-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_16479777-16643551

-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_12-snap.3214-T1
Valid prediction for snap_scaffold_12-snap.3218-T1
Valid prediction for Augustus_model.g21044.t1
Valid prediction for Augustus_model.g21039.t1
Valid prediction for GlimmerHMM_glimmerT_31508-T1
Valid prediction for snap_scaffold_12-snap.3209-T1
Valid prediction for GlimmerHMM_glimmerT_31503-T1
Valid prediction for Augustus_model.g21040.t1
Valid prediction for snap_scaffold_12-snap.3194-T1
Valid prediction for Augustus_model.g21046.t1
Valid prediction for GeneMark_model.54298_t
Valid prediction for GlimmerHMM_glimmerT_31490-T1
Valid prediction for Augustus_model.g21034.t1
Valid prediction for GeneMark_model.54311_t
Valid prediction for Augustus_model.g21028.t1
Valid prediction for GlimmerHMM_glimmerT_31504-T1
Valid prediction for Augustus_model.g21042.t1
Valid prediction for GlimmerHMM_glimmerT_31515-T1
Valid prediction for GlimmerHMM_glimmerT_31500-T1
Valid prediction for Augustus_model.g21038.t1
Couldn't classify 129937, 130323
Sorry, prediction pasa_asmbl_9155.p1 fails validation.
(TCA)	 CG	129937-130323	GT	GGG
Valid prediction for GlimmerHMM_glimmerT_31512-T1
Valid prediction for GlimmerHMM_glimmerT_31502-T1
Valid prediction for GlimmerHMM_glimmerT_31511-T1
Valid prediction for snap_scaffold_12-snap.3225-T1
Valid prediction for snap_scaffold_12-snap.3213-T1
Valid prediction for GeneMark_model.54312_t
Valid prediction for GlimmerHMM_glimmerT_31505-T1
Valid prediction for GeneMark_model.54302_t
Valid prediction for snap_scaffold_12-snap.3224-T1
Valid prediction for snap_scaffold_12-snap.3215-T1
Couldn't classify 143120, 143449
Sorry, prediction pasa_asmbl_9213.p2 fails validation.
(GGG)	 GG	143120-143449	AG	AGA
Valid prediction for GeneMark_model.54307_t
Valid prediction for Augustus_model.g21043.t1
Valid prediction for GlimmerHMM_glimmerT_31497-T1
Valid prediction for GeneMark_model.54315_t
Valid prediction for GeneMark_model.54310_t
Valid prediction for Augustus_model.g21024.t1
Valid prediction for GeneMark_model.54297_t
Valid prediction for GlimmerHMM_glimmerT_31510-T1
Valid prediction for snap_scaffold_12-snap.3220-T1
Valid prediction for Augustus_model.g21033.t1
Valid prediction for snap_scaffold_12-snap.3219-T1
Valid prediction for GeneMark_model.54299_t
Valid prediction for Augustus_model.g21041.t1
Valid prediction for GeneMark_model.54314_t
Valid prediction for snap_scaffold_12-snap.3221-T1
Couldn't classify 108984, 110309
Sorry, prediction pasa_asmbl_8272.p1 fails validation.
(ATG)	 TG	108984-110309	GG	GTG

-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.g21032.t1
Valid prediction for snap_scaffold_12-snap.3202-T1
Valid prediction for CodingQuarry_transcript_10500-T1
Valid prediction for Augustus_model.g21045.t1
Valid prediction for GlimmerHMM_glimmerT_31506-T1
Valid prediction for Augustus_model.g21030.t1
Valid prediction for GlimmerHMM_glimmerT_31514-T1
Couldn't classify 20621, 21034
Sorry, prediction pasa_asmbl_9167.p1 fails validation.
(GAC)	 GT	20621-21034	CC	TTC
Valid prediction for GeneMark_model.54317_t
Valid prediction for snap_scaffold_12-snap.3197-T1
Valid prediction for GlimmerHMM_glimmerT_31487-T1
Valid prediction for GlimmerHMM_glimmerT_31498-T1
Valid prediction for Augustus_model.g21026.t1
Valid prediction for snap_scaffold_12-snap.3204-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.3206-T1
Valid prediction for GeneMark_model.54304_t
Valid prediction for GlimmerHMM_glimmerT_31513-T1
Valid prediction for snap_scaffold_12-snap.3201-T1
Valid prediction for Augustus_model.g21036.t1
Couldn't classify 89500, 89823
Sorry, prediction pasa_asmbl_8270.p1 fails validation.
(ATG)	 TC	89500-89823	GA	AGG
Valid prediction for snap_scaffold_12-snap.3199-T1
Valid prediction for HiQ_model.g21031.t1
Valid prediction for GlimmerHMM_glimmerT_31507-T1
Valid prediction for GeneMark_model.54316_t
Valid prediction for GlimmerHMM_glimmerT_31493-T1
Valid prediction for snap_scaffold_12-snap.3208-T1
Couldn't classify 149533, 150096
Sorry, prediction pasa_asmbl_8265.p1 fails validation.
(TTT)	 AT	149533-150096	AG	AGA
Valid prediction for GeneMark_model.54318_t
Valid prediction for GlimmerHMM_glimmerT_31489-T1
Valid prediction for GeneMark_model.54303_t
Valid prediction for GlimmerHMM_glimmerT_31491-T1
Valid prediction for Augustus_model.g21029.t1
Valid prediction for GlimmerHMM_glimmerT_31492-T1
Valid prediction for snap_scaffold_12-snap.3223-T1
Valid prediction for GeneMark_model.54300_t
Valid prediction for snap_scaffold_12-snap.3198-T1
Valid prediction for snap_scaffold_12-snap.3203-T1
Couldn't classify 23215, 23565
Sorry, prediction pasa_asmbl_9162.p1 fails validation.
(CGC)	 GG	23215-23565	TA	AGT
Valid prediction for Augustus_model.g21037.t1
Valid prediction for snap_scaffold_12-snap.3196-T1
Valid prediction for GlimmerHMM_glimmerT_31509-T1
Valid prediction for GlimmerHMM_glimmerT_31499-T1
Valid prediction for Augustus_model.g21027.t1
Valid prediction for snap_scaffold_12-snap.3210-T1
Valid prediction for snap_scaffold_12-snap.3207-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.54305_t
Valid prediction for GeneMark_model.54313_t
Valid prediction for GlimmerHMM_glimmerT_31496-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.3222-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31488-T1
Valid prediction for snap_scaffold_12-snap.3205-T1
Valid prediction for CodingQuarry_transcript_10501-T1
Valid prediction for snap_scaffold_12-snap.3195-T1
Valid prediction for GeneMark_model.54306_t
Valid prediction for snap_scaffold_12-snap.3200-T1
Valid prediction for Augustus_model.g21035.t1
Valid prediction for Augustus_model.g21025.t1
Valid prediction for pasa_asmbl_8269.p1
Valid prediction for GlimmerHMM_glimmerT_31501-T1
Valid prediction for CodingQuarry_transcript_10499-T1
Valid prediction for GeneMark_model.54309_t
Valid prediction for snap_scaffold_12-snap.3216-T1
Valid prediction for snap_scaffold_12-snap.3212-T1
Valid prediction for snap_scaffold_12-snap.3217-T1
Valid prediction for snap_scaffold_12-snap.3211-T1
Valid prediction for GlimmerHMM_glimmerT_31495-T1
Valid prediction for pasa_asmbl_8267.p1
Valid prediction for GeneMark_model.54301_t
Valid prediction for GlimmerHMM_glimmerT_31494-T1

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

-building trellis in range 1 - 163775
-exon list size: 274


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.3    
3.6    
4.0    
4.3    
4.7    
5.1    
5.4    
5.8    
6.2    
6.5    
6.9    
7.2    
7.6    
8.0    
8.3    
8.7    
9.1    
9.4    
9.8    
10.1    
10.5    
10.9    
11.2    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.8    
14.1    
14.5    
14.9    
15.2    
15.6    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.1    
18.5    
18.8    
19.2    
19.6    
19.9    
20.3    
20.7    
21.0    
21.4    
21.7    
22.1    
22.5    
22.8    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.2    
27.5    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.1    
30.4    
30.8    
31.2    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.1    
35.5    
35.9    
36.2    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.8    
39.1    
39.5    
39.9    
40.2    
40.6    
40.9    
41.3    
41.7    
42.0    
42.4    
42.8    
43.1    
43.5    
43.8    
44.2    
44.6    
44.9    
45.3    
45.7    
46.0    
46.4    
46.7    
47.1    
47.5    
47.8    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.2    
52.5    
52.9    
53.3    
53.6    
54.0    
54.3    
54.7    
55.1    
55.4    
55.8    
56.2    
56.5    
56.9    
57.2    
57.6    
58.0    
58.3    
58.7    
59.1    
59.4    
59.8    
60.1    
60.5    
60.9    
61.2    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.8    
64.1    
64.5    
64.9    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.8    
69.2    
69.6    
69.9    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.5    
72.8    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.2    
77.5    
77.9    
78.3    
78.6    
79.0    
79.3    
79.7    
80.1    
80.4    
80.8    
81.2    
81.5    
81.9    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.4    
84.8    
85.1    
85.5    
85.9    
86.2    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.8    
89.1    
89.5    
89.9    
90.2    
90.6    
90.9    
91.3    
91.7    
92.0    
92.4    
92.8    
93.1    
93.5    
93.8    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.7    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 26 predictions from path traversal
GOT 5prime partial gene.

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