-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_1415781-1704573

-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_16-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_38658-T1
Valid prediction for snap_scaffold_16-snap.231-T1
Valid prediction for snap_scaffold_16-snap.241-T1
Valid prediction for GeneMark_model.66093_t
Valid prediction for GlimmerHMM_glimmerT_38651-T1
Valid prediction for snap_scaffold_16-snap.227-T1
Valid prediction for snap_scaffold_16-snap.225-T1
Valid prediction for GeneMark_model.66086_t
Valid prediction for GeneMark_model.66083_t
Valid prediction for GlimmerHMM_glimmerT_38641-T1
Valid prediction for GeneMark_model.66105_t
Valid prediction for snap_scaffold_16-snap.222-T1
Valid prediction for Augustus_model.g25942.t1
Valid prediction for snap_scaffold_16-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_38645-T1
Valid prediction for Augustus_model.g25933.t1
Valid prediction for GeneMark_model.66110_t
Valid prediction for GeneMark_model.66100_t
Valid prediction for GlimmerHMM_glimmerT_38656-T1
Valid prediction for CodingQuarry_transcript_19862-T1
Valid prediction for GeneMark_model.66103_t
Valid prediction for snap_scaffold_16-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_38654-T1
Valid prediction for GlimmerHMM_glimmerT_38664-T1
Valid prediction for pasa_asmbl_16873.p1
Valid prediction for GlimmerHMM_glimmerT_38660-T1
Valid prediction for GlimmerHMM_glimmerT_38642-T1
Valid prediction for GeneMark_model.66082_t
Valid prediction for GlimmerHMM_glimmerT_38646-T1
Couldn't classify 78656, 78715
Couldn't classify 93250, 93391
Sorry, prediction pasa_asmbl_16869.p1 fails validation.
(GAG)	 AA	78656-78715	GT	AGG
(GTG)	 AG	79265-79401	GT	AGG
(CTA)	 AG	81990-82153	GT	AGG
(GCA)	 AG	84156-84268	GT	GGG
(AAT)	 AG	84491-84554	GT	CGG
(ATG)	 AG	84892-84989	GT	AAG
(ATT)	 AG	87678-87779	GT	AAG
(GAA)	 AG	89933-90058	GT	ATG
(GAA)	 AG	90321-90442	GT	ATG
(GGA)	 AG	91603-91707	GT	AGG
(GAA)	 AG	92629-92754	GT	GTG
(TGG)	 AG	93250-93391	GT	TGG
-recovered pasa_asmbl_16869.p1, initial, 84892, 84989
-recovered pasa_asmbl_16869.p1, internal, 79265, 79401
-recovered pasa_asmbl_16869.p1, internal, 81990, 82153
-recovered pasa_asmbl_16869.p1, internal, 84156, 84268
-recovered pasa_asmbl_16869.p1, internal, 84491, 84554
-recovered pasa_asmbl_16869.p1, internal, 84892, 84989
-recovered pasa_asmbl_16869.p1, internal, 87678, 87779
-recovered pasa_asmbl_16869.p1, internal, 89933, 90058
-recovered pasa_asmbl_16869.p1, internal, 90321, 90442
-recovered pasa_asmbl_16869.p1, internal, 91603, 91707
-recovered pasa_asmbl_16869.p1, internal, 92629, 92754
-recovered pasa_asmbl_16869.p1, internal, 93250, 93391
Valid prediction for CodingQuarry_transcript_19863-T1
Valid prediction for GeneMark_model.66085_t
Valid prediction for GeneMark_model.66090_t
Valid prediction for GlimmerHMM_glimmerT_38648-T1
Valid prediction for GlimmerHMM_glimmerT_38644-T1
Valid prediction for Augustus_model.g25935.t1
Valid prediction for GeneMark_model.66094_t
Valid prediction for GeneMark_model.66108_t
Valid prediction for GeneMark_model.66112_t
Valid prediction for GeneMark_model.66080_t
Valid prediction for snap_scaffold_16-snap.244-T1
Valid prediction for GeneMark_model.66097_t
Valid prediction for snap_scaffold_16-snap.230-T1
Valid prediction for GeneMark_model.66099_t
Valid prediction for snap_scaffold_16-snap.220-T1
Valid prediction for snap_scaffold_16-snap.243-T1
Couldn't classify 61216, 61394
Sorry, prediction pasa_asmbl_16864.p1 fails validation.
(ATG)	 CA	59885-59958	GT	TGG
(GTA)	 AG	60640-60733	GT	AAG
(GTC)	 AG	60834-60876	GT	AGG
(CCC)	 AG	61216-61394	CT	CCC
-recovered pasa_asmbl_16864.p1, initial, 59885, 59958
-recovered pasa_asmbl_16864.p1, internal, 60640, 60733
-recovered pasa_asmbl_16864.p1, internal, 60834, 60876
Valid prediction for snap_scaffold_16-snap.239-T1
Couldn't classify 61905, 62066
Sorry, prediction pasa_asmbl_16868.p2 fails validation.
(CTG)	 AG	61905-62066	GT	AGG
(ATT)	 AG	62629-62790	GT	TCG
(GAT)	 AG	62997-63032	TG	AGT
-recovered pasa_asmbl_16868.p2, terminal, 62997, 63032
-recovered pasa_asmbl_16868.p2, internal, 61905, 62066
-recovered pasa_asmbl_16868.p2, internal, 62629, 62790
Valid prediction for snap_scaffold_16-snap.226-T1
Valid prediction for GeneMark_model.66095_t
Valid prediction for GeneMark_model.66084_t
Valid prediction for GlimmerHMM_glimmerT_38663-T1
Valid prediction for snap_scaffold_16-snap.232-T1
Valid prediction for snap_scaffold_16-snap.228-T1
Valid prediction for snap_scaffold_16-snap.246-T1
Valid prediction for HiQ_model.g25934.t1
Valid prediction for GlimmerHMM_glimmerT_38653-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.66104_t
Valid prediction for GeneMark_model.66088_t
Valid prediction for snap_scaffold_16-snap.233-T1
Valid prediction for snap_scaffold_16-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_38655-T1
Valid prediction for GlimmerHMM_glimmerT_38662-T1
Valid prediction for GlimmerHMM_glimmerT_38661-T1
Valid prediction for GlimmerHMM_glimmerT_38659-T1
Valid prediction for Augustus_model.g25938.t1
Valid prediction for GeneMark_model.66111_t
Valid prediction for snap_scaffold_16-snap.235-T1
Valid prediction for GeneMark_model.66101_t
Valid prediction for snap_scaffold_16-snap.237-T1
Valid prediction for GeneMark_model.66092_t
Valid prediction for GeneMark_model.66096_t
Valid prediction for Augustus_model.g25940.t1
Valid prediction for snap_scaffold_16-snap.224-T1
Valid prediction for snap_scaffold_16-snap.236-T1
Valid prediction for GeneMark_model.66106_t
Valid prediction for GlimmerHMM_glimmerT_38643-T1
Valid prediction for GeneMark_model.66109_t
Valid prediction for GlimmerHMM_glimmerT_38647-T1
Valid prediction for GlimmerHMM_glimmerT_38652-T1
Valid prediction for GeneMark_model.66087_t
Valid prediction for snap_scaffold_16-snap.247-T1
Valid prediction for GeneMark_model.66089_t
Valid prediction for snap_scaffold_16-snap.240-T1
Valid prediction for Augustus_model.g25936.t1
Valid prediction for snap_scaffold_16-snap.221-T1
Valid prediction for Augustus_model.g25939.t1
Valid prediction for snap_scaffold_16-snap.245-T1
Valid prediction for snap_scaffold_16-snap.223-T1
Valid prediction for snap_scaffold_16-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_38650-T1
Valid prediction for GeneMark_model.66098_t
Valid prediction for GeneMark_model.66091_t
Valid prediction for GlimmerHMM_glimmerT_38649-T1
Valid prediction for Augustus_model.g25941.t1
Valid prediction for snap_scaffold_16-snap.238-T1
Valid prediction for GeneMark_model.66081_t
Valid prediction for GlimmerHMM_glimmerT_38657-T1
Valid prediction for GeneMark_model.66107_t
Valid prediction for GeneMark_model.66102_t
Valid prediction for Augustus_model.g25937.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 255836, rend_intergenic: 251906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 288793
-exon list size: 352


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 255836, rend_intergenic: 251906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13642
-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 2532 - 13642
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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