-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_29

-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_29-snap.6-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_60913-T1
Valid prediction for GlimmerHMM_glimmerT_60910-T1
Valid prediction for snap_scaffold_29-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_60909-T1
Valid prediction for GlimmerHMM_glimmerT_60908-T1
add_exon() Sorry, GlimmerHMM_glimmerT_60908-T1 1956-2202-terminal-1 is invalid.
Valid prediction for GeneMark_model.106123_t
Valid prediction for snap_scaffold_29-snap.8-T1
Valid prediction for Augustus_model.g40531.t1
Valid prediction for snap_scaffold_29-snap.3-T1
Valid prediction for GeneMark_model.106122_t
Valid prediction for GeneMark_model.106125_t
Valid prediction for GlimmerHMM_glimmerT_60918-T1
Couldn't classify 1606, 1754
Sorry, prediction GeneMark_model.106118_t fails validation.
(GTG)	 AG	1606-1754	GT	GTG
(AGC)	 AG	2010-2198	GT	TGG
(GAG)	 AG	2254-2263	GT	GGG
(CAC)	 AG	2481-2675	GT	AGG
(GGA)	 AG	2824-2865	GT	GAG
(TCC)	 AG	4859-4930	GT	TGG
(GAC)	 AG	5257-5300	GT	AGG
(GGT)	 AG	5698-5707	AG	AAA
-recovered GeneMark_model.106118_t, terminal, 5698, 5707
-recovered GeneMark_model.106118_t, internal, 1606, 1754
-recovered GeneMark_model.106118_t, internal, 2010, 2198
-recovered GeneMark_model.106118_t, internal, 2254, 2263
-recovered GeneMark_model.106118_t, internal, 2481, 2675
-recovered GeneMark_model.106118_t, internal, 2824, 2865
-recovered GeneMark_model.106118_t, internal, 4859, 4930
-recovered GeneMark_model.106118_t, internal, 5257, 5300
Valid prediction for snap_scaffold_29-snap.2-T1
Couldn't classify 1606, 1754
Sorry, prediction Augustus_model.g40526.t1 fails validation.
(GTG)	 AG	1606-1754	GT	GTG
(TTG)	 AG	1956-2198	GT	TGG
(CAT)	 AG	2504-2675	GT	AGG
(GGA)	 AG	2824-2865	GT	GAG
(TCC)	 AG	4859-4960	AA	GAA
-recovered Augustus_model.g40526.t1, terminal, 4859, 4960
-recovered Augustus_model.g40526.t1, internal, 1606, 1754
-recovered Augustus_model.g40526.t1, internal, 1956, 2198
-recovered Augustus_model.g40526.t1, internal, 2504, 2675
-recovered Augustus_model.g40526.t1, internal, 2824, 2865
Valid prediction for Augustus_model.g40535.t1
Valid prediction for snap_scaffold_29-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_60920-T1
Valid prediction for GlimmerHMM_glimmerT_60921-T1
Valid prediction for GlimmerHMM_glimmerT_60917-T1
Valid prediction for snap_scaffold_29-snap.1-T1
Valid prediction for snap_scaffold_29-snap.5-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 GlimmerHMM_glimmerT_60916-T1
Valid prediction for GlimmerHMM_glimmerT_60912-T1
Valid prediction for snap_scaffold_29-snap.13-T1
Valid prediction for Augustus_model.g40530.t1
Valid prediction for GlimmerHMM_glimmerT_60927-T1
Valid prediction for GlimmerHMM_glimmerT_60925-T1
Valid prediction for Augustus_model.g40528.t1
Couldn't classify 47201, 47421
Sorry, prediction pasa_asmbl_38585.p1 fails validation.
(AAT)	 CC	47201-47421	GT	AGG
(GTC)	 AG	49179-49284	TG	GAT
-recovered pasa_asmbl_38585.p1, terminal, 49179, 49284
Valid prediction for Augustus_model.g40527.t1
Valid prediction for Augustus_model.g40534.t1
Valid prediction for GlimmerHMM_glimmerT_60915-T1
Valid prediction for snap_scaffold_29-snap.4-T1
Couldn't classify 715, 1188
Sorry, prediction pasa_asmbl_38589.p1 fails validation.
(TCC)	 CT	715-1188	AA	ATA
Valid prediction for GlimmerHMM_glimmerT_60911-T1
Valid prediction for GlimmerHMM_glimmerT_60924-T1
Valid prediction for Augustus_model.g40532.t1
Valid prediction for GeneMark_model.106120_t
Valid prediction for snap_scaffold_29-snap.11-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 184, 648
Sorry, prediction pasa_asmbl_38590.p1 fails validation.
(CCA)	 AC	184-648	CC	CAC
Valid prediction for Augustus_model.g40529.t1
Valid prediction for GlimmerHMM_glimmerT_60919-T1
Valid prediction for GeneMark_model.106126_t
Valid prediction for GlimmerHMM_glimmerT_60923-T1
Valid prediction for snap_scaffold_29-snap.12-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.106121_t
Valid prediction for snap_scaffold_29-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_60928-T1
add_exon() Sorry, GlimmerHMM_glimmerT_60928-T1 2532-2898-terminal-1 is invalid.
Valid prediction for GeneMark_model.106119_t
Valid prediction for GlimmerHMM_glimmerT_60926-T1
Valid prediction for GlimmerHMM_glimmerT_60922-T1
Couldn't classify 396, 1065
Sorry, prediction snap_scaffold_29-snap.14-T1 fails validation.
(TCC)	 AG	396-1065	GT	TGG
(CCC)	 AG	1244-1520	GT	TGG
(ATT)	 AG	2507-2898	TC	GAT
-recovered snap_scaffold_29-snap.14-T1, terminal, 2507, 2898
-recovered snap_scaffold_29-snap.14-T1, internal, 396, 1065
-recovered snap_scaffold_29-snap.14-T1, internal, 1244, 1520
Valid prediction for Augustus_model.g40533.t1
Valid prediction for GlimmerHMM_glimmerT_60914-T1

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

-building trellis in range 1 - 58417
-exon list size: 223


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.7    
3.1    
3.6    
4.0    
4.4    
4.9    
5.3    
5.8    
6.2    
6.7    
7.1    
7.6    
8.0    
8.4    
8.9    
9.3    
9.8    
10.2    
10.7    
11.1    
11.6    
12.0    
12.4    
12.9    
13.3    
13.8    
14.2    
14.7    
15.1    
15.6    
16.0    
16.4    
16.9    
17.3    
17.8    
18.2    
18.7    
19.1    
19.6    
20.0    
20.4    
20.9    
21.3    
21.8    
22.2    
22.7    
23.1    
23.6    
24.0    
24.4    
24.9    
25.3    
25.8    
26.2    
26.7    
27.1    
27.6    
28.0    
28.4    
28.9    
29.3    
29.8    
30.2    
30.7    
31.1    
31.6    
32.0    
32.4    
32.9    
33.3    
33.8    
34.2    
34.7    
35.1    
35.6    
36.0    
36.4    
36.9    
37.3    
37.8    
38.2    
38.7    
39.1    
39.6    
40.0    
40.4    
40.9    
41.3    
41.8    
42.2    
42.7    
43.1    
43.6    
44.0    
44.4    
44.9    
45.3    
45.8    
46.2    
46.7    
47.1    
47.6    
48.0    
48.4    
48.9    
49.3    
49.8    
50.2    
50.7    
51.1    
51.6    
52.0    
52.4    
52.9    
53.3    
53.8    
54.2    
54.7    
55.1    
55.6    
56.0    
56.4    
56.9    
57.3    
57.8    
58.2    
58.7    
59.1    
59.6    
60.0    
60.4    
60.9    
61.3    
61.8    
62.2    
62.7    
63.1    
63.6    
64.0    
64.4    
64.9    
65.3    
65.8    
66.2    
66.7    
67.1    
67.6    
68.0    
68.4    
68.9    
69.3    
69.8    
70.2    
70.7    
71.1    
71.6    
72.0    
72.4    
72.9    
73.3    
73.8    
74.2    
74.7    
75.1    
75.6    
76.0    
76.4    
76.9    
77.3    
77.8    
78.2    
78.7    
79.1    
79.6    
80.0    
80.4    
80.9    
81.3    
81.8    
82.2    
82.7    
83.1    
83.6    
84.0    
84.4    
84.9    
85.3    
85.8    
86.2    
86.7    
87.1    
87.6    
88.0    
88.4    
88.9    
89.3    
89.8    
90.2    
90.7    
91.1    
91.6    
92.0    
92.4    
92.9    
93.3    
93.8    
94.2    
94.7    
95.1    
95.6    
96.0    
96.4    
96.9    
97.3    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 22 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support