-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_1332420-1585617

-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_34018-T1
Valid prediction for GlimmerHMM_glimmerT_34028-T1
Valid prediction for GeneMark_model.58251_t
Valid prediction for CodingQuarry_transcript_15516-T1
Valid prediction for GeneMark_model.58257_t
Valid prediction for Augustus_model.g22888.t1
Valid prediction for GlimmerHMM_glimmerT_34025-T1
Valid prediction for snap_scaffold_14-snap.239-T1
Valid prediction for GeneMark_model.58246_t
Valid prediction for snap_scaffold_14-snap.241-T1
Valid prediction for GeneMark_model.58239_t
Couldn't classify 120209, 120796
Sorry, prediction pasa_asmbl_12865.p1 fails validation.
(AGT)	 CC	120209-120796	AT	GAA
Valid prediction for GlimmerHMM_glimmerT_34027-T1
Valid prediction for GeneMark_model.58247_t
Valid prediction for Augustus_model.g22883.t1
Valid prediction for GlimmerHMM_glimmerT_34044-T1
Valid prediction for Augustus_model.g22880.t1
Valid prediction for snap_scaffold_14-snap.255-T1
Valid prediction for snap_scaffold_14-snap.250-T1
Valid prediction for snap_scaffold_14-snap.251-T1
Valid prediction for snap_scaffold_14-snap.252-T1
Valid prediction for snap_scaffold_14-snap.235-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34023-T1
Valid prediction for Augustus_model.g22898.t1
Valid prediction for GlimmerHMM_glimmerT_34045-T1
Valid prediction for GlimmerHMM_glimmerT_34037-T1
Valid prediction for GlimmerHMM_glimmerT_34036-T1
Valid prediction for Augustus_model.g22894.t1
Valid prediction for snap_scaffold_14-snap.230-T1
Couldn't classify 12866, 13027
Sorry, prediction pasa_asmbl_11796.p1 fails validation.
(AAG)	 CA	12866-13027	GT	AGG
(GGT)	 AG	13104-13281	GT	AGG
(GTG)	 AG	15298-15518	AT	AAA
-recovered pasa_asmbl_11796.p1, terminal, 15298, 15518
-recovered pasa_asmbl_11796.p1, internal, 13104, 13281
Valid prediction for GeneMark_model.58250_t
Valid prediction for GlimmerHMM_glimmerT_34049-T1
Valid prediction for GlimmerHMM_glimmerT_34017-T1
Valid prediction for GeneMark_model.58235_t
Valid prediction for snap_scaffold_14-snap.256-T1
Valid prediction for CodingQuarry_transcript_15509-T1
Valid prediction for Augustus_model.g22901.t1
Valid prediction for Augustus_model.g22893.t1
Valid prediction for GeneMark_model.58243_t
Valid prediction for snap_scaffold_14-snap.244-T1
Valid prediction for snap_scaffold_14-snap.236-T1
Valid prediction for Augustus_model.g22902.t1
Valid prediction for GeneMark_model.58262_t
Valid prediction for Augustus_model.g22884.t1
Valid prediction for Augustus_model.g22900.t1
Couldn't classify 39368, 39967
Sorry, prediction pasa_asmbl_12854.p1 fails validation.
(GGG)	 CC	39368-39967	AT	GGA
Valid prediction for snap_scaffold_14-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_34047-T1
Valid prediction for GlimmerHMM_glimmerT_34043-T1
Couldn't classify 226216, 226361
Sorry, prediction pasa_asmbl_11799.p1 fails validation.
(CAA)	 TA	226216-226361	GT	AGG
(GCT)	 AG	226463-226650	GT	TGG
(GTG)	 AG	226732-226885	GT	GGG
(GAG)	 AG	227028-227091	GT	AGG
(TAT)	 AG	227186-227278	GT	AGG
(GCT)	 AG	227469-227630	CC	AGC
-recovered pasa_asmbl_11799.p1, terminal, 227469, 227630
-recovered pasa_asmbl_11799.p1, internal, 226463, 226650
-recovered pasa_asmbl_11799.p1, internal, 226732, 226885
-recovered pasa_asmbl_11799.p1, internal, 227028, 227091
-recovered pasa_asmbl_11799.p1, internal, 227186, 227278
Valid prediction for snap_scaffold_14-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_34016-T1
Valid prediction for Augustus_model.g22873.t1
Valid prediction for GlimmerHMM_glimmerT_34050-T1
Valid prediction for HiQ_model.g22875.t1
Valid prediction for GeneMark_model.58260_t
Valid prediction for snap_scaffold_14-snap.219-T1
Valid prediction for Augustus_model.g22890.t1
Valid prediction for snap_scaffold_14-snap.221-T1
Valid prediction for GlimmerHMM_glimmerT_34026-T1
Valid prediction for GlimmerHMM_glimmerT_34039-T1
Valid prediction for GeneMark_model.58242_t
Valid prediction for GeneMark_model.58253_t
Valid prediction for GlimmerHMM_glimmerT_34030-T1
Valid prediction for Augustus_model.g22885.t1
Valid prediction for GlimmerHMM_glimmerT_34035-T1
Valid prediction for snap_scaffold_14-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_34033-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 snap_scaffold_14-snap.228-T1
Valid prediction for GlimmerHMM_glimmerT_34029-T1
Valid prediction for GeneMark_model.58244_t
Valid prediction for snap_scaffold_14-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_34024-T1
Valid prediction for GlimmerHMM_glimmerT_34019-T1
Valid prediction for GeneMark_model.58258_t
Valid prediction for Augustus_model.g22876.t1
Valid prediction for pasa_asmbl_12860.p1
Valid prediction for snap_scaffold_14-snap.240-T1
Valid prediction for Augustus_model.g22897.t1
Valid prediction for pasa_asmbl_12858.p1
Valid prediction for Augustus_model.g22879.t1
Valid prediction for GeneMark_model.58259_t
Valid prediction for GeneMark_model.58256_t
Valid prediction for GlimmerHMM_glimmerT_34046-T1
Valid prediction for GlimmerHMM_glimmerT_34020-T1
Valid prediction for snap_scaffold_14-snap.237-T1
Valid prediction for CodingQuarry_transcript_15515-T1
Valid prediction for GeneMark_model.58237_t
Valid prediction for Augustus_model.g22881.t1
Valid prediction for GlimmerHMM_glimmerT_34038-T1
Valid prediction for GlimmerHMM_glimmerT_34032-T1
Valid prediction for snap_scaffold_14-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_34031-T1
Valid prediction for GeneMark_model.58240_t
Valid prediction for GeneMark_model.58234_t
Valid prediction for Augustus_model.g22892.t1
Valid prediction for pasa_asmbl_12870.p1
Valid prediction for GlimmerHMM_glimmerT_34041-T1
Valid prediction for Augustus_model.g22886.t1
Valid prediction for snap_scaffold_14-snap.233-T1
Valid prediction for GeneMark_model.58255_t
Valid prediction for snap_scaffold_14-snap.225-T1
Valid prediction for HiQ_model.g22895.t1
Valid prediction for snap_scaffold_14-snap.231-T1
Couldn't classify 178706, 178846
Sorry, prediction pasa_asmbl_12861.p1 fails validation.
(GGT)	 CA	178706-178846	GT	AGG
(GTG)	 AG	179445-179544	GT	AGG
(CCT)	 AG	181006-181277	GG	GAG
-recovered pasa_asmbl_12861.p1, terminal, 181006, 181277
-recovered pasa_asmbl_12861.p1, internal, 179445, 179544
Valid prediction for HiQ_model.g22887.t1
Valid prediction for GeneMark_model.58249_t
Valid prediction for snap_scaffold_14-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_34022-T1
Valid prediction for Augustus_model.g22878.t1
Valid prediction for Augustus_model.g22877.t1
Valid prediction for GlimmerHMM_glimmerT_34042-T1
Valid prediction for snap_scaffold_14-snap.232-T1
Valid prediction for Augustus_model.g22889.t1
Valid prediction for GeneMark_model.58245_t
Valid prediction for GlimmerHMM_glimmerT_34048-T1
Valid prediction for snap_scaffold_14-snap.249-T1
Valid prediction for snap_scaffold_14-snap.248-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34021-T1
Valid prediction for pasa_asmbl_12866.p1
Valid prediction for GeneMark_model.58261_t
Valid prediction for GeneMark_model.58254_t
Valid prediction for snap_scaffold_14-snap.222-T1
Valid prediction for snap_scaffold_14-snap.224-T1
Valid prediction for Augustus_model.g22882.t1
Valid prediction for snap_scaffold_14-snap.257-T1
Valid prediction for GeneMark_model.58236_t
Valid prediction for CodingQuarry_transcript_15512-T1
Valid prediction for snap_scaffold_14-snap.246-T1
Valid prediction for snap_scaffold_14-snap.238-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34034-T1
Valid prediction for Augustus_model.g22874.t1
Valid prediction for Augustus_model.g22896.t1
Valid prediction for Augustus_model.g22891.t1
Couldn't classify 167973, 168056
Couldn't classify 174330, 174629
Sorry, prediction pasa_asmbl_12862.p1 fails validation.
(AGC)	 GG	167973-168056	GT	TGG
(ATA)	 AG	168820-168970	GT	AGG
(ATC)	 AG	169177-169265	GT	ATG
(CTC)	 AG	172115-172238	GT	TGG
(GTG)	 AG	172357-172553	GT	TGG
(GGT)	 AG	173007-173186	GT	CGG
(GTT)	 AG	174330-174629	TA	GTT
-recovered pasa_asmbl_12862.p1, internal, 168820, 168970
-recovered pasa_asmbl_12862.p1, internal, 169177, 169265
-recovered pasa_asmbl_12862.p1, internal, 172115, 172238
-recovered pasa_asmbl_12862.p1, internal, 172357, 172553
-recovered pasa_asmbl_12862.p1, internal, 173007, 173186
Valid prediction for snap_scaffold_14-snap.227-T1
Valid prediction for HiQ_model.g22899.t1
Valid prediction for GlimmerHMM_glimmerT_34040-T1
Valid prediction for CodingQuarry_transcript_15513-T1
Valid prediction for snap_scaffold_14-snap.254-T1
Valid prediction for snap_scaffold_14-snap.223-T1
Valid prediction for snap_scaffold_14-snap.229-T1
Valid prediction for snap_scaffold_14-snap.245-T1
Valid prediction for CodingQuarry_transcript_15514-T1
Valid prediction for snap_scaffold_14-snap.226-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 240419, rend_intergenic: 236445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253198
-exon list size: 442


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
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2.9    
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3.8    
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4.3    
4.5    
4.7    
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5.9    
6.1    
6.3    
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6.8    
7.0    
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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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 240419, rend_intergenic: 236445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 240420 - 253198
-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
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 240420 - 252604
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 240420 - 251007
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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