-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_1055529-1284173

-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.g34703.t1
Valid prediction for Augustus_model.g34679.t1
Valid prediction for snap_scaffold_23-snap.179-T1
Valid prediction for snap_scaffold_23-snap.188-T1
Valid prediction for GeneMark_model.89789_t
Valid prediction for GlimmerHMM_glimmerT_51643-T1
Valid prediction for GeneMark_model.89807_t
Valid prediction for snap_scaffold_23-snap.186-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51645-T1
Valid prediction for GeneMark_model.89799_t
Valid prediction for GlimmerHMM_glimmerT_51641-T1
Valid prediction for snap_scaffold_23-snap.173-T1
Valid prediction for snap_scaffold_23-snap.167-T1
Couldn't classify 65933, 66080
Sorry, prediction pasa_asmbl_30612.p1 fails validation.
(ATG)	 AG	63736-63910	GT	AGG
(TCA)	 AG	64459-64618	GT	AGG
(ATT)	 AG	65933-66080	GT	AGG
-recovered pasa_asmbl_30612.p1, initial, 63736, 63910
add_exon() Sorry, pasa_asmbl_30612.p1 64459-64618-terminal-3 is invalid.
-recovered pasa_asmbl_30612.p1, terminal, 64459, 64618
-recovered pasa_asmbl_30612.p1, internal, 63736, 63910
-recovered pasa_asmbl_30612.p1, internal, 64459, 64618
-recovered pasa_asmbl_30612.p1, internal, 65933, 66080
Valid prediction for snap_scaffold_23-snap.166-T1
Valid prediction for snap_scaffold_23-snap.170-T1
Valid prediction for snap_scaffold_23-snap.184-T1
Valid prediction for snap_scaffold_23-snap.171-T1
Valid prediction for GeneMark_model.89791_t
Valid prediction for GeneMark_model.89809_t
Valid prediction for HiQ_model.g34685.t1
Valid prediction for GlimmerHMM_glimmerT_51660-T1
Valid prediction for Augustus_model.g34699.t1
Valid prediction for GlimmerHMM_glimmerT_51655-T1
Valid prediction for snap_scaffold_23-snap.180-T1
Valid prediction for snap_scaffold_23-snap.164-T1
Valid prediction for snap_scaffold_23-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_51638-T1
Valid prediction for GlimmerHMM_glimmerT_51653-T1
Couldn't classify 144564, 144655
Sorry, prediction pasa_asmbl_30621.p1 fails validation.
(ATG)	 CG	132716-132748	GT	AGG
(ACT)	 AG	133312-133410	GT	TGG
(TCT)	 AG	133623-133716	GT	TGG
(ATG)	 AG	133914-134030	GT	TGG
(AGC)	 AG	134152-134303	GT	AGG
(GGG)	 AG	134505-134680	GT	TGG
(GGC)	 AG	135208-135364	GT	CGG
(TGC)	 AG	135984-136206	GT	TGG
(ATA)	 AG	137997-138112	GT	GGG
(ACT)	 AG	138725-138897	GT	CGG
(GAA)	 AG	139077-139123	GT	AGG
(CTC)	 AG	139663-140019	GT	AGG
(CTA)	 AG	141945-142175	GT	GGG
(GTC)	 AG	143482-143697	GT	AGG
(ATG)	 AG	144564-144655	GT	GGG
-recovered pasa_asmbl_30621.p1, initial, 132716, 132748
add_exon() Sorry, pasa_asmbl_30621.p1 133914-134030-initial-1 is invalid.
-recovered pasa_asmbl_30621.p1, initial, 133914, 134030
add_exon() Sorry, pasa_asmbl_30621.p1 144564-144655-initial-1 is invalid.
-recovered pasa_asmbl_30621.p1, initial, 144564, 144655
-recovered pasa_asmbl_30621.p1, internal, 133312, 133410
-recovered pasa_asmbl_30621.p1, internal, 133623, 133716
-recovered pasa_asmbl_30621.p1, internal, 133914, 134030
-recovered pasa_asmbl_30621.p1, internal, 134152, 134303
-recovered pasa_asmbl_30621.p1, internal, 134505, 134680
-recovered pasa_asmbl_30621.p1, internal, 135208, 135364
-recovered pasa_asmbl_30621.p1, internal, 135984, 136206
-recovered pasa_asmbl_30621.p1, internal, 137997, 138112
-recovered pasa_asmbl_30621.p1, internal, 138725, 138897
-recovered pasa_asmbl_30621.p1, internal, 139077, 139123
-recovered pasa_asmbl_30621.p1, internal, 139663, 140019
-recovered pasa_asmbl_30621.p1, internal, 141945, 142175
-recovered pasa_asmbl_30621.p1, internal, 143482, 143697
-recovered pasa_asmbl_30621.p1, internal, 144564, 144655
Valid prediction for GeneMark_model.89797_t
Valid prediction for Augustus_model.g34684.t1
Valid prediction for CodingQuarry_transcript_35477-T1
Valid prediction for Augustus_model.g34700.t1
Valid prediction for Augustus_model.g34683.t1
Valid prediction for GlimmerHMM_glimmerT_51647-T1
Valid prediction for snap_scaffold_23-snap.168-T1
Valid prediction for Augustus_model.g34677.t1
Valid prediction for GeneMark_model.89804_t
Valid prediction for snap_scaffold_23-snap.174-T1
Valid prediction for GeneMark_model.89796_t
Valid prediction for Augustus_model.g34702.t1
Valid prediction for snap_scaffold_23-snap.163-T1
Valid prediction for snap_scaffold_23-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_51639-T1
Valid prediction for Augustus_model.g34686.t1
Valid prediction for snap_scaffold_23-snap.162-T1
Valid prediction for GeneMark_model.89794_t
Valid prediction for Augustus_model.g34681.t1
Couldn't classify 69173, 69305
Sorry, prediction pasa_asmbl_30613.p1 fails validation.
(AAA)	 AG	69173-69305	GT	ATG
(TAC)	 AG	69535-69733	GT	TTG
(GAA)	 AG	69991-70121	GT	CGG
(GAA)	 AG	71458-71675	GT	AGG
(GAA)	 AG	73001-73093	AC	GAA
-recovered pasa_asmbl_30613.p1, terminal, 73001, 73093
-recovered pasa_asmbl_30613.p1, internal, 69173, 69305
-recovered pasa_asmbl_30613.p1, internal, 69535, 69733
-recovered pasa_asmbl_30613.p1, internal, 69991, 70121
-recovered pasa_asmbl_30613.p1, internal, 71458, 71675
Valid prediction for GeneMark_model.89785_t
Valid prediction for GlimmerHMM_glimmerT_51632-T1
Valid prediction for snap_scaffold_23-snap.172-T1
Valid prediction for GeneMark_model.89802_t
Valid prediction for GeneMark_model.89798_t
Valid prediction for GeneMark_model.89786_t
Valid prediction for snap_scaffold_23-snap.159-T1
Valid prediction for snap_scaffold_23-snap.165-T1
Valid prediction for GeneMark_model.89806_t
Valid prediction for Augustus_model.g34674.t1
Valid prediction for snap_scaffold_23-snap.189-T1
Valid prediction for GeneMark_model.89792_t
Valid prediction for Augustus_model.g34701.t1
Valid prediction for GlimmerHMM_glimmerT_51657-T1
Valid prediction for Augustus_model.g34689.t1
Valid prediction for GlimmerHMM_glimmerT_51661-T1
Valid prediction for snap_scaffold_23-snap.155-T1
Valid prediction for Augustus_model.g34697.t1
Valid prediction for snap_scaffold_23-snap.160-T1
Valid prediction for snap_scaffold_23-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_51637-T1
Valid prediction for Augustus_model.g34693.t1
Valid prediction for GlimmerHMM_glimmerT_51663-T1
Valid prediction for GlimmerHMM_glimmerT_51646-T1
Valid prediction for snap_scaffold_23-snap.187-T1
Valid prediction for snap_scaffold_23-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_51648-T1
Valid prediction for GlimmerHMM_glimmerT_51662-T1
Valid prediction for Augustus_model.g34691.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 HiQ_model.g34692.t1
Valid prediction for snap_scaffold_23-snap.161-T1
Valid prediction for GeneMark_model.89805_t
Valid prediction for GlimmerHMM_glimmerT_51656-T1
Valid prediction for snap_scaffold_23-snap.182-T1
Valid prediction for CodingQuarry_transcript_35478-T1
Valid prediction for GeneMark_model.89803_t
Valid prediction for GeneMark_model.89801_t
Valid prediction for HiQ_model.g34680.t1
Valid prediction for GlimmerHMM_glimmerT_51636-T1
Valid prediction for Augustus_model.g34682.t1
Valid prediction for GeneMark_model.89808_t
Valid prediction for GlimmerHMM_glimmerT_51658-T1
Valid prediction for snap_scaffold_23-snap.158-T1
Valid prediction for snap_scaffold_23-snap.177-T1
Valid prediction for snap_scaffold_23-snap.175-T1
Valid prediction for GlimmerHMM_glimmerT_51631-T1
Valid prediction for GlimmerHMM_glimmerT_51644-T1
Valid prediction for GlimmerHMM_glimmerT_51659-T1
Valid prediction for Augustus_model.g34694.t1
Valid prediction for snap_scaffold_23-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_51635-T1
Valid prediction for GeneMark_model.89784_t
Valid prediction for GlimmerHMM_glimmerT_51651-T1
Valid prediction for snap_scaffold_23-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_51664-T1
Valid prediction for snap_scaffold_23-snap.181-T1
Valid prediction for snap_scaffold_23-snap.178-T1
Valid prediction for snap_scaffold_23-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_51642-T1
Valid prediction for GeneMark_model.89793_t
Valid prediction for GlimmerHMM_glimmerT_51640-T1
Valid prediction for GeneMark_model.89788_t
Valid prediction for Augustus_model.g34704.t1
Valid prediction for Augustus_model.g34687.t1
Valid prediction for Augustus_model.g34688.t1
Valid prediction for GeneMark_model.89810_t
Valid prediction for GeneMark_model.89790_t
Valid prediction for HiQ_model.g34678.t1
Valid prediction for GlimmerHMM_glimmerT_51650-T1
Valid prediction for snap_scaffold_23-snap.193-T1
Valid prediction for Augustus_model.g34690.t1
Valid prediction for GlimmerHMM_glimmerT_51649-T1
Valid prediction for snap_scaffold_23-snap.192-T1
Valid prediction for Augustus_model.g34698.t1
Valid prediction for GlimmerHMM_glimmerT_51654-T1
Valid prediction for GlimmerHMM_glimmerT_51652-T1
Valid prediction for Augustus_model.g34695.t1
Valid prediction for GlimmerHMM_glimmerT_51634-T1
Valid prediction for GeneMark_model.89787_t
Valid prediction for GlimmerHMM_glimmerT_51633-T1
Valid prediction for Augustus_model.g34675.t1
Valid prediction for Augustus_model.g34673.t1
Couldn't classify 147640, 147786
Sorry, prediction pasa_asmbl_31344.p1 fails validation.
(ATG)	 TC	138374-138471	GT	AGG
(GCC)	 AG	139319-139448	GT	TGG
(AGT)	 AG	140077-140198	GT	ATG
(TTT)	 AG	142570-142633	GT	AGG
(GCA)	 AG	142739-142832	GT	ACG
(CGT)	 AG	143346-143516	GT	CAG
(ACT)	 AG	143611-143670	GT	AGG
(TGA)	 AG	143866-144069	GT	AGG
(GAA)	 AG	144812-144919	GT	AGG
(AAT)	 AG	145096-145202	GT	ACG
(GTG)	 AG	147175-147288	GT	CGG
(AAC)	 AG	147640-147786	AG	CTA
-recovered pasa_asmbl_31344.p1, initial, 138374, 138471
add_exon() Sorry, pasa_asmbl_31344.p1 143866-144069-terminal-1 is invalid.
-recovered pasa_asmbl_31344.p1, terminal, 143866, 144069
-recovered pasa_asmbl_31344.p1, internal, 139319, 139448
-recovered pasa_asmbl_31344.p1, internal, 140077, 140198
-recovered pasa_asmbl_31344.p1, internal, 142570, 142633
-recovered pasa_asmbl_31344.p1, internal, 142739, 142832
-recovered pasa_asmbl_31344.p1, internal, 143346, 143516
-recovered pasa_asmbl_31344.p1, internal, 143611, 143670
-recovered pasa_asmbl_31344.p1, internal, 143866, 144069
-recovered pasa_asmbl_31344.p1, internal, 144812, 144919
-recovered pasa_asmbl_31344.p1, internal, 145096, 145202
-recovered pasa_asmbl_31344.p1, internal, 147175, 147288
Valid prediction for GeneMark_model.89795_t
Valid prediction for snap_scaffold_23-snap.183-T1
Valid prediction for Augustus_model.g34696.t1
Valid prediction for snap_scaffold_23-snap.157-T1
Valid prediction for Augustus_model.g34676.t1

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

-building trellis in range 1 - 228645
-exon list size: 401


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 205669 - 228645
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 207623 - 228645
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 207623 - 220035
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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