-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_1961129-2223065

-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 CodingQuarry_transcript_2548-T1
Valid prediction for GlimmerHMM_glimmerT_276-T1
Valid prediction for GlimmerHMM_glimmerT_277-T1
Valid prediction for HiQ_model.g212.t1
Valid prediction for pasa_asmbl_1530.p1
Valid prediction for HiQ_model.g205.t1
Valid prediction for GlimmerHMM_glimmerT_267-T1
Valid prediction for Augustus_model.g215.t1
Valid prediction for CodingQuarry_transcript_2545-T1
Valid prediction for GlimmerHMM_glimmerT_264-T1
Valid prediction for GlimmerHMM_glimmerT_263-T1
Valid prediction for snap_scaffold_1-snap.331-T1
Valid prediction for Augustus_model.g201.t1
Valid prediction for snap_scaffold_1-snap.333-T1
Valid prediction for GlimmerHMM_glimmerT_254-T1
Valid prediction for GlimmerHMM_glimmerT_266-T1
Valid prediction for pasa_asmbl_1533.p1
Valid prediction for snap_scaffold_1-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_252-T1
Valid prediction for snap_scaffold_1-snap.334-T1
Valid prediction for HiQ_model.g218.t1
Valid prediction for HiQ_model.g203.t1
Valid prediction for GlimmerHMM_glimmerT_256-T1
Valid prediction for Augustus_model.g206.t1
Valid prediction for GlimmerHMM_glimmerT_270-T1
Valid prediction for CodingQuarry_transcript_2544-T1
Valid prediction for CodingQuarry_transcript_2546-T1
Valid prediction for pasa_asmbl_1526.p1
Couldn't classify 119018, 119110
Sorry, prediction pasa_asmbl_1532.p1 fails validation.
(GCC)	 AG	119018-119110	GT	AGG
(ATA)	 AG	121148-121252	GT	AGG
(GTG)	 AG	121444-121675	GT	TGG
(GGA)	 AG	122236-122348	GT	TGG
(GAA)	 AG	123568-123624	GT	AAG
-recovered pasa_asmbl_1532.p1, terminal, 123568, 123624
-recovered pasa_asmbl_1532.p1, internal, 119018, 119110
-recovered pasa_asmbl_1532.p1, internal, 121148, 121252
-recovered pasa_asmbl_1532.p1, internal, 121444, 121675
-recovered pasa_asmbl_1532.p1, internal, 122236, 122348
-recovered pasa_asmbl_1532.p1, internal, 123568, 123624
Valid prediction for snap_scaffold_1-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_274-T1
Valid prediction for GlimmerHMM_glimmerT_261-T1
Valid prediction for GlimmerHMM_glimmerT_255-T1
Valid prediction for snap_scaffold_1-snap.343-T1
Valid prediction for Augustus_model.g211.t1
Valid prediction for snap_scaffold_1-snap.341-T1
Sorry, intron length (3) is less than minimum required (10)

-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_1-snap.340-T1
Valid prediction for snap_scaffold_1-snap.356-T1
Couldn't classify 255830, 256055
Sorry, prediction pasa_asmbl_92.p1 fails validation.
(GTT)	 TG	255830-256055	GT	GGG
(AAG)	 AG	256330-257135	CT	AGC
-recovered pasa_asmbl_92.p1, terminal, 256330, 257135
Valid prediction for snap_scaffold_1-snap.359-T1
Couldn't classify 189657, 189758
Sorry, prediction pasa_asmbl_108.p1 fails validation.
(AGA)	 AG	189657-189758	GT	AGG
(AAT)	 AG	189967-190073	GT	AAG
(GGC)	 AG	190433-190553	GT	AGG
(AAT)	 AG	190828-190896	AC	AAA
-recovered pasa_asmbl_108.p1, terminal, 190828, 190896
-recovered pasa_asmbl_108.p1, internal, 189657, 189758
-recovered pasa_asmbl_108.p1, internal, 189967, 190073
-recovered pasa_asmbl_108.p1, internal, 190433, 190553
Valid prediction for snap_scaffold_1-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_257-T1
Valid prediction for GlimmerHMM_glimmerT_250-T1
Couldn't classify 212743, 212908
Couldn't classify 215799, 215909
Sorry, prediction pasa_asmbl_104.p1 fails validation.
(GAG)	 AG	212743-212908	GT	CTG
(ATG)	 AG	213080-213320	GT	AGG
(ACA)	 AG	214061-214176	GT	AGG
(GTA)	 AG	214378-214514	GT	AGG
(ATT)	 AG	215799-215909	GG	TAG
add_exon() Sorry, pasa_asmbl_104.p1 213080-213320-initial-1 is invalid.
-recovered pasa_asmbl_104.p1, initial, 213080, 213320
-recovered pasa_asmbl_104.p1, internal, 212743, 212908
-recovered pasa_asmbl_104.p1, internal, 213080, 213320
-recovered pasa_asmbl_104.p1, internal, 214061, 214176
-recovered pasa_asmbl_104.p1, internal, 214378, 214514
Couldn't classify 252397, 252592
Sorry, prediction pasa_asmbl_95.p1 fails validation.
(GAA)	 CT	252397-252592	GT	AGG
(ACC)	 AG	253068-253984	AG	GAA
-recovered pasa_asmbl_95.p1, terminal, 253068, 253984
Valid prediction for GlimmerHMM_glimmerT_248-T1
Valid prediction for pasa_asmbl_98.p1
Couldn't classify 101568, 101737
Couldn't classify 105042, 105228
Sorry, prediction pasa_asmbl_112.p1 fails validation.
(GGA)	 CA	101568-101737	GT	AGG
(TAA)	 AG	101981-102085	GT	AGG
(CGC)	 AG	102233-102344	GT	AGG
(TTA)	 AG	102438-103329	GT	AGG
(GTA)	 AG	103477-103570	GT	AGG
(TGA)	 AG	105042-105228	GG	AAG
-recovered pasa_asmbl_112.p1, internal, 101981, 102085
-recovered pasa_asmbl_112.p1, internal, 102233, 102344
-recovered pasa_asmbl_112.p1, internal, 102438, 103329
-recovered pasa_asmbl_112.p1, internal, 103477, 103570
Valid prediction for HiQ_model.g199.t1
Valid prediction for snap_scaffold_1-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_273-T1
Valid prediction for Augustus_model.g198.t1
Valid prediction for snap_scaffold_1-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_269-T1
Valid prediction for GlimmerHMM_glimmerT_260-T1
Valid prediction for CodingQuarry_transcript_2542-T1
Valid prediction for Augustus_model.g210.t1
Valid prediction for snap_scaffold_1-snap.328-T1
Valid prediction for Augustus_model.g222.t1
Valid prediction for CodingQuarry_transcript_2549-T1
Valid prediction for snap_scaffold_1-snap.337-T1
Valid prediction for HiQ_model.g200.t1
Valid prediction for snap_scaffold_1-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_251-T1
Valid prediction for HiQ_model.g209.t1
Valid prediction for snap_scaffold_1-snap.352-T1
Valid prediction for snap_scaffold_1-snap.329-T1
Valid prediction for Augustus_model.g219.t1
Valid prediction for snap_scaffold_1-snap.339-T1
Valid prediction for snap_scaffold_1-snap.347-T1
Valid prediction for GlimmerHMM_glimmerT_258-T1
Valid prediction for snap_scaffold_1-snap.346-T1
Couldn't classify 185491, 185823
Sorry, prediction pasa_asmbl_1284.p1 fails validation.
(CTA)	 CA	185491-185823	AG	CCA
Valid prediction for snap_scaffold_1-snap.350-T1
Valid prediction for CodingQuarry_transcript_2547-T1
Valid prediction for snap_scaffold_1-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_271-T1
Valid prediction for snap_scaffold_1-snap.357-T1
Valid prediction for Augustus_model.g220.t1
Valid prediction for Augustus_model.g216.t1
Valid prediction for snap_scaffold_1-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_262-T1
Valid prediction for HiQ_model.g214.t1
Valid prediction for pasa_asmbl_111.p1
Valid prediction for snap_scaffold_1-snap.326-T1
Valid prediction for snap_scaffold_1-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_275-T1
Valid prediction for Augustus_model.g221.t1
Valid prediction for snap_scaffold_1-snap.348-T1
Valid prediction for Augustus_model.g207.t1
Couldn't classify 203694, 203902
Couldn't classify 209535, 209702
Sorry, prediction pasa_asmbl_105.p1 fails validation.
(AGT)	 AG	203694-203902	GT	AGG
(GTT)	 AG	204684-204900	GT	AGG
(CAA)	 AG	206913-207096	GT	AGG
(GCA)	 AG	209141-209292	GT	GAG
(CTA)	 AG	209535-209702	GT	AGG
-recovered pasa_asmbl_105.p1, internal, 203694, 203902
-recovered pasa_asmbl_105.p1, internal, 204684, 204900
-recovered pasa_asmbl_105.p1, internal, 206913, 207096
-recovered pasa_asmbl_105.p1, internal, 209141, 209292
-recovered pasa_asmbl_105.p1, internal, 209535, 209702
Couldn't classify 76696, 76851
Sorry, prediction pasa_asmbl_116.p2 fails validation.
(GCC)	 GG	76696-76851	GT	AGG
(GAC)	 AG	77880-78122	AT	GAA
-recovered pasa_asmbl_116.p2, terminal, 77880, 78122
Valid prediction for CodingQuarry_transcript_2541-T1
Valid prediction for GlimmerHMM_glimmerT_265-T1
Couldn't classify 198560, 198729
Sorry, prediction pasa_asmbl_106.p1 fails validation.
(ATG)	 AG	195997-196336	GT	GGG
(GTC)	 AG	198560-198729	GT	AGG
-recovered pasa_asmbl_106.p1, initial, 195997, 196336
-recovered pasa_asmbl_106.p1, internal, 195997, 196336
-recovered pasa_asmbl_106.p1, internal, 198560, 198729
Valid prediction for CodingQuarry_transcript_2543-T1
Valid prediction for Augustus_model.g204.t1
Valid prediction for snap_scaffold_1-snap.335-T1
Valid prediction for snap_scaffold_1-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_259-T1
Valid prediction for GlimmerHMM_glimmerT_249-T1
Valid prediction for snap_scaffold_1-snap.358-T1
Valid prediction for Augustus_model.g202.t1
Valid prediction for snap_scaffold_1-snap.355-T1
Valid prediction for Augustus_model.g208.t1
Valid prediction for GlimmerHMM_glimmerT_272-T1
Valid prediction for Augustus_model.g213.t1
Valid prediction for Augustus_model.g217.t1
Valid prediction for snap_scaffold_1-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_268-T1
Valid prediction for snap_scaffold_1-snap.349-T1
Valid prediction for snap_scaffold_1-snap.342-T1
Valid prediction for GlimmerHMM_glimmerT_253-T1

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

-building trellis in range 1 - 261937
-exon list size: 299


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
11.0    
11.3    
11.6    
12.0    
12.3    
12.6    
13.0    
13.3    
13.6    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.3    
18.6    
18.9    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.6    
28.9    
29.2    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.2    
35.5    
35.9    
36.2    
36.5    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.5    
63.8    
64.1    
64.5    
64.8    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.8    
71.1    
71.4    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.1    
81.4    
81.7    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.4    
86.7    
87.0    
87.4    
87.7    
88.0    
88.4    
88.7    
89.0    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 28 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 247601 - 261937
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 251532 - 261937
-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