-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_7453385-7781123

-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_12460-T1
Valid prediction for Augustus_model.g8253.t1
Valid prediction for Augustus_model.g8255.t1
Valid prediction for GeneMark_model.21222_t
Valid prediction for GlimmerHMM_glimmerT_12473-T1
Valid prediction for snap_scaffold_5-snap.1505-T1
Valid prediction for GeneMark_model.21218_t
Valid prediction for GlimmerHMM_glimmerT_12464-T1
Valid prediction for CodingQuarry_transcript_51999-T1
Valid prediction for GeneMark_model.21228_t
Valid prediction for Augustus_model.g8263.t1
Valid prediction for GlimmerHMM_glimmerT_12461-T1
Valid prediction for HiQ_model.g8267.t1
Valid prediction for GeneMark_model.21216_t
Valid prediction for CodingQuarry_transcript_51998-T1
Valid prediction for snap_scaffold_5-snap.1522-T1
Valid prediction for Augustus_model.g8254.t1
Valid prediction for GlimmerHMM_glimmerT_12475-T1
Couldn't classify 278727, 279311
Sorry, prediction pasa_asmbl_44166.p1 fails validation.
(GTC)	 GG	278727-279311	GT	AGG
(GTT)	 AG	279489-279950	GT	AGG
(ACC)	 AG	280046-280162	GT	AGG
(ATT)	 AG	280512-280627	GT	AAG
(ATA)	 AG	281351-281453	GT	AGG
(ATC)	 AG	281877-281966	GT	TGG
(AAA)	 AG	282883-283104	TG	AGT
-recovered pasa_asmbl_44166.p1, terminal, 282883, 283104
-recovered pasa_asmbl_44166.p1, internal, 279489, 279950
-recovered pasa_asmbl_44166.p1, internal, 280046, 280162
-recovered pasa_asmbl_44166.p1, internal, 280512, 280627
-recovered pasa_asmbl_44166.p1, internal, 281351, 281453
-recovered pasa_asmbl_44166.p1, internal, 281877, 281966
Valid prediction for pasa_asmbl_44168.p1
Valid prediction for GeneMark_model.21231_t
Valid prediction for GeneMark_model.21214_t
Valid prediction for GeneMark_model.21229_t
Valid prediction for GlimmerHMM_glimmerT_12467-T1
Valid prediction for Augustus_model.g8270.t1
Valid prediction for GlimmerHMM_glimmerT_12462-T1
Valid prediction for GeneMark_model.21212_t
Valid prediction for snap_scaffold_5-snap.1501-T1
Valid prediction for snap_scaffold_5-snap.1513-T1
Valid prediction for GeneMark_model.21211_t
Valid prediction for snap_scaffold_5-snap.1499-T1
Couldn't classify 180709, 181005
Sorry, prediction pasa_asmbl_45570.p1 fails validation.
(ATG)	 CC	180709-181005	TT	CAT
Valid prediction for snap_scaffold_5-snap.1518-T1
Valid prediction for Augustus_model.g8266.t1
Valid prediction for GeneMark_model.21220_t
Valid prediction for Augustus_model.g8256.t1
Valid prediction for snap_scaffold_5-snap.1523-T1
Valid prediction for Augustus_model.g8271.t1
Valid prediction for CodingQuarry_transcript_52002-T1
Valid prediction for snap_scaffold_5-snap.1503-T1
Valid prediction for GeneMark_model.21208_t
Valid prediction for GlimmerHMM_glimmerT_12476-T1
Valid prediction for GeneMark_model.21235_t
Valid prediction for GeneMark_model.21217_t
Valid prediction for snap_scaffold_5-snap.1504-T1
Valid prediction for snap_scaffold_5-snap.1500-T1
Couldn't classify 253766, 253843
Sorry, prediction pasa_asmbl_44162.p1 fails validation.
(CTC)	 GT	253766-253843	GT	AGG
(GTG)	 AG	254025-254151	GT	ATG
(TTG)	 AG	254328-254513	GT	GGG
(GGC)	 AG	254584-254663	GT	AGG
(GTG)	 AG	254823-254990	GT	AGG
(GGT)	 AG	255360-255460	GT	CGG
(GAT)	 AG	255566-255767	TT	GAT
-recovered pasa_asmbl_44162.p1, terminal, 255566, 255767
-recovered pasa_asmbl_44162.p1, internal, 254025, 254151
-recovered pasa_asmbl_44162.p1, internal, 254328, 254513
-recovered pasa_asmbl_44162.p1, internal, 254584, 254663
-recovered pasa_asmbl_44162.p1, internal, 254823, 254990
-recovered pasa_asmbl_44162.p1, internal, 255360, 255460
Valid prediction for GeneMark_model.21219_t
Valid prediction for GeneMark_model.21224_t

-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 Augustus_model.g8261.t1
Couldn't classify 58548, 58640
Couldn't classify 62192, 62230
Sorry, prediction pasa_asmbl_46323.p1 fails validation.
(CGC)	 GA	58548-58640	GT	AGG
(TTC)	 AG	60736-60936	GC	AGG
(ATG)	 AG	61762-61857	GT	GTG
(GAA)	 AG	62192-62230	GC	AAG
-recovered pasa_asmbl_46323.p1, initial, 61762, 61857
-recovered pasa_asmbl_46323.p1, internal, 60736, 60936
-recovered pasa_asmbl_46323.p1, internal, 61762, 61857
-recovered pasa_asmbl_46323.p1, internal, 62192, 62230
Valid prediction for GeneMark_model.21227_t
Valid prediction for GeneMark_model.21215_t
Valid prediction for snap_scaffold_5-snap.1512-T1
Valid prediction for Augustus_model.g8252.t1
Valid prediction for snap_scaffold_5-snap.1497-T1
Valid prediction for GeneMark_model.21221_t
Valid prediction for CodingQuarry_transcript_52000-T1
Valid prediction for GeneMark_model.21205_t
Valid prediction for snap_scaffold_5-snap.1511-T1
Valid prediction for GeneMark_model.21230_t
Valid prediction for snap_scaffold_5-snap.1502-T1
Valid prediction for snap_scaffold_5-snap.1510-T1
Valid prediction for GeneMark_model.21232_t
Valid prediction for GlimmerHMM_glimmerT_12479-T1
Valid prediction for GeneMark_model.21226_t
Valid prediction for GlimmerHMM_glimmerT_12470-T1
Valid prediction for GlimmerHMM_glimmerT_12465-T1
Valid prediction for HiQ_model.g8264.t1
Valid prediction for GlimmerHMM_glimmerT_12466-T1
Valid prediction for snap_scaffold_5-snap.1515-T1
Valid prediction for snap_scaffold_5-snap.1507-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_12468-T1
Valid prediction for GlimmerHMM_glimmerT_12463-T1
Valid prediction for snap_scaffold_5-snap.1525-T1
Valid prediction for GeneMark_model.21206_t
Valid prediction for GlimmerHMM_glimmerT_12472-T1
Valid prediction for Augustus_model.g8257.t1
Valid prediction for GeneMark_model.21210_t
Valid prediction for Augustus_model.g8259.t1
Valid prediction for snap_scaffold_5-snap.1508-T1
Valid prediction for GeneMark_model.21223_t
Valid prediction for snap_scaffold_5-snap.1506-T1
Valid prediction for Augustus_model.g8258.t1
Valid prediction for Augustus_model.g8262.t1
Valid prediction for Augustus_model.g8269.t1
Valid prediction for snap_scaffold_5-snap.1520-T1
Valid prediction for Augustus_model.g8265.t1
Valid prediction for snap_scaffold_5-snap.1517-T1
Valid prediction for pasa_asmbl_45571.p1
Valid prediction for Augustus_model.g8268.t1
Valid prediction for GeneMark_model.21207_t
Valid prediction for snap_scaffold_5-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_12469-T1
Valid prediction for GlimmerHMM_glimmerT_12474-T1
Valid prediction for snap_scaffold_5-snap.1516-T1
Valid prediction for GlimmerHMM_glimmerT_12471-T1
Valid prediction for GeneMark_model.21234_t
Valid prediction for snap_scaffold_5-snap.1498-T1
Valid prediction for GeneMark_model.21225_t
Valid prediction for GlimmerHMM_glimmerT_12478-T1
Couldn't classify 63675, 63743
Sorry, prediction CodingQuarry_transcript_52001-T1 fails validation.
(ATG)	 CG	62922-62951	GT	AGG
(GTG)	 AG	63143-63281	GT	CCG
(CTC)	 AG	63675-63743	TG	GGT
(CAT)	 AG	65009-65095	GT	AGG
(GGA)	 AG	65571-65716	AT	GAA
-recovered CodingQuarry_transcript_52001-T1, initial, 62922, 62951
-recovered CodingQuarry_transcript_52001-T1, terminal, 65571, 65716
-recovered CodingQuarry_transcript_52001-T1, internal, 63143, 63281
-recovered CodingQuarry_transcript_52001-T1, internal, 65009, 65095
Valid prediction for Augustus_model.g8260.t1
Valid prediction for snap_scaffold_5-snap.1514-T1
Valid prediction for GeneMark_model.21233_t
Valid prediction for snap_scaffold_5-snap.1524-T1
Valid prediction for snap_scaffold_5-snap.1496-T1
Valid prediction for snap_scaffold_5-snap.1519-T1
Valid prediction for Augustus_model.g8251.t1
Valid prediction for GeneMark_model.21213_t
Valid prediction for GlimmerHMM_glimmerT_12477-T1

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

-building trellis in range 1 - 327739
-exon list size: 427


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
7.7    
7.9    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 296899 - 327739
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 296899 - 323542
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 296899 - 316600
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 296899 - 315861
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 296899 - 311832
-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