-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_305863-488066

-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.g34598.t1
Valid prediction for snap_scaffold_24-snap.89-T1
Valid prediction for snap_scaffold_24-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_51871-T1
Couldn't classify 135005, 135301
Sorry, prediction pasa_asmbl_32013.p1 fails validation.
(AAC)	 GC	135005-135301	GA	AGG
Couldn't classify 7501, 7587
Couldn't classify 14712, 14848
Sorry, prediction pasa_asmbl_32007.p1 fails validation.
(GGC)	 CT	7501-7587	GT	AGG
(CGT)	 AG	8508-8597	GT	TGG
(TGG)	 AG	9065-9198	GT	TGG
(GGA)	 AG	9451-9532	GT	AGG
(GAG)	 AG	10215-10452	GT	AGG
(AGG)	 AG	11074-11204	GT	GGG
(GAG)	 AG	11356-11424	GT	TGG
(TTC)	 AG	11597-11686	GT	TTG
(GTG)	 AG	12401-12483	GT	AGG
(TTC)	 AG	12668-12783	GT	CAG
(TAT)	 AG	14712-14848	CA	ACC
-recovered pasa_asmbl_32007.p1, internal, 8508, 8597
-recovered pasa_asmbl_32007.p1, internal, 9065, 9198
-recovered pasa_asmbl_32007.p1, internal, 9451, 9532
-recovered pasa_asmbl_32007.p1, internal, 10215, 10452
-recovered pasa_asmbl_32007.p1, internal, 11074, 11204
-recovered pasa_asmbl_32007.p1, internal, 11356, 11424
-recovered pasa_asmbl_32007.p1, internal, 11597, 11686
-recovered pasa_asmbl_32007.p1, internal, 12401, 12483
-recovered pasa_asmbl_32007.p1, internal, 12668, 12783
Valid prediction for snap_scaffold_24-snap.70-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 30448, 30605
Sorry, prediction pasa_asmbl_32008.p1 fails validation.
(ATG)	 GC	27881-28103	GT	TGG
(GTG)	 AG	28284-28412	GT	AGG
(GCG)	 AG	30448-30605	GG	GGG
-recovered pasa_asmbl_32008.p1, initial, 27881, 28103
-recovered pasa_asmbl_32008.p1, internal, 28284, 28412
Valid prediction for CodingQuarry_transcript_37215-T1
Valid prediction for GlimmerHMM_glimmerT_51874-T1
Valid prediction for snap_scaffold_24-snap.86-T1
Valid prediction for GlimmerHMM_glimmerT_51875-T1
Valid prediction for GlimmerHMM_glimmerT_51883-T1
Valid prediction for Augustus_model.g34596.t1
Valid prediction for pasa_asmbl_32017.p1
Valid prediction for GlimmerHMM_glimmerT_51862-T1
Valid prediction for snap_scaffold_24-snap.111-T1
Valid prediction for Augustus_model.g34599.t1
Valid prediction for GlimmerHMM_glimmerT_51873-T1
Valid prediction for snap_scaffold_24-snap.79-T1
Valid prediction for pasa_asmbl_32014.p2
Valid prediction for snap_scaffold_24-snap.95-T1
Valid prediction for Augustus_model.g34586.t1
Valid prediction for snap_scaffold_24-snap.84-T1
Couldn't classify 134726, 134836
Sorry, prediction pasa_asmbl_32012.p1 fails validation.
(ATG)	 TG	133352-133462	GT	AGG
(CTT)	 AG	133539-133697	GT	TCG
(AGC)	 AG	134221-134385	GT	AGG
(GAG)	 AG	134726-134836	AA	AGA
-recovered pasa_asmbl_32012.p1, initial, 133352, 133462
-recovered pasa_asmbl_32012.p1, internal, 133539, 133697
-recovered pasa_asmbl_32012.p1, internal, 134221, 134385
Valid prediction for HiQ_model.g34597.t1
Valid prediction for Augustus_model.g34592.t1
Valid prediction for GlimmerHMM_glimmerT_51872-T1
Valid prediction for snap_scaffold_24-snap.106-T1
Valid prediction for GlimmerHMM_glimmerT_51878-T1
Valid prediction for snap_scaffold_24-snap.100-T1
Valid prediction for snap_scaffold_24-snap.76-T1
Valid prediction for snap_scaffold_24-snap.109-T1
Valid prediction for HiQ_model.g34588.t1
Valid prediction for snap_scaffold_24-snap.81-T1
Valid prediction for Augustus_model.g34594.t1
Valid prediction for GlimmerHMM_glimmerT_51879-T1
Valid prediction for GlimmerHMM_glimmerT_51865-T1
Valid prediction for snap_scaffold_24-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_51870-T1
Valid prediction for HiQ_model.g34593.t1
Valid prediction for snap_scaffold_24-snap.73-T1
Valid prediction for Augustus_model.g34595.t1
Valid prediction for snap_scaffold_24-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_51880-T1
Valid prediction for snap_scaffold_24-snap.77-T1
Valid prediction for CodingQuarry_transcript_37216-T1
Valid prediction for snap_scaffold_24-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_51877-T1
Valid prediction for CodingQuarry_transcript_37217-T1
Valid prediction for snap_scaffold_24-snap.99-T1
Valid prediction for GlimmerHMM_glimmerT_51882-T1
Valid prediction for pasa_asmbl_32010.p1
Valid prediction for GlimmerHMM_glimmerT_51869-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 GlimmerHMM_glimmerT_51868-T1
Valid prediction for Augustus_model.g34587.t1
Valid prediction for Augustus_model.g34591.t1
Valid prediction for snap_scaffold_24-snap.80-T1
Valid prediction for snap_scaffold_24-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_51876-T1
Valid prediction for snap_scaffold_24-snap.108-T1
Valid prediction for snap_scaffold_24-snap.105-T1
Valid prediction for snap_scaffold_24-snap.97-T1
Couldn't classify 140048, 140246
Couldn't classify 140352, 140461
Sorry, prediction CodingQuarry_transcript_37214-T1 fails validation.
(ATG)	 TG	139473-139556	GT	CCG
(GGC)	 AG	140048-140246	AA	GGA
(TGG)	 GG	140352-140461	GC	AAG
-recovered CodingQuarry_transcript_37214-T1, initial, 139473, 139556
Valid prediction for snap_scaffold_24-snap.74-T1
Valid prediction for snap_scaffold_24-snap.98-T1
Valid prediction for snap_scaffold_24-snap.72-T1
Valid prediction for snap_scaffold_24-snap.110-T1
Valid prediction for snap_scaffold_24-snap.85-T1
Valid prediction for snap_scaffold_24-snap.96-T1
Valid prediction for snap_scaffold_24-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_51863-T1
Valid prediction for GlimmerHMM_glimmerT_51881-T1
Valid prediction for snap_scaffold_24-snap.103-T1
Valid prediction for snap_scaffold_24-snap.88-T1
Valid prediction for snap_scaffold_24-snap.91-T1
Valid prediction for snap_scaffold_24-snap.104-T1
Valid prediction for snap_scaffold_24-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_51861-T1
Valid prediction for Augustus_model.g34590.t1
Valid prediction for snap_scaffold_24-snap.115-T1
Valid prediction for snap_scaffold_24-snap.113-T1
Valid prediction for snap_scaffold_24-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_51864-T1
Valid prediction for Augustus_model.g34589.t1
Valid prediction for snap_scaffold_24-snap.75-T1
Valid prediction for snap_scaffold_24-snap.71-T1
Valid prediction for snap_scaffold_24-snap.82-T1
Valid prediction for snap_scaffold_24-snap.117-T1
Valid prediction for snap_scaffold_24-snap.92-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_51867-T1
Valid prediction for GlimmerHMM_glimmerT_51866-T1
Valid prediction for snap_scaffold_24-snap.118-T1
Valid prediction for snap_scaffold_24-snap.94-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.116-T1
Valid prediction for pasa_asmbl_32704.p1
Valid prediction for snap_scaffold_24-snap.78-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17300, rend_intergenic: 7425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25743, rend_intergenic: 18469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47220, rend_intergenic: 46445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50608, rend_intergenic: 49182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56833, rend_intergenic: 51631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59635, rend_intergenic: 56967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62085, rend_intergenic: 60181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69909, rend_intergenic: 67696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88008, rend_intergenic: 69945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93377, rend_intergenic: 88030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105814, rend_intergenic: 93785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107585, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118963, rend_intergenic: 115761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133892, rend_intergenic: 121112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141968, rend_intergenic: 137916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145621, rend_intergenic: 144703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149756, rend_intergenic: 146854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176253, rend_intergenic: 150092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182204
-exon list size: 486


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 17300, rend_intergenic: 7425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25743, rend_intergenic: 18469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47220, rend_intergenic: 46445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50608, rend_intergenic: 49182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56833, rend_intergenic: 51631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59635, rend_intergenic: 56967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62085, rend_intergenic: 60181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69909, rend_intergenic: 67696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88008, rend_intergenic: 69945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93377, rend_intergenic: 88030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105814, rend_intergenic: 93785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107585, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118963, rend_intergenic: 115761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133892, rend_intergenic: 121112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141968, rend_intergenic: 137916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145621, rend_intergenic: 144703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149756, rend_intergenic: 146854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176253, rend_intergenic: 150092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support