-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_11932752-12278201

-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 GeneMark_model.35821_t
Valid prediction for HiQ_model.g14085.t1
Valid prediction for GlimmerHMM_glimmerT_21002-T1
Couldn't classify 26902, 26917
Sorry, prediction pasa_asmbl_52292.p1 fails validation.
(AGA)	 CC	26902-26917	GT	TCG
(CAT)	 AG	27051-27161	GT	AGG
(AGT)	 AG	27365-27492	GT	AGG
(GTT)	 AG	27642-27754	GT	AGG
(GTA)	 AG	27862-27968	GT	GGG
(CTG)	 AG	28174-28305	GT	GGG
(GTC)	 AG	28574-28650	AG	GAA
-recovered pasa_asmbl_52292.p1, terminal, 28574, 28650
-recovered pasa_asmbl_52292.p1, internal, 27051, 27161
-recovered pasa_asmbl_52292.p1, internal, 27365, 27492
-recovered pasa_asmbl_52292.p1, internal, 27642, 27754
-recovered pasa_asmbl_52292.p1, internal, 27862, 27968
-recovered pasa_asmbl_52292.p1, internal, 28174, 28305
Valid prediction for snap_scaffold_8-snap.2229-T1
Valid prediction for snap_scaffold_8-snap.2208-T1
Valid prediction for snap_scaffold_8-snap.2237-T1
Valid prediction for HiQ_model.g14079.t1
Valid prediction for CodingQuarry_transcript_59692-T1
Couldn't classify 26543, 26656
Sorry, prediction pasa_asmbl_52291.p1 fails validation.
(ATG)	 CG	25335-25415	GT	AGG
(AAT)	 AG	26058-26100	GT	AGG
(CAC)	 AG	26193-26266	GT	AGG
(GTA)	 AG	26543-26656	TT	ACT
-recovered pasa_asmbl_52291.p1, initial, 25335, 25415
-recovered pasa_asmbl_52291.p1, internal, 26058, 26100
-recovered pasa_asmbl_52291.p1, internal, 26193, 26266
Valid prediction for GlimmerHMM_glimmerT_20986-T1
Couldn't classify 143652, 143957
Sorry, prediction pasa_asmbl_52298.p1 fails validation.
(TCA)	 TT	143652-143957	TG	AAT
Valid prediction for Augustus_model.g14081.t1
Valid prediction for snap_scaffold_8-snap.2234-T1
Valid prediction for GeneMark_model.35822_t
Couldn't classify 15471, 15896
Sorry, prediction pasa_asmbl_52289.p1 fails validation.
(AGC)	 GT	15471-15896	GT	AGG
(AAC)	 AG	17018-17085	GT	AGG
(GTA)	 AG	17369-17513	GT	CGG
(TAC)	 AG	17822-17914	GT	AGG
(ACA)	 AG	18210-18265	GT	ATG
(GCG)	 AG	18412-18478	GT	AGG
(TGC)	 AG	18974-19080	GT	TGG
(CTT)	 AG	19275-19317	GT	AGG
(TGG)	 AG	19448-19519	GT	AGG
(GAG)	 AG	19946-20076	GT	TGG
(GTA)	 AG	21820-21877	GT	AGG
(CGT)	 AG	22364-22624	GT	AGG
(AAC)	 AG	22750-22862	GT	AGG
(ATA)	 AG	23015-23099	GG	AAG
-recovered pasa_asmbl_52289.p1, terminal, 23015, 23099
-recovered pasa_asmbl_52289.p1, internal, 17018, 17085
-recovered pasa_asmbl_52289.p1, internal, 17369, 17513
-recovered pasa_asmbl_52289.p1, internal, 17822, 17914
-recovered pasa_asmbl_52289.p1, internal, 18210, 18265
-recovered pasa_asmbl_52289.p1, internal, 18412, 18478
-recovered pasa_asmbl_52289.p1, internal, 18974, 19080
-recovered pasa_asmbl_52289.p1, internal, 19275, 19317
-recovered pasa_asmbl_52289.p1, internal, 19448, 19519
-recovered pasa_asmbl_52289.p1, internal, 19946, 20076
-recovered pasa_asmbl_52289.p1, internal, 21820, 21877
-recovered pasa_asmbl_52289.p1, internal, 22364, 22624
-recovered pasa_asmbl_52289.p1, internal, 22750, 22862
Valid prediction for GlimmerHMM_glimmerT_20996-T1
Valid prediction for snap_scaffold_8-snap.2212-T1
Valid prediction for GeneMark_model.35798_t
Valid prediction for snap_scaffold_8-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_20995-T1
Valid prediction for GeneMark_model.35824_t
Valid prediction for snap_scaffold_8-snap.2216-T1
Valid prediction for snap_scaffold_8-snap.2225-T1
Valid prediction for snap_scaffold_8-snap.2209-T1
Valid prediction for GeneMark_model.35799_t
Valid prediction for snap_scaffold_8-snap.2210-T1
Valid prediction for GeneMark_model.35807_t
Valid prediction for GeneMark_model.35828_t
Valid prediction for GeneMark_model.35818_t
Valid prediction for GlimmerHMM_glimmerT_20997-T1
Valid prediction for GlimmerHMM_glimmerT_20984-T1
Valid prediction for GeneMark_model.35827_t
Valid prediction for GeneMark_model.35816_t
Valid prediction for CodingQuarry_transcript_59691-T1
Valid prediction for GlimmerHMM_glimmerT_20988-T1
Valid prediction for snap_scaffold_8-snap.2227-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.35810_t
Valid prediction for snap_scaffold_8-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_20991-T1
Valid prediction for snap_scaffold_8-snap.2239-T1
Valid prediction for snap_scaffold_8-snap.2223-T1
Valid prediction for snap_scaffold_8-snap.2236-T1
Valid prediction for HiQ_model.g14084.t1
Valid prediction for Augustus_model.g14093.t1
Couldn't classify 100575, 100636
Sorry, prediction pasa_asmbl_52296.p1 fails validation.
(GGT)	 CA	100575-100636	GT	TGG
(GGA)	 AG	101107-101167	GT	TGG
(GGC)	 AG	102341-102418	GT	AGG
(CAT)	 AG	102687-102776	GT	AGG
(CTG)	 AG	102961-103026	GT	AGG
(GCC)	 AG	103141-103191	GT	TGG
(AAT)	 AG	103304-103396	TT	AGT
-recovered pasa_asmbl_52296.p1, terminal, 103304, 103396
-recovered pasa_asmbl_52296.p1, internal, 101107, 101167
-recovered pasa_asmbl_52296.p1, internal, 102341, 102418
-recovered pasa_asmbl_52296.p1, internal, 102687, 102776
-recovered pasa_asmbl_52296.p1, internal, 102961, 103026
-recovered pasa_asmbl_52296.p1, internal, 103141, 103191
Valid prediction for GlimmerHMM_glimmerT_21001-T1
Valid prediction for Augustus_model.g14087.t1
Valid prediction for GeneMark_model.35814_t
Valid prediction for GeneMark_model.35802_t
Valid prediction for GlimmerHMM_glimmerT_20979-T1
Valid prediction for snap_scaffold_8-snap.2235-T1
Valid prediction for CodingQuarry_transcript_59690-T1
Valid prediction for snap_scaffold_8-snap.2211-T1
Valid prediction for pasa_asmbl_52293.p1
Valid prediction for GeneMark_model.35831_t
Valid prediction for snap_scaffold_8-snap.2228-T1
Valid prediction for Augustus_model.g14080.t1
Valid prediction for GeneMark_model.35805_t
Valid prediction for GlimmerHMM_glimmerT_20980-T1
Valid prediction for snap_scaffold_8-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_21000-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 GeneMark_model.35817_t
Valid prediction for GlimmerHMM_glimmerT_20989-T1
Couldn't classify 285271, 285487
Couldn't classify 296857, 297008
Sorry, prediction pasa_asmbl_53178.p1 fails validation.
(GGC)	 CA	285271-285487	GT	AGG
(GCT)	 AG	287151-287296	GT	AAG
(CTC)	 AG	287619-287657	GT	AGG
(GTG)	 AG	290620-290753	GT	AGG
(CTA)	 AG	290849-290981	GT	AGG
(GAG)	 AG	291090-291296	GT	AGG
(GTA)	 AG	291538-291666	GT	AGG
(GCG)	 AG	293046-293190	GT	AGG
(ATG)	 AG	294494-294622	GT	AGG
(GTG)	 AG	296468-296587	GT	CTG
(TGT)	 AG	296857-297008	TC	GCT
add_exon() Sorry, pasa_asmbl_53178.p1 294494-294622-initial-1 is invalid.
-recovered pasa_asmbl_53178.p1, initial, 294494, 294622
-recovered pasa_asmbl_53178.p1, internal, 287151, 287296
-recovered pasa_asmbl_53178.p1, internal, 287619, 287657
-recovered pasa_asmbl_53178.p1, internal, 290620, 290753
-recovered pasa_asmbl_53178.p1, internal, 290849, 290981
-recovered pasa_asmbl_53178.p1, internal, 291090, 291296
-recovered pasa_asmbl_53178.p1, internal, 291538, 291666
-recovered pasa_asmbl_53178.p1, internal, 293046, 293190
-recovered pasa_asmbl_53178.p1, internal, 294494, 294622
-recovered pasa_asmbl_53178.p1, internal, 296468, 296587
Valid prediction for GlimmerHMM_glimmerT_20992-T1
Valid prediction for GeneMark_model.35797_t
Valid prediction for HiQ_model.g14090.t1
Couldn't classify 297379, 297930
Sorry, prediction pasa_asmbl_53177.p1 fails validation.
(AGG)	 GC	297379-297930	AT	AGA
Valid prediction for GeneMark_model.35809_t
Couldn't classify 65097, 65607
Sorry, prediction pasa_asmbl_53634.p1 fails validation.
(CTA)	 AC	65097-65607	GT	AGG
(AGC)	 AG	66358-66479	GT	AGG
(TCT)	 AG	66608-66740	GT	AGG
(GTT)	 AG	67304-67411	GT	AGG
(GCT)	 AG	67909-68019	GT	AGG
(ATC)	 AG	68278-68390	GT	AGG
(TTA)	 AG	68695-68859	CC	AGC
add_exon() Sorry, pasa_asmbl_53634.p1 67304-67411-terminal-1 is invalid.
-recovered pasa_asmbl_53634.p1, terminal, 67304, 67411
-recovered pasa_asmbl_53634.p1, terminal, 68695, 68859
-recovered pasa_asmbl_53634.p1, internal, 66358, 66479
-recovered pasa_asmbl_53634.p1, internal, 66608, 66740
-recovered pasa_asmbl_53634.p1, internal, 67304, 67411
-recovered pasa_asmbl_53634.p1, internal, 67909, 68019
-recovered pasa_asmbl_53634.p1, internal, 68278, 68390
Valid prediction for GlimmerHMM_glimmerT_20981-T1
Valid prediction for GeneMark_model.35823_t
Valid prediction for GlimmerHMM_glimmerT_20993-T1
Couldn't classify 298261, 298413
Sorry, prediction pasa_asmbl_53174.p1 fails validation.
(GTC)	 AG	298261-298413	GT	AGG
(GAT)	 AG	298778-298991	GT	AGG
(GCT)	 AG	299579-299688	GT	AGG
(CTG)	 AG	299953-300128	GT	AGG
(GTT)	 AG	300397-300564	GT	GGG
(GGT)	 AG	301287-301470	GT	CCG
(GAC)	 AG	301706-301960	GT	AGG
(GTC)	 AG	302639-302756	GT	CAG
(ACG)	 AG	303494-303656	GT	AGG
(GAG)	 AG	303792-303856	GT	TGG
(ACG)	 AG	303970-304106	CC	GAC
-recovered pasa_asmbl_53174.p1, terminal, 303970, 304106
-recovered pasa_asmbl_53174.p1, internal, 298261, 298413
-recovered pasa_asmbl_53174.p1, internal, 298778, 298991
-recovered pasa_asmbl_53174.p1, internal, 299579, 299688
-recovered pasa_asmbl_53174.p1, internal, 299953, 300128
-recovered pasa_asmbl_53174.p1, internal, 300397, 300564
-recovered pasa_asmbl_53174.p1, internal, 301287, 301470
-recovered pasa_asmbl_53174.p1, internal, 301706, 301960
-recovered pasa_asmbl_53174.p1, internal, 302639, 302756
-recovered pasa_asmbl_53174.p1, internal, 303494, 303656
-recovered pasa_asmbl_53174.p1, internal, 303792, 303856
Valid prediction for snap_scaffold_8-snap.2207-T1
Valid prediction for pasa_asmbl_53182.p2
Valid prediction for GlimmerHMM_glimmerT_20977-T1
Valid prediction for Augustus_model.g14089.t1
Valid prediction for snap_scaffold_8-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_20999-T1
Valid prediction for GlimmerHMM_glimmerT_20983-T1
Valid prediction for GeneMark_model.35813_t
Valid prediction for Augustus_model.g14082.t1
Valid prediction for HiQ_model.g14091.t1
Valid prediction for GeneMark_model.35804_t
Valid prediction for CodingQuarry_transcript_59696-T1
Valid prediction for snap_scaffold_8-snap.2220-T1
Valid prediction for snap_scaffold_8-snap.2224-T1
Valid prediction for GeneMark_model.35811_t
Valid prediction for GlimmerHMM_glimmerT_21003-T1
Valid prediction for Augustus_model.g14083.t1
Valid prediction for snap_scaffold_8-snap.2214-T1
Valid prediction for Augustus_model.g14092.t1
Valid prediction for snap_scaffold_8-snap.2219-T1
Valid prediction for GeneMark_model.35833_t
Valid prediction for pasa_asmbl_53185.p1
Valid prediction for GlimmerHMM_glimmerT_20987-T1
Valid prediction for GeneMark_model.35832_t
Valid prediction for snap_scaffold_8-snap.2240-T1
Valid prediction for snap_scaffold_8-snap.2226-T1
Valid prediction for GeneMark_model.35801_t
Valid prediction for GeneMark_model.35806_t
Valid prediction for snap_scaffold_8-snap.2230-T1
Valid prediction for Augustus_model.g14078.t1
Valid prediction for snap_scaffold_8-snap.2232-T1
Valid prediction for Augustus_model.g14088.t1
Valid prediction for snap_scaffold_8-snap.2238-T1
Valid prediction for Augustus_model.g14086.t1
Valid prediction for GeneMark_model.35819_t
Valid prediction for GlimmerHMM_glimmerT_20978-T1
Valid prediction for snap_scaffold_8-snap.2231-T1
Valid prediction for GeneMark_model.35830_t
Valid prediction for GlimmerHMM_glimmerT_20985-T1
Valid prediction for GeneMark_model.35826_t
Valid prediction for GeneMark_model.35800_t
Valid prediction for GlimmerHMM_glimmerT_20994-T1
Valid prediction for GlimmerHMM_glimmerT_20998-T1
Valid prediction for GeneMark_model.35808_t
Valid prediction for GeneMark_model.35812_t
Valid prediction for GlimmerHMM_glimmerT_20990-T1
Valid prediction for snap_scaffold_8-snap.2206-T1
Valid prediction for GeneMark_model.35820_t
Valid prediction for GeneMark_model.35803_t
Valid prediction for snap_scaffold_8-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_20982-T1
Valid prediction for CodingQuarry_transcript_59693-T1
Valid prediction for snap_scaffold_8-snap.2222-T1
Valid prediction for GeneMark_model.35829_t
Valid prediction for pasa_asmbl_53179.p1
Valid prediction for GeneMark_model.35825_t
Valid prediction for GeneMark_model.35815_t
Valid prediction for CodingQuarry_transcript_59695-T1
Valid prediction for snap_scaffold_8-snap.2215-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 165179, rend_intergenic: 157768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172315, rend_intergenic: 166161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 345450
-exon list size: 536


building trellis

0.2    
0.4    
0.6    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 165179, rend_intergenic: 157768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172315, rend_intergenic: 166161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support