-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_9550698-9671191

-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 GlimmerHMM_glimmerT_60849-T1
Valid prediction for GlimmerHMM_glimmerT_60862-T1
Couldn't classify 84343, 84502
Sorry, prediction pasa_asmbl_38569.p1 fails validation.
(TAC)	 CG	84343-84502	GT	AGG
(GTA)	 AG	84752-84939	GT	AGG
(GTG)	 AG	85141-85419	AG	AGA
-recovered pasa_asmbl_38569.p1, terminal, 85141, 85419
-recovered pasa_asmbl_38569.p1, internal, 84752, 84939
Valid prediction for GeneMark_model.106050_t
Valid prediction for snap_scaffold_28-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_60860-T1
Valid prediction for snap_scaffold_28-snap.2157-T1
Valid prediction for GeneMark_model.106036_t
Valid prediction for snap_scaffold_28-snap.2163-T1
Valid prediction for GeneMark_model.106045_t
Valid prediction for GeneMark_model.106028_t
Valid prediction for GlimmerHMM_glimmerT_60863-T1
Valid prediction for snap_scaffold_28-snap.2164-T1
Valid prediction for Augustus_model.g40504.t1
Valid prediction for GlimmerHMM_glimmerT_60857-T1
Valid prediction for snap_scaffold_28-snap.2161-T1
Couldn't classify 84121, 84221
Sorry, prediction pasa_asmbl_38568.p1 fails validation.
(ATG)	 AC	77906-77975	GT	AGG
(GAA)	 AG	78655-78786	GT	AGG
(GGA)	 AG	79488-79594	GT	AGG
(GTG)	 AG	79759-79833	GT	AGG
(GTT)	 AG	80208-80404	GT	CGG
(GTT)	 AG	80693-80849	GT	GAG
(GTG)	 AG	80964-81077	GT	AGG
(GTG)	 AG	81305-81395	GT	AGG
(GGA)	 AG	82236-82390	GT	AGG
(GTG)	 AG	82496-82601	GT	GGG
(GAA)	 AG	82708-82854	GT	TGG
(GGT)	 AG	83036-83209	GT	CGG
(GCA)	 AG	83668-83796	GT	AGG
(ATG)	 AG	83884-84033	GT	CAG
(GTA)	 AG	84121-84221	GT	AGG
-recovered pasa_asmbl_38568.p1, initial, 77906, 77975
add_exon() Sorry, pasa_asmbl_38568.p1 83884-84033-initial-1 is invalid.
-recovered pasa_asmbl_38568.p1, initial, 83884, 84033
add_exon() Sorry, pasa_asmbl_38568.p1 78655-78786-terminal-1 is invalid.
-recovered pasa_asmbl_38568.p1, terminal, 78655, 78786
add_exon() Sorry, pasa_asmbl_38568.p1 81305-81395-terminal-3 is invalid.
-recovered pasa_asmbl_38568.p1, terminal, 81305, 81395
-recovered pasa_asmbl_38568.p1, internal, 78655, 78786
-recovered pasa_asmbl_38568.p1, internal, 79488, 79594
-recovered pasa_asmbl_38568.p1, internal, 79759, 79833
-recovered pasa_asmbl_38568.p1, internal, 80208, 80404
-recovered pasa_asmbl_38568.p1, internal, 80693, 80849
-recovered pasa_asmbl_38568.p1, internal, 80964, 81077
-recovered pasa_asmbl_38568.p1, internal, 81305, 81395
-recovered pasa_asmbl_38568.p1, internal, 82236, 82390
-recovered pasa_asmbl_38568.p1, internal, 82496, 82601
-recovered pasa_asmbl_38568.p1, internal, 82708, 82854
-recovered pasa_asmbl_38568.p1, internal, 83036, 83209
-recovered pasa_asmbl_38568.p1, internal, 83668, 83796
-recovered pasa_asmbl_38568.p1, internal, 83884, 84033
-recovered pasa_asmbl_38568.p1, internal, 84121, 84221
Valid prediction for Augustus_model.g40507.t1
Valid prediction for GlimmerHMM_glimmerT_60854-T1
Valid prediction for GeneMark_model.106053_t
Valid prediction for GeneMark_model.106040_t
Valid prediction for HiQ_model.g40508.t1
Valid prediction for snap_scaffold_28-snap.2158-T1
Valid prediction for GlimmerHMM_glimmerT_60859-T1
Valid prediction for CodingQuarry_transcript_43663-T1
Valid prediction for Augustus_model.g40510.t1
Valid prediction for HiQ_model.g40500.t1
Valid prediction for CodingQuarry_transcript_43664-T1
Couldn't classify 90391, 90541
Couldn't classify 91728, 91735
Sorry, prediction pasa_asmbl_38492.p1 fails validation.
(GAT)	 CC	90391-90541	GT	CAG
(GTA)	 AG	90629-90729	GT	AGG
(GCC)	 AG	91277-91478	GT	AGG
(GTA)	 AG	91728-91735	TG	GCT
-recovered pasa_asmbl_38492.p1, internal, 90629, 90729
-recovered pasa_asmbl_38492.p1, internal, 91277, 91478
Valid prediction for snap_scaffold_28-snap.2170-T1
Valid prediction for HiQ_model.g40503.t1
Valid prediction for GlimmerHMM_glimmerT_60861-T1
Valid prediction for snap_scaffold_28-snap.2154-T1
Valid prediction for snap_scaffold_28-snap.2172-T1
Valid prediction for GlimmerHMM_glimmerT_60851-T1
Valid prediction for GeneMark_model.106047_t
Valid prediction for snap_scaffold_28-snap.2175-T1
Valid prediction for GeneMark_model.106038_t
Couldn't classify 46107, 46338
Sorry, prediction pasa_asmbl_38490.p1 fails validation.
(GAT)	 TG	46107-46338	GT	AGG
(GCA)	 AG	47040-47236	GT	AGG
(GAG)	 AG	47371-47649	TG	GAT
-recovered pasa_asmbl_38490.p1, terminal, 47371, 47649
-recovered pasa_asmbl_38490.p1, internal, 47040, 47236
Valid prediction for GeneMark_model.106042_t
Valid prediction for snap_scaffold_28-snap.2166-T1
Valid prediction for GeneMark_model.106048_t
Valid prediction for snap_scaffold_28-snap.2168-T1
Valid prediction for GlimmerHMM_glimmerT_60848-T1
Couldn't classify 33477, 33509
Sorry, prediction pasa_asmbl_38489.p1 fails validation.
(TTC)	 CA	33477-33509	GT	AGG
(GAA)	 AG	34726-34821	GT	CTG
(GAT)	 AG	34961-35147	GT	AGG
(TCA)	 AG	35904-36058	TC	GAT
-recovered pasa_asmbl_38489.p1, terminal, 35904, 36058
-recovered pasa_asmbl_38489.p1, internal, 34726, 34821
-recovered pasa_asmbl_38489.p1, internal, 34961, 35147
Valid prediction for Augustus_model.g40497.t1
Valid prediction for GeneMark_model.106041_t
Valid prediction for GlimmerHMM_glimmerT_60852-T1
Couldn't classify 13449, 13542
Sorry, prediction pasa_asmbl_38485.p1 fails validation.
(CAG)	 AC	13449-13542	GT	TGG
(CAG)	 AG	15018-15182	GT	AGG
(GTT)	 AG	15420-15496	GT	AGG
(GCT)	 AG	15948-16122	GT	GGG
(GCC)	 AG	16354-16459	GT	AAG
(CTT)	 AG	16592-16638	GT	GGG
(ACA)	 AG	16841-17993	GT	AGG
(GCT)	 AG	18264-18431	GT	TGG
(TGA)	 AG	18578-18785	GG	GAG
-recovered pasa_asmbl_38485.p1, terminal, 18578, 18785
-recovered pasa_asmbl_38485.p1, internal, 15018, 15182
-recovered pasa_asmbl_38485.p1, internal, 15420, 15496
-recovered pasa_asmbl_38485.p1, internal, 15948, 16122
-recovered pasa_asmbl_38485.p1, internal, 16354, 16459
-recovered pasa_asmbl_38485.p1, internal, 16592, 16638
-recovered pasa_asmbl_38485.p1, internal, 16841, 17993
-recovered pasa_asmbl_38485.p1, internal, 18264, 18431
Valid prediction for GeneMark_model.106037_t
Valid prediction for GlimmerHMM_glimmerT_60865-T1
Valid prediction for GeneMark_model.106052_t
Valid prediction for HiQ_model.g40506.t1
Valid prediction for snap_scaffold_28-snap.2150-T1
Valid prediction for GeneMark_model.106033_t
Valid prediction for Augustus_model.g40502.t1
Valid prediction for GeneMark_model.106049_t
Valid prediction for snap_scaffold_28-snap.2173-T1
Valid prediction for GeneMark_model.106030_t
Valid prediction for GeneMark_model.106044_t
Valid prediction for GeneMark_model.106032_t

-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.106039_t
Valid prediction for CodingQuarry_transcript_43665-T1
Valid prediction for CodingQuarry_transcript_43662-T1
Valid prediction for GlimmerHMM_glimmerT_60864-T1
Valid prediction for pasa_asmbl_37851.p1
Valid prediction for snap_scaffold_28-snap.2151-T1
Valid prediction for pasa_asmbl_37850.p1
Valid prediction for snap_scaffold_28-snap.2174-T1
Valid prediction for snap_scaffold_28-snap.2152-T1
Valid prediction for snap_scaffold_28-snap.2167-T1
Valid prediction for snap_scaffold_28-snap.2160-T1
Valid prediction for Augustus_model.g40509.t1
Valid prediction for snap_scaffold_28-snap.2169-T1
Valid prediction for GeneMark_model.106034_t
Valid prediction for snap_scaffold_28-snap.2162-T1
Valid prediction for HiQ_model.g40498.t1
Valid prediction for GeneMark_model.106035_t
Valid prediction for GlimmerHMM_glimmerT_60855-T1
Valid prediction for Augustus_model.g40501.t1
Valid prediction for GeneMark_model.106031_t
Valid prediction for Augustus_model.g40505.t1
Couldn't classify 28052, 28384
Sorry, prediction pasa_asmbl_38494.p1 fails validation.
(ATG)	 AC	28052-28384	AG	GGA
Valid prediction for GeneMark_model.106051_t
Valid prediction for Augustus_model.g40499.t1
Valid prediction for GlimmerHMM_glimmerT_60858-T1
Valid prediction for GeneMark_model.106043_t
Valid prediction for snap_scaffold_28-snap.2171-T1
Valid prediction for GlimmerHMM_glimmerT_60856-T1
Couldn't classify 77027, 77202
Couldn't classify 77471, 77633
Sorry, prediction pasa_asmbl_37932.p1 fails validation.
(CTT)	 AG	77027-77202	GT	AGG
(ACA)	 AG	77471-77633	GT	AGG
-recovered pasa_asmbl_37932.p1, internal, 77027, 77202
-recovered pasa_asmbl_37932.p1, internal, 77471, 77633
Valid prediction for GlimmerHMM_glimmerT_60847-T1
Valid prediction for snap_scaffold_28-snap.2176-T1
Valid prediction for snap_scaffold_28-snap.2159-T1
Valid prediction for GlimmerHMM_glimmerT_60850-T1
Valid prediction for GlimmerHMM_glimmerT_60853-T1
Valid prediction for GeneMark_model.106046_t
Valid prediction for snap_scaffold_28-snap.2149-T1
Valid prediction for CodingQuarry_transcript_43661-T1
Valid prediction for snap_scaffold_28-snap.2153-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.2155-T1
Valid prediction for snap_scaffold_28-snap.2165-T1
Valid prediction for GeneMark_model.106029_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10350, rend_intergenic: 4549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18785, rend_intergenic: 10365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25216, rend_intergenic: 22531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43456, rend_intergenic: 39797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66795, rend_intergenic: 61509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74532, rend_intergenic: 71594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85419, rend_intergenic: 79693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117456, rend_intergenic: 113549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 120494
-exon list size: 397


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
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3.8    
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5.3    
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7.3    
7.5    
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9.5    
9.8    
10.0    
10.3    
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10.8    
11.0    
11.3    
11.5    
11.8    
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12.3    
12.5    
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13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
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16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
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    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
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    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
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61.9    
62.2    
62.4    
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62.9    
63.2    
63.4    
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63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
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65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
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    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 10350, rend_intergenic: 4549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18785, rend_intergenic: 10365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25216, rend_intergenic: 22531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43456, rend_intergenic: 39797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66795, rend_intergenic: 61509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74532, rend_intergenic: 71594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85419, rend_intergenic: 79693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117456, rend_intergenic: 113549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support