-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_5720805-5920282

-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 Augustus_model.g29060.t1
Valid prediction for GeneMark_model.74886_t
Valid prediction for GeneMark_model.74882_t
Valid prediction for GeneMark_model.74893_t
Valid prediction for CodingQuarry_transcript_23721-T1
Valid prediction for GeneMark_model.74879_t
Valid prediction for GeneMark_model.74884_t
Valid prediction for snap_scaffold_18-snap.1227-T1
Valid prediction for snap_scaffold_18-snap.1208-T1
Valid prediction for snap_scaffold_18-snap.1203-T1
Valid prediction for snap_scaffold_18-snap.1229-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43407-T1
Valid prediction for GeneMark_model.74900_t
Valid prediction for Augustus_model.g29058.t1
Couldn't classify 50819, 50867
Couldn't classify 51926, 51930
Sorry, prediction pasa_asmbl_20633.p1 fails validation.
(TCG)	 CC	50819-50867	GT	CAG
(GTA)	 AG	50957-51082	GT	AGG
(AGC)	 AG	51299-51535	GT	AGG
(TTC)	 AG	51705-51815	GT	TTG
(ACC)	 AG	51926-51930	AC	CCA
-recovered pasa_asmbl_20633.p1, internal, 50957, 51082
-recovered pasa_asmbl_20633.p1, internal, 51299, 51535
-recovered pasa_asmbl_20633.p1, internal, 51705, 51815
Valid prediction for GeneMark_model.74892_t
Valid prediction for HiQ_model.g29061.t1
Valid prediction for snap_scaffold_18-snap.1209-T1
Valid prediction for GeneMark_model.74887_t
Valid prediction for snap_scaffold_18-snap.1216-T1
Valid prediction for GlimmerHMM_glimmerT_43418-T1
Valid prediction for Augustus_model.g29052.t1
Valid prediction for GlimmerHMM_glimmerT_43426-T1
Valid prediction for snap_scaffold_18-snap.1204-T1
Valid prediction for GeneMark_model.74895_t
Valid prediction for Augustus_model.g29063.t1
Valid prediction for snap_scaffold_18-snap.1205-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1210-T1
Valid prediction for snap_scaffold_18-snap.1218-T1
Valid prediction for CodingQuarry_transcript_23726-T1
Valid prediction for snap_scaffold_18-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_43405-T1
Valid prediction for GeneMark_model.74889_t
Valid prediction for pasa_asmbl_20630.p1
Valid prediction for snap_scaffold_18-snap.1214-T1
Valid prediction for pasa_asmbl_20635.p1
Valid prediction for GeneMark_model.74911_t
Valid prediction for snap_scaffold_18-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_43414-T1
Valid prediction for Augustus_model.g29056.t1
Couldn't classify 75192, 75572
Sorry, prediction pasa_asmbl_20640.p1 fails validation.
(TTT)	 CG	75192-75572	GG	GAG
Valid prediction for GeneMark_model.74875_t
Valid prediction for Augustus_model.g29053.t1
Valid prediction for GlimmerHMM_glimmerT_43427-T1
Valid prediction for snap_scaffold_18-snap.1217-T1
Valid prediction for Augustus_model.g29055.t1
Valid prediction for pasa_asmbl_20628.p1
Valid prediction for GeneMark_model.74901_t
Valid prediction for snap_scaffold_18-snap.1206-T1
Couldn't classify 184643, 184740
Couldn't classify 185021, 185321
Sorry, prediction CodingQuarry_transcript_23727-T1 fails validation.
(ATG)	 GG	184643-184740	CT	ACC
(CTC)	 AC	185021-185321	AG	GAA
Valid prediction for snap_scaffold_18-snap.1207-T1
Valid prediction for snap_scaffold_18-snap.1220-T1
Valid prediction for CodingQuarry_transcript_23724-T1
Couldn't classify 120200, 120270
Couldn't classify 125356, 125415
Sorry, prediction pasa_asmbl_20645.p1 fails validation.
(CCC)	 GC	120200-120270	GT	AAG
(TGG)	 AG	121381-121448	GT	CGG
(AGC)	 AG	124060-124127	GT	AGG
(CAC)	 AG	124295-124456	GT	AGG
(AAT)	 AG	125059-125208	GT	AGG
(GCG)	 AG	125356-125415	AA	TCA
-recovered pasa_asmbl_20645.p1, internal, 121381, 121448
-recovered pasa_asmbl_20645.p1, internal, 124060, 124127
-recovered pasa_asmbl_20645.p1, internal, 124295, 124456
-recovered pasa_asmbl_20645.p1, internal, 125059, 125208
Valid prediction for CodingQuarry_transcript_23722-T1
Valid prediction for GlimmerHMM_glimmerT_43409-T1
Valid prediction for GlimmerHMM_glimmerT_43413-T1
Valid prediction for GlimmerHMM_glimmerT_43410-T1
Valid prediction for HiQ_model.g29050.t1
Valid prediction for snap_scaffold_18-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_43404-T1
Valid prediction for HiQ_model.g29057.t1
Valid prediction for GlimmerHMM_glimmerT_43416-T1
Valid prediction for GeneMark_model.74914_t
Valid prediction for Augustus_model.g29054.t1
Valid prediction for GeneMark_model.74881_t
Valid prediction for GeneMark_model.74891_t
Valid prediction for Augustus_model.g29051.t1
Valid prediction for GeneMark_model.74903_t
Valid prediction for GeneMark_model.74899_t
Valid prediction for GlimmerHMM_glimmerT_43412-T1
Valid prediction for GlimmerHMM_glimmerT_43417-T1
Valid prediction for GlimmerHMM_glimmerT_43406-T1
Valid prediction for GlimmerHMM_glimmerT_43421-T1
Valid prediction for GeneMark_model.74907_t
Valid prediction for snap_scaffold_18-snap.1221-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_18-snap.1232-T1
Valid prediction for GlimmerHMM_glimmerT_43411-T1
Valid prediction for GeneMark_model.74913_t
Valid prediction for GeneMark_model.74904_t
Valid prediction for Augustus_model.g29066.t1
Valid prediction for GlimmerHMM_glimmerT_43425-T1
Valid prediction for Augustus_model.g29065.t1
Couldn't classify 7316, 7690
Sorry, prediction pasa_asmbl_19919.p1 fails validation.
(TTC)	 CA	7316-7690	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_43424-T1
Valid prediction for GlimmerHMM_glimmerT_43428-T1
Valid prediction for Augustus_model.g29062.t1
Valid prediction for snap_scaffold_18-snap.1215-T1
Valid prediction for HiQ_model.g29059.t1
Valid prediction for snap_scaffold_18-snap.1231-T1
Valid prediction for snap_scaffold_18-snap.1233-T1
Valid prediction for snap_scaffold_18-snap.1223-T1
Valid prediction for snap_scaffold_18-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_43422-T1
Valid prediction for snap_scaffold_18-snap.1224-T1
Valid prediction for GeneMark_model.74910_t
Valid prediction for GeneMark_model.74915_t
Valid prediction for snap_scaffold_18-snap.1211-T1
Valid prediction for GeneMark_model.74883_t
Valid prediction for GeneMark_model.74905_t
Valid prediction for GlimmerHMM_glimmerT_43423-T1
Couldn't classify 46962, 47009
Couldn't classify 50374, 50511
Sorry, prediction pasa_asmbl_19912.p2 fails validation.
(GTG)	 AG	46962-47009	GT	ACG
(GTT)	 AG	48443-48563	GT	AGG
(AGC)	 AG	49397-49530	GT	AGG
(GCA)	 AG	50374-50511	GG	TGG
add_exon() Sorry, pasa_asmbl_19912.p2 48443-48563-terminal-3 is invalid.
-recovered pasa_asmbl_19912.p2, terminal, 48443, 48563
-recovered pasa_asmbl_19912.p2, internal, 46962, 47009
-recovered pasa_asmbl_19912.p2, internal, 48443, 48563
-recovered pasa_asmbl_19912.p2, internal, 49397, 49530
Valid prediction for GeneMark_model.74885_t
Valid prediction for GlimmerHMM_glimmerT_43419-T1
Valid prediction for GeneMark_model.74909_t
Valid prediction for GeneMark_model.74906_t
Valid prediction for Augustus_model.g29064.t1
Valid prediction for snap_scaffold_18-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_43415-T1
Valid prediction for GeneMark_model.74897_t
Valid prediction for GlimmerHMM_glimmerT_43420-T1
Valid prediction for CodingQuarry_transcript_23728-T1
Valid prediction for GeneMark_model.74902_t
Valid prediction for GeneMark_model.74890_t
Valid prediction for GeneMark_model.74898_t
Valid prediction for GlimmerHMM_glimmerT_43408-T1
Valid prediction for snap_scaffold_18-snap.1225-T1
Valid prediction for GeneMark_model.74894_t
Valid prediction for GeneMark_model.74880_t
Valid prediction for GeneMark_model.74908_t
Valid prediction for pasa_asmbl_19920.p1
Valid prediction for GeneMark_model.74912_t
Valid prediction for snap_scaffold_18-snap.1230-T1
Valid prediction for CodingQuarry_transcript_23725-T1
Valid prediction for snap_scaffold_18-snap.1219-T1
Valid prediction for pasa_asmbl_19910.p1
Valid prediction for GeneMark_model.74888_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49065, rend_intergenic: 38394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199478
-exon list size: 527


building trellis

0.2    
0.4    
0.6    
0.8    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.6    
9.8    
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    
12.7    
12.9    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.8    
20.0    
20.2    
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    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
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    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
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    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
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    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
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    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 49065, rend_intergenic: 38394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support