-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_11043176-11228216

-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_20-snap.2359-T1
Valid prediction for snap_scaffold_20-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_47956-T1
Valid prediction for Augustus_model.g32020.t1
Valid prediction for GeneMark_model.83571_t
Valid prediction for HiQ_model.g32032.t1
Valid prediction for CodingQuarry_transcript_30602-T1
Valid prediction for GlimmerHMM_glimmerT_47953-T1
Valid prediction for snap_scaffold_20-snap.2361-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g32025.t1
Valid prediction for Augustus_model.g32021.t1
Valid prediction for GeneMark_model.83578_t
Valid prediction for Augustus_model.g32030.t1
Valid prediction for GeneMark_model.83576_t
Valid prediction for GeneMark_model.83574_t
Valid prediction for pasa_asmbl_26165.p1
Valid prediction for GeneMark_model.83573_t
Valid prediction for pasa_asmbl_26164.p1
Valid prediction for GeneMark_model.83586_t
Valid prediction for GeneMark_model.83569_t
Valid prediction for GeneMark_model.83582_t
Valid prediction for Augustus_model.g32036.t1
Valid prediction for Augustus_model.g32027.t1
Valid prediction for CodingQuarry_transcript_30598-T1
Valid prediction for GlimmerHMM_glimmerT_47959-T1
Valid prediction for GeneMark_model.83585_t
Valid prediction for GlimmerHMM_glimmerT_47981-T1
Valid prediction for GlimmerHMM_glimmerT_47970-T1
Valid prediction for Augustus_model.g32026.t1
Valid prediction for snap_scaffold_20-snap.2373-T1
Valid prediction for snap_scaffold_20-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_47979-T1
Valid prediction for HiQ_model.g32028.t1
Valid prediction for Augustus_model.g32019.t1
Valid prediction for snap_scaffold_20-snap.2367-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47972-T1
Valid prediction for GlimmerHMM_glimmerT_47961-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_26171.p1
Valid prediction for snap_scaffold_20-snap.2360-T1
Valid prediction for Augustus_model.g32024.t1
Valid prediction for GlimmerHMM_glimmerT_47968-T1
Valid prediction for GlimmerHMM_glimmerT_47955-T1
Valid prediction for GlimmerHMM_glimmerT_47974-T1
Valid prediction for Augustus_model.g32018.t1
Valid prediction for snap_scaffold_20-snap.2362-T1
Valid prediction for Augustus_model.g32029.t1
Valid prediction for GlimmerHMM_glimmerT_47965-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_47964-T1
Valid prediction for GlimmerHMM_glimmerT_47957-T1
Valid prediction for snap_scaffold_20-snap.2366-T1
Valid prediction for HiQ_model.g32031.t1
Valid prediction for CodingQuarry_transcript_30599-T1
Valid prediction for snap_scaffold_20-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_47954-T1
Valid prediction for snap_scaffold_20-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_47973-T1
Valid prediction for GlimmerHMM_glimmerT_47977-T1
Couldn't classify 44060, 44147
Couldn't classify 45741, 45781
Sorry, prediction pasa_asmbl_27074.p1 fails validation.
(CGG)	 CT	44060-44147	GT	TGG
(CAA)	 AG	44910-44970	GT	AAG
(GTG)	 AG	45410-45540	GT	AGG
(ATC)	 AG	45741-45781	GG	GGG
-recovered pasa_asmbl_27074.p1, internal, 44910, 44970
-recovered pasa_asmbl_27074.p1, internal, 45410, 45540
Valid prediction for snap_scaffold_20-snap.2380-T1
Valid prediction for snap_scaffold_20-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_47984-T1
Valid prediction for snap_scaffold_20-snap.2387-T1
Valid prediction for snap_scaffold_20-snap.2363-T1
Valid prediction for Augustus_model.g32035.t1
Valid prediction for snap_scaffold_20-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_47952-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.83590_t
Valid prediction for snap_scaffold_20-snap.2383-T1
Valid prediction for CodingQuarry_transcript_30600-T1
Valid prediction for GeneMark_model.83583_t
Valid prediction for GlimmerHMM_glimmerT_47980-T1
Valid prediction for Augustus_model.g32037.t1
Valid prediction for pasa_asmbl_27055.p1
Valid prediction for GlimmerHMM_glimmerT_47976-T1
Valid prediction for GlimmerHMM_glimmerT_47966-T1
Valid prediction for GeneMark_model.83580_t
Valid prediction for snap_scaffold_20-snap.2358-T1
Valid prediction for GeneMark_model.83589_t
Valid prediction for snap_scaffold_20-snap.2375-T1
Valid prediction for Augustus_model.g32039.t1
Valid prediction for GeneMark_model.83572_t
Valid prediction for GeneMark_model.83570_t
Valid prediction for Augustus_model.g32017.t1
Couldn't classify 52287, 52374
Couldn't classify 56434, 56461
Sorry, prediction pasa_asmbl_27070.p1 fails validation.
(ACA)	 CA	52287-52374	GT	AGG
(TGA)	 AG	53172-53336	GT	AAG
(ATA)	 AG	54564-54677	GT	CAG
(ACA)	 AG	55006-55119	GT	AAG
(GGG)	 AG	55414-55527	GT	CGG
(GCA)	 AG	55792-55908	GT	GAG
(ATT)	 AG	56055-56082	GT	TGG
(CTA)	 AG	56434-56461	GA	GGG
-recovered pasa_asmbl_27070.p1, internal, 53172, 53336
-recovered pasa_asmbl_27070.p1, internal, 54564, 54677
-recovered pasa_asmbl_27070.p1, internal, 55006, 55119
-recovered pasa_asmbl_27070.p1, internal, 55414, 55527
-recovered pasa_asmbl_27070.p1, internal, 55792, 55908
-recovered pasa_asmbl_27070.p1, internal, 56055, 56082
Valid prediction for GlimmerHMM_glimmerT_47983-T1
Couldn't classify 97757, 98059
Sorry, prediction pasa_asmbl_27063.p1 fails validation.
(GTT)	 AG	97757-98059	GT	AGG
(AGG)	 AG	98294-98523	GT	GAG
(GCA)	 AG	98768-99099	GT	TGG
(TGT)	 AG	99281-99421	GT	AGG
(GCA)	 AG	99598-99849	GT	TGG
(GTG)	 AG	100594-100794	GT	CCG
(ATA)	 AG	101180-101413	GT	CAG
(GTG)	 AG	102841-102978	GT	CGG
(ACA)	 AG	104661-104789	GT	TGG
(AAG)	 AG	105049-105192	GT	AGG
(ATG)	 AG	105618-105746	GT	AGG
(AGC)	 AG	107770-108003	GT	GTG
(GTA)	 AG	108211-108383	GT	CAG
(CAC)	 AG	109814-109940	GT	ACG
(AGC)	 AG	110126-110297	GT	GGG
(ACG)	 AG	110376-110533	GT	TGG
(GTA)	 AG	110817-110940	GT	AGG
(GGA)	 AG	111257-111369	GT	AGG
(GGT)	 AG	112365-112483	GA	GAG
add_exon() Sorry, pasa_asmbl_27063.p1 105618-105746-initial-1 is invalid.
-recovered pasa_asmbl_27063.p1, initial, 105618, 105746
-recovered pasa_asmbl_27063.p1, terminal, 112365, 112483
-recovered pasa_asmbl_27063.p1, internal, 97757, 98059
-recovered pasa_asmbl_27063.p1, internal, 98294, 98523
-recovered pasa_asmbl_27063.p1, internal, 98768, 99099
-recovered pasa_asmbl_27063.p1, internal, 99281, 99421
-recovered pasa_asmbl_27063.p1, internal, 99598, 99849
-recovered pasa_asmbl_27063.p1, internal, 100594, 100794
-recovered pasa_asmbl_27063.p1, internal, 101180, 101413
-recovered pasa_asmbl_27063.p1, internal, 102841, 102978
-recovered pasa_asmbl_27063.p1, internal, 104661, 104789
-recovered pasa_asmbl_27063.p1, internal, 105049, 105192
-recovered pasa_asmbl_27063.p1, internal, 105618, 105746
-recovered pasa_asmbl_27063.p1, internal, 107770, 108003
-recovered pasa_asmbl_27063.p1, internal, 108211, 108383
-recovered pasa_asmbl_27063.p1, internal, 109814, 109940
-recovered pasa_asmbl_27063.p1, internal, 110126, 110297
-recovered pasa_asmbl_27063.p1, internal, 110376, 110533
-recovered pasa_asmbl_27063.p1, internal, 110817, 110940
-recovered pasa_asmbl_27063.p1, internal, 111257, 111369
Valid prediction for snap_scaffold_20-snap.2379-T1
Valid prediction for snap_scaffold_20-snap.2365-T1
Valid prediction for HiQ_model.g32023.t1
Valid prediction for snap_scaffold_20-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_47960-T1
Couldn't classify 48864, 48978
Couldn't classify 51369, 51386
Sorry, prediction pasa_asmbl_27072.p1 fails validation.
(GCG)	 TA	48864-48978	GT	CAG
(ATG)	 AG	49172-49285	GT	CGG
(ATG)	 AG	50112-50225	GT	AAG
(ATG)	 AG	50928-50974	GT	AGG
(GAC)	 AG	51369-51386	AA	ACA
add_exon() Sorry, pasa_asmbl_27072.p1 49172-49285-initial-1 is invalid.
-recovered pasa_asmbl_27072.p1, initial, 49172, 49285
add_exon() Sorry, pasa_asmbl_27072.p1 50112-50225-initial-1 is invalid.
-recovered pasa_asmbl_27072.p1, initial, 50112, 50225
-recovered pasa_asmbl_27072.p1, initial, 50928, 50974
-recovered pasa_asmbl_27072.p1, internal, 49172, 49285
-recovered pasa_asmbl_27072.p1, internal, 50112, 50225
-recovered pasa_asmbl_27072.p1, internal, 50928, 50974
Valid prediction for GeneMark_model.83587_t
Valid prediction for GlimmerHMM_glimmerT_47963-T1
Valid prediction for GlimmerHMM_glimmerT_47969-T1
Valid prediction for GeneMark_model.83584_t
Valid prediction for GlimmerHMM_glimmerT_47971-T1
Valid prediction for pasa_asmbl_27062.p1
Valid prediction for snap_scaffold_20-snap.2374-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g32038.t1
Couldn't classify 63283, 63381
Sorry, prediction pasa_asmbl_27069.p1 fails validation.
(TGG)	 GC	63283-63381	GT	AAG
(GGC)	 AG	63624-63755	GT	TCG
(TCA)	 AG	63931-64081	GT	CGG
(ATT)	 AG	64311-64828	CA	AGC
-recovered pasa_asmbl_27069.p1, terminal, 64311, 64828
-recovered pasa_asmbl_27069.p1, internal, 63624, 63755
-recovered pasa_asmbl_27069.p1, internal, 63931, 64081
Valid prediction for snap_scaffold_20-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_47962-T1
Valid prediction for snap_scaffold_20-snap.2384-T1
Valid prediction for GlimmerHMM_glimmerT_47967-T1
Valid prediction for HiQ_model.g32022.t1
Valid prediction for Augustus_model.g32034.t1
Valid prediction for GeneMark_model.83581_t
Valid prediction for GeneMark_model.83579_t
Valid prediction for GeneMark_model.83588_t
Valid prediction for snap_scaffold_20-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_47975-T1
Valid prediction for GlimmerHMM_glimmerT_47958-T1
Valid prediction for GeneMark_model.83577_t
Valid prediction for snap_scaffold_20-snap.2369-T1
Valid prediction for CodingQuarry_transcript_30601-T1
Valid prediction for GlimmerHMM_glimmerT_47982-T1
Valid prediction for Augustus_model.g32033.t1
Valid prediction for GeneMark_model.83568_t
Valid prediction for GlimmerHMM_glimmerT_47978-T1
Valid prediction for snap_scaffold_20-snap.2381-T1
Valid prediction for snap_scaffold_20-snap.2370-T1
Valid prediction for snap_scaffold_20-snap.2378-T1
Valid prediction for snap_scaffold_20-snap.2376-T1

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

-building trellis in range 1 - 185041
-exon list size: 442


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.0    
2.3    
2.5    
2.7    
2.9    
3.2    
3.4    
3.6    
3.8    
4.1    
4.3    
4.5    
4.7    
5.0    
5.2    
5.4    
5.6    
5.9    
6.1    
6.3    
6.5    
6.8    
7.0    
7.2    
7.4    
7.7    
7.9    
8.1    
8.3    
8.6    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.2    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.2    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support