-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_13090495-13407804

-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.g7046.t1
Valid prediction for GeneMark_model.17401_t
Valid prediction for Augustus_model.g7033.t1
Valid prediction for snap_scaffold_4-snap.2758-T1
Couldn't classify 295947, 296050
Sorry, prediction pasa_asmbl_43118.p1 fails validation.
(GGT)	 AG	295947-296050	GT	AGG
(CGA)	 AG	298388-298463	GT	AGG
(AAA)	 AG	298941-299519	AA	AGA
-recovered pasa_asmbl_43118.p1, terminal, 298941, 299519
-recovered pasa_asmbl_43118.p1, internal, 295947, 296050
-recovered pasa_asmbl_43118.p1, internal, 298388, 298463
Valid prediction for GeneMark_model.17413_t
Valid prediction for GeneMark_model.17407_t
Valid prediction for GeneMark_model.17424_t
Valid prediction for snap_scaffold_4-snap.2763-T1
Valid prediction for GeneMark_model.17419_t
Valid prediction for Augustus_model.g7044.t1
Couldn't classify 81001, 81259
Couldn't classify 81837, 81958
Sorry, prediction pasa_asmbl_43576.p1 fails validation.
(TCA)	 CT	81001-81259	GT	CGG
(GTA)	 AG	81837-81958	AA	ACA
Valid prediction for snap_scaffold_4-snap.2760-T1
Valid prediction for GlimmerHMM_glimmerT_10696-T1
Valid prediction for GlimmerHMM_glimmerT_10698-T1
Valid prediction for GeneMark_model.17421_t
Valid prediction for CodingQuarry_transcript_49083-T1
Valid prediction for GeneMark_model.17399_t
Valid prediction for GeneMark_model.17405_t
Valid prediction for Augustus_model.g7039.t1
Valid prediction for GeneMark_model.17411_t
Valid prediction for GlimmerHMM_glimmerT_10703-T1
Valid prediction for Augustus_model.g7040.t1
Valid prediction for snap_scaffold_4-snap.2779-T1
Valid prediction for GeneMark_model.17396_t
Valid prediction for GeneMark_model.17426_t
Valid prediction for GeneMark_model.17425_t
Valid prediction for GeneMark_model.17393_t
Valid prediction for Augustus_model.g7045.t1
Valid prediction for Augustus_model.g7037.t1
Valid prediction for GeneMark_model.17410_t
Valid prediction for GeneMark_model.17400_t
Valid prediction for snap_scaffold_4-snap.2767-T1
Valid prediction for snap_scaffold_4-snap.2761-T1
Valid prediction for Augustus_model.g7038.t1
Valid prediction for snap_scaffold_4-snap.2756-T1
Valid prediction for GeneMark_model.17423_t
Valid prediction for GeneMark_model.17409_t
Valid prediction for snap_scaffold_4-snap.2777-T1
Valid prediction for snap_scaffold_4-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_10706-T1
Valid prediction for GlimmerHMM_glimmerT_10701-T1
Valid prediction for snap_scaffold_4-snap.2764-T1
Valid prediction for snap_scaffold_4-snap.2751-T1
Valid prediction for GeneMark_model.17403_t
Valid prediction for GeneMark_model.17420_t
Valid prediction for Augustus_model.g7035.t1
Valid prediction for snap_scaffold_4-snap.2778-T1
Valid prediction for snap_scaffold_4-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_10694-T1
Valid prediction for GlimmerHMM_glimmerT_10708-T1
Couldn't classify 282336, 282356
Couldn't classify 284118, 284537
Sorry, prediction pasa_asmbl_43117.p1 fails validation.
(ATT)	 TC	282336-282356	GT	AGG
(CAG)	 AG	284118-284537	AA	AGA
Valid prediction for GeneMark_model.17427_t
Valid prediction for GlimmerHMM_glimmerT_10702-T1
Valid prediction for GlimmerHMM_glimmerT_10709-T1
Valid prediction for snap_scaffold_4-snap.2770-T1
Valid prediction for snap_scaffold_4-snap.2762-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_10711-T1
Valid prediction for GlimmerHMM_glimmerT_10697-T1
Valid prediction for snap_scaffold_4-snap.2780-T1
Valid prediction for snap_scaffold_4-snap.2768-T1
Valid prediction for GlimmerHMM_glimmerT_10707-T1
Valid prediction for Augustus_model.g7031.t1
Valid prediction for pasa_asmbl_41726.p1
Valid prediction for GlimmerHMM_glimmerT_10693-T1
Valid prediction for snap_scaffold_4-snap.2771-T1
Valid prediction for snap_scaffold_4-snap.2775-T1
Valid prediction for snap_scaffold_4-snap.2769-T1
Valid prediction for Augustus_model.g7043.t1
Valid prediction for GeneMark_model.17416_t
Valid prediction for HiQ_model.g7030.t1
Valid prediction for snap_scaffold_4-snap.2773-T1
Valid prediction for GeneMark_model.17406_t
Valid prediction for snap_scaffold_4-snap.2781-T1
Valid prediction for CodingQuarry_transcript_49080-T1
Valid prediction for GlimmerHMM_glimmerT_10704-T1
Valid prediction for Augustus_model.g7042.t1
Valid prediction for snap_scaffold_4-snap.2757-T1
Valid prediction for snap_scaffold_4-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_10692-T1
Valid prediction for GlimmerHMM_glimmerT_10710-T1
Valid prediction for pasa_asmbl_41730.p1
Valid prediction for GeneMark_model.17428_t
Valid prediction for GeneMark_model.17415_t
Valid prediction for GeneMark_model.17418_t
Valid prediction for Augustus_model.g7048.t1
Valid prediction for GeneMark_model.17408_t
Valid prediction for GeneMark_model.17404_t
Valid prediction for snap_scaffold_4-snap.2752-T1
Valid prediction for HiQ_model.g7036.t1
Valid prediction for pasa_asmbl_41716.p1
Valid prediction for Augustus_model.g7032.t1
Valid prediction for snap_scaffold_4-snap.2772-T1
Valid prediction for CodingQuarry_transcript_49081-T1
Valid prediction for CodingQuarry_transcript_49076-T1
Valid prediction for GeneMark_model.17394_t
Valid prediction for GlimmerHMM_glimmerT_10690-T1
Couldn't classify 4003, 4140
Couldn't classify 4621, 4772
Sorry, prediction pasa_asmbl_41738.p1 fails validation.
(GAT)	 AG	4003-4140	GT	AGG
(CCC)	 AG	4363-4510	GT	CGG
(CTG)	 AG	4621-4772	CC	AGC
-recovered pasa_asmbl_41738.p1, internal, 4003, 4140
-recovered pasa_asmbl_41738.p1, internal, 4363, 4510
Valid prediction for pasa_asmbl_41713.p1
Valid prediction for GeneMark_model.17397_t
Couldn't classify 289391, 289525
Sorry, prediction pasa_asmbl_41721.p1 fails validation.
(AGC)	 TC	289391-289525	GT	AGG
(GTA)	 AG	290448-290595	GT	CGG
(CTG)	 AG	290856-290953	AT	AGA
-recovered pasa_asmbl_41721.p1, terminal, 290856, 290953
-recovered pasa_asmbl_41721.p1, internal, 290448, 290595
Valid prediction for snap_scaffold_4-snap.2759-T1
Valid prediction for GeneMark_model.17395_t
Valid prediction for Augustus_model.g7028.t1
Couldn't classify 5361, 5468
Sorry, prediction pasa_asmbl_42396.p1 fails validation.
(CAC)	 AG	5361-5468	GT	AGG
(AGG)	 AG	5597-5725	GT	AGG
(GAT)	 AG	6001-6234	GT	AGG
(CTC)	 AG	6426-6700	GT	AAG
(GAC)	 AG	7016-7338	GT	TGG
(TGA)	 AG	7430-7555	GT	AGG
(TTG)	 AG	7657-7781	GC	GAG
-recovered pasa_asmbl_42396.p1, terminal, 7657, 7781
-recovered pasa_asmbl_42396.p1, internal, 5361, 5468
-recovered pasa_asmbl_42396.p1, internal, 5597, 5725
-recovered pasa_asmbl_42396.p1, internal, 6001, 6234
-recovered pasa_asmbl_42396.p1, internal, 6426, 6700
-recovered pasa_asmbl_42396.p1, internal, 7016, 7338
-recovered pasa_asmbl_42396.p1, internal, 7430, 7555
-recovered pasa_asmbl_42396.p1, internal, 7657, 7781
Valid prediction for snap_scaffold_4-snap.2753-T1
Valid prediction for GeneMark_model.17398_t
Valid prediction for GlimmerHMM_glimmerT_10705-T1
Valid prediction for GeneMark_model.17417_t
Valid prediction for CodingQuarry_transcript_49078-T1
Valid prediction for GlimmerHMM_glimmerT_10695-T1
Valid prediction for snap_scaffold_4-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_10699-T1
Valid prediction for GeneMark_model.17414_t
Valid prediction for GeneMark_model.17412_t
Valid prediction for GeneMark_model.17402_t
Valid prediction for GeneMark_model.17422_t
Valid prediction for HiQ_model.g7034.t1
Valid prediction for Augustus_model.g7047.t1
Valid prediction for snap_scaffold_4-snap.2765-T1
Valid prediction for GlimmerHMM_glimmerT_10691-T1
Couldn't classify 280507, 280595
Sorry, prediction pasa_asmbl_41723.p2 fails validation.
(AGG)	 CA	280507-280595	GT	AGG
(GGC)	 AG	282422-282604	GT	AGG
(GAT)	 AG	283409-283463	GG	AAG
-recovered pasa_asmbl_41723.p2, terminal, 283409, 283463
-recovered pasa_asmbl_41723.p2, internal, 282422, 282604
Valid prediction for GlimmerHMM_glimmerT_10700-T1
Valid prediction for CodingQuarry_transcript_49077-T1
Valid prediction for CodingQuarry_transcript_49079-T1
Valid prediction for Augustus_model.g7041.t1
Valid prediction for HiQ_model.g7029.t1
Valid prediction for snap_scaffold_4-snap.2754-T1

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

-building trellis in range 1 - 317310
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support