-snap.892-T1
Valid prediction for GlimmerHMM_glimmerT_52178-T1
Valid prediction for snap_scaffold_23-snap.895-T1
Valid prediction for Augustus_model.g35089.t1
Couldn't classify 295777, 295863
Sorry, prediction pasa_asmbl_30837.p1 fails validation.
(TTT)	 GA	295777-295863	GT	AGG
(GCA)	 AG	296563-296670	GT	AGG
(GAA)	 AG	296860-296954	GT	GGG
(TCC)	 AG	297185-297278	GT	TGG
(CAA)	 AG	297380-297452	GT	TGG
(ATG)	 AG	297680-297812	GT	GTG
(GGA)	 AG	297885-298014	GT	AGG
(AAC)	 AG	298109-298198	GT	TGG
(GTG)	 AG	298354-298461	GT	ATG
(ATT)	 AG	298592-298687	GT	AGG
(CGT)	 AG	298859-298955	GT	GGG
(GTA)	 AG	299540-299594	GT	GGG
(AAT)	 AG	300407-300524	GT	ATG
(TGT)	 AG	300760-300833	GT	ACG
(CAT)	 AG	301115-301208	TT	GAT
add_exon() Sorry, pasa_asmbl_30837.p1 297680-297812-initial-1 is invalid.
-recovered pasa_asmbl_30837.p1, initial, 297680, 297812
-recovered pasa_asmbl_30837.p1, terminal, 301115, 301208
-recovered pasa_asmbl_30837.p1, internal, 296563, 296670
-recovered pasa_asmbl_30837.p1, internal, 296860, 296954
-recovered pasa_asmbl_30837.p1, internal, 297185, 297278
-recovered pasa_asmbl_30837.p1, internal, 297380, 297452
-recovered pasa_asmbl_30837.p1, internal, 297680, 297812
-recovered pasa_asmbl_30837.p1, internal, 297885, 298014
-recovered pasa_asmbl_30837.p1, internal, 298109, 298198
-recovered pasa_asmbl_30837.p1, internal, 298354, 298461
-recovered pasa_asmbl_30837.p1, internal, 298592, 298687
-recovered pasa_asmbl_30837.p1, internal, 298859, 298955
-recovered pasa_asmbl_30837.p1, internal, 299540, 299594
-recovered pasa_asmbl_30837.p1, internal, 300407, 300524
-recovered pasa_asmbl_30837.p1, internal, 300760, 300833
Valid prediction for GeneMark_model.90559_t
Valid prediction for GeneMark_model.90554_t
Valid prediction for GlimmerHMM_glimmerT_52164-T1
Valid prediction for snap_scaffold_23-snap.894-T1
Valid prediction for GeneMark_model.90553_t
Valid prediction for snap_scaffold_23-snap.891-T1
Valid prediction for Augustus_model.g35088.t1
Valid prediction for snap_scaffold_23-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_52176-T1
Valid prediction for snap_scaffold_23-snap.896-T1
Valid prediction for snap_scaffold_23-snap.886-T1
Couldn't classify 34904, 34937
Couldn't classify 38534, 38728
Sorry, prediction pasa_asmbl_30827.p1 fails validation.
(TTT)	 AG	34904-34937	GT	AGG
(GTC)	 AG	35578-35736	GT	AGG
(GTG)	 AG	36793-36917	GT	AGG
(GTT)	 AG	38534-38728	GT	AAG
add_exon() Sorry, pasa_asmbl_30827.p1 35578-35736-terminal-1 is invalid.
-recovered pasa_asmbl_30827.p1, terminal, 35578, 35736
-recovered pasa_asmbl_30827.p1, internal, 34904, 34937
-recovered pasa_asmbl_30827.p1, internal, 35578, 35736
-recovered pasa_asmbl_30827.p1, internal, 36793, 36917
-recovered pasa_asmbl_30827.p1, internal, 38534, 38728
Valid prediction for HiQ_model.g35076.t1
Valid prediction for GeneMark_model.90537_t
Valid prediction for snap_scaffold_23-snap.884-T1
Valid prediction for CodingQuarry_transcript_35578-T1
Valid prediction for Augustus_model.g35083.t1
Valid prediction for GlimmerHMM_glimmerT_52172-T1
Valid prediction for CodingQuarry_transcript_35579-T1
Valid prediction for GlimmerHMM_glimmerT_52192-T1
Valid prediction for GeneMark_model.90552_t
Valid prediction for Augustus_model.g35077.t1
Valid prediction for HiQ_model.g35103.t1
Valid prediction for GeneMark_model.90544_t
Valid prediction for CodingQuarry_transcript_35581-T1
Valid prediction for snap_scaffold_23-snap.870-T1
Valid prediction for snap_scaffold_23-snap.897-T1
Valid prediction for GlimmerHMM_glimmerT_52167-T1
Valid prediction for HiQ_model.g35097.t1
Valid prediction for Augustus_model.g35085.t1
Couldn't classify 138245, 138749
Couldn't classify 140123, 140256
Sorry, prediction pasa_asmbl_31239.p1 fails validation.
(AGT)	 TC	138245-138749	GT	AGG
(GTG)	 AG	140123-140256	CC	GAC
Valid prediction for pasa_asmbl_30830.p1
Valid prediction for snap_scaffold_23-snap.875-T1
Valid prediction for GeneMark_model.90539_t
Valid prediction for snap_scaffold_23-snap.905-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52190-T1
Valid prediction for Augustus_model.g35086.t1
Valid prediction for snap_scaffold_23-snap.899-T1
Valid prediction for snap_scaffold_23-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_52162-T1
Valid prediction for GeneMark_model.90542_t
Valid prediction for GlimmerHMM_glimmerT_52188-T1
Valid prediction for Augustus_model.g35084.t1
Valid prediction for GlimmerHMM_glimmerT_52183-T1
Valid prediction for GeneMark_model.90547_t
Valid prediction for snap_scaffold_23-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_52179-T1
Valid prediction for GlimmerHMM_glimmerT_52181-T1
Valid prediction for snap_scaffold_23-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_52180-T1
Valid prediction for snap_scaffold_23-snap.890-T1
Valid prediction for snap_scaffold_23-snap.877-T1
Valid prediction for GeneMark_model.90558_t
Valid prediction for snap_scaffold_23-snap.883-T1
Valid prediction for GeneMark_model.90543_t
Valid prediction for GeneMark_model.90555_t
Valid prediction for snap_scaffold_23-snap.893-T1
Valid prediction for Augustus_model.g35093.t1
Valid prediction for Augustus_model.g35081.t1
Valid prediction for snap_scaffold_23-snap.885-T1
Valid prediction for GeneMark_model.90549_t
Valid prediction for Augustus_model.g35078.t1
Valid prediction for snap_scaffold_23-snap.888-T1
Valid prediction for snap_scaffold_23-snap.889-T1
Valid prediction for GeneMark_model.90548_t
Valid prediction for snap_scaffold_23-snap.898-T1
Valid prediction for GlimmerHMM_glimmerT_52174-T1
Valid prediction for GlimmerHMM_glimmerT_52161-T1
Valid prediction for snap_scaffold_23-snap.887-T1
Valid prediction for GeneMark_model.90545_t
Valid prediction for GlimmerHMM_glimmerT_52169-T1
Valid prediction for Augustus_model.g35094.t1
Valid prediction for GeneMark_model.90550_t
Valid prediction for GeneMark_model.90538_t
Valid prediction for snap_scaffold_23-snap.872-T1
Valid prediction for Augustus_model.g35082.t1
Valid prediction for snap_scaffold_23-snap.874-T1
Valid prediction for snap_scaffold_23-snap.871-T1
Valid prediction for GeneMark_model.90540_t
Valid prediction for snap_scaffold_23-snap.876-T1
Valid prediction for Augustus_model.g35091.t1
Valid prediction for GeneMark_model.90563_t
Valid prediction for Augustus_model.g35098.t1
Valid prediction for GlimmerHMM_glimmerT_52160-T1
Valid prediction for GlimmerHMM_glimmerT_52168-T1
Valid prediction for Augustus_model.g35075.t1
Valid prediction for pasa_asmbl_30828.p1
Valid prediction for GeneMark_model.90546_t
Valid prediction for Augustus_model.g35092.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 HiQ_model.g35074.t1
Valid prediction for Augustus_model.g35102.t1
Valid prediction for pasa_asmbl_31595.p1
Valid prediction for GlimmerHMM_glimmerT_52165-T1
Valid prediction for GeneMark_model.90564_t
Valid prediction for GlimmerHMM_glimmerT_52159-T1
Valid prediction for GeneMark_model.90536_t
Valid prediction for snap_scaffold_23-snap.904-T1
Valid prediction for snap_scaffold_23-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_52163-T1
Valid prediction for GeneMark_model.90551_t
Valid prediction for GlimmerHMM_glimmerT_52182-T1
Valid prediction for GlimmerHMM_glimmerT_52191-T1
Valid prediction for snap_scaffold_23-snap.880-T1
Valid prediction for GeneMark_model.90565_t
Valid prediction for Augustus_model.g35100.t1
Valid prediction for snap_scaffold_23-snap.902-T1
Valid prediction for Augustus_model.g35090.t1
Valid prediction for Augustus_model.g35080.t1
Valid prediction for GeneMark_model.90562_t
Valid prediction for GlimmerHMM_glimmerT_52186-T1
Valid prediction for Augustus_model.g35099.t1
Valid prediction for GeneMark_model.90560_t
Valid prediction for GlimmerHMM_glimmerT_52185-T1
Valid prediction for GlimmerHMM_glimmerT_52189-T1
Valid prediction for GeneMark_model.90541_t
Valid prediction for GlimmerHMM_glimmerT_52184-T1
Valid prediction for GlimmerHMM_glimmerT_52171-T1
Valid prediction for GlimmerHMM_glimmerT_52187-T1
Valid prediction for snap_scaffold_23-snap.907-T1
Valid prediction for snap_scaffold_23-snap.906-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52170-T1
Valid prediction for Augustus_model.g35079.t1
Valid prediction for GlimmerHMM_glimmerT_52177-T1
Valid prediction for pasa_asmbl_31593.p1
Valid prediction for HiQ_model.g35096.t1
Valid prediction for snap_scaffold_23-snap.869-T1
Valid prediction for snap_scaffold_23-snap.868-T1
Valid prediction for GeneMark_model.90556_t
Valid prediction for Augustus_model.g35101.t1
Valid prediction for GlimmerHMM_glimmerT_52173-T1
Valid prediction for snap_scaffold_23-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_52166-T1
Valid prediction for snap_scaffold_23-snap.901-T1
Valid prediction for snap_scaffold_23-snap.879-T1
Valid prediction for Augustus_model.g35095.t1
Valid prediction for snap_scaffold_23-snap.900-T1
Valid prediction for Augustus_model.g35087.t1
Valid prediction for GlimmerHMM_glimmerT_52175-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 339433
-exon list size: 436


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16474
-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
	-no exons in range 1457 - 16474

-building DP trellis

-building trellis in range 301209 - 339433
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 301209 - 317789
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 301209 - 314536
-exon list size: 1


building trellis

33.3    
66.7    
-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 317852 - 339433
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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
	-no exons in range 317852 - 329191

-building DP trellis

-building trellis in range 329263 - 339433
-exon list size: 1


building trellis

33.3    
66.7    
-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