-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_3615668-3797101

-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_18-snap.763-T1
Valid prediction for snap_scaffold_18-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_42046-T1
Valid prediction for snap_scaffold_18-snap.780-T1
Valid prediction for Augustus_model.g28008.t1
Valid prediction for pasa_asmbl_20473.p1
Valid prediction for GlimmerHMM_glimmerT_42047-T1
Valid prediction for pasa_asmbl_20476.p1
Valid prediction for snap_scaffold_18-snap.760-T1
Valid prediction for HiQ_model.g28011.t1
Valid prediction for snap_scaffold_18-snap.757-T1
Valid prediction for HiQ_model.g28003.t1
Valid prediction for pasa_asmbl_20474.p1
Valid prediction for CodingQuarry_transcript_23717-T1
Valid prediction for GlimmerHMM_glimmerT_42061-T1
Valid prediction for snap_scaffold_18-snap.777-T1
Valid prediction for Augustus_model.g28005.t1
Valid prediction for snap_scaffold_18-snap.758-T1
Valid prediction for Augustus_model.g28012.t1
Valid prediction for GlimmerHMM_glimmerT_42064-T1
Valid prediction for GlimmerHMM_glimmerT_42058-T1
Valid prediction for snap_scaffold_18-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_42066-T1
Valid prediction for GlimmerHMM_glimmerT_42051-T1
Valid prediction for GlimmerHMM_glimmerT_42056-T1
Valid prediction for GlimmerHMM_glimmerT_42072-T1
Valid prediction for snap_scaffold_18-snap.764-T1
Valid prediction for snap_scaffold_18-snap.747-T1
Valid prediction for snap_scaffold_18-snap.765-T1
Valid prediction for snap_scaffold_18-snap.770-T1
Valid prediction for snap_scaffold_18-snap.773-T1
Valid prediction for pasa_asmbl_20466.p1
Valid prediction for snap_scaffold_18-snap.746-T1
Valid prediction for snap_scaffold_18-snap.768-T1
Valid prediction for GlimmerHMM_glimmerT_42069-T1
Valid prediction for GlimmerHMM_glimmerT_42053-T1
Valid prediction for snap_scaffold_18-snap.769-T1
Valid prediction for snap_scaffold_18-snap.762-T1
Valid prediction for CodingQuarry_transcript_23720-T1
Valid prediction for HiQ_model.g28017.t1
Valid prediction for snap_scaffold_18-snap.778-T1
Valid prediction for snap_scaffold_18-snap.753-T1
Valid prediction for HiQ_model.g28009.t1
Valid prediction for Augustus_model.g28004.t1
Valid prediction for GlimmerHMM_glimmerT_42057-T1
Valid prediction for GlimmerHMM_glimmerT_42071-T1
Valid prediction for GlimmerHMM_glimmerT_42065-T1
Valid prediction for pasa_asmbl_20478.p1
Valid prediction for snap_scaffold_18-snap.750-T1
Valid prediction for HiQ_model.g28019.t1
Valid prediction for snap_scaffold_18-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_42054-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_42048-T1
Valid prediction for GlimmerHMM_glimmerT_42073-T1
Valid prediction for GlimmerHMM_glimmerT_42049-T1
Valid prediction for snap_scaffold_18-snap.779-T1
Valid prediction for Augustus_model.g28007.t1
Valid prediction for pasa_asmbl_19770.p1
Valid prediction for snap_scaffold_18-snap.755-T1
Valid prediction for snap_scaffold_18-snap.772-T1
Valid prediction for snap_scaffold_18-snap.775-T1
Valid prediction for CodingQuarry_transcript_23721-T1
Valid prediction for GlimmerHMM_glimmerT_42063-T1
Valid prediction for GlimmerHMM_glimmerT_42059-T1
Valid prediction for snap_scaffold_18-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_42060-T1
Valid prediction for Augustus_model.g28014.t1
Valid prediction for GlimmerHMM_glimmerT_42068-T1
Valid prediction for snap_scaffold_18-snap.754-T1
Valid prediction for snap_scaffold_18-snap.781-T1
Valid prediction for HiQ_model.g28018.t1
Valid prediction for GlimmerHMM_glimmerT_42045-T1
Valid prediction for GlimmerHMM_glimmerT_42050-T1
Valid prediction for GlimmerHMM_glimmerT_42062-T1
Valid prediction for GlimmerHMM_glimmerT_42070-T1
Valid prediction for snap_scaffold_18-snap.752-T1
Valid prediction for snap_scaffold_18-snap.766-T1
Valid prediction for Augustus_model.g28013.t1
Valid prediction for snap_scaffold_18-snap.771-T1
Valid prediction for snap_scaffold_18-snap.745-T1
Valid prediction for snap_scaffold_18-snap.751-T1
Valid prediction for snap_scaffold_18-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_42055-T1
Couldn't classify 56671, 57625
Couldn't classify 59229, 59410
Sorry, prediction pasa_asmbl_19767.p1 fails validation.
(TTC)	 TC	56671-57625	GT	AGG
(TCC)	 AG	59229-59410	CA	CGC
Valid prediction for GlimmerHMM_glimmerT_42052-T1
Valid prediction for snap_scaffold_18-snap.776-T1
Valid prediction for Augustus_model.g28016.t1
Valid prediction for GlimmerHMM_glimmerT_42067-T1
Valid prediction for snap_scaffold_18-snap.774-T1
Valid prediction for pasa_asmbl_19775.p1
Valid prediction for snap_scaffold_18-snap.756-T1
Valid prediction for CodingQuarry_transcript_23719-T1
Valid prediction for Augustus_model.g28010.t1
Valid prediction for Augustus_model.g28015.t1
Valid prediction for Augustus_model.g28006.t1
Couldn't classify 3950, 4141
Sorry, prediction pasa_asmbl_19778.p1 fails validation.
(TTC)	 GC	3950-4141	GT	AGG
(GAG)	 AG	4367-4480	GT	AGG
(ATT)	 AG	4710-4787	GT	AGG
(ACG)	 AG	4924-5019	GT	TGG
(GCT)	 AG	5138-5244	GT	AGG
(CCC)	 AG	5347-5416	GT	AGG
(GCA)	 AG	5635-5727	GT	AGG
(ACA)	 AG	5955-6083	GT	TGG
(GAC)	 AG	6461-6679	GT	CGG
(CTG)	 AG	6922-6976	GT	CCG
(GAA)	 AG	7173-7312	CA	GAC
-recovered pasa_asmbl_19778.p1, terminal, 7173, 7312
-recovered pasa_asmbl_19778.p1, internal, 4367, 4480
-recovered pasa_asmbl_19778.p1, internal, 4710, 4787
-recovered pasa_asmbl_19778.p1, internal, 4924, 5019
-recovered pasa_asmbl_19778.p1, internal, 5138, 5244
-recovered pasa_asmbl_19778.p1, internal, 5347, 5416
-recovered pasa_asmbl_19778.p1, internal, 5635, 5727
-recovered pasa_asmbl_19778.p1, internal, 5955, 6083
-recovered pasa_asmbl_19778.p1, internal, 6461, 6679
-recovered pasa_asmbl_19778.p1, internal, 6922, 6976
Valid prediction for snap_scaffold_18-snap.749-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30969, rend_intergenic: 29199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40545, rend_intergenic: 33406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70796, rend_intergenic: 64612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128589, rend_intergenic: 122016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132469, rend_intergenic: 129843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144080, rend_intergenic: 141228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156445, rend_intergenic: 151231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166878, rend_intergenic: 165110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181431, rend_intergenic: 174168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181434
-exon list size: 338


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.6    
2.9    
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3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
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5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
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10.0    
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10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
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16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
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22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
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54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
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57.1    
57.4    
57.6    
57.9    
58.2    
58.5    
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59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
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62.9    
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64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.6    
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68.2    
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69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
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75.3    
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81.2    
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82.4    
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83.2    
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84.1    
84.4    
84.7    
85.0    
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86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
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94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 30969, rend_intergenic: 29199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40545, rend_intergenic: 33406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70796, rend_intergenic: 64612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128589, rend_intergenic: 122016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132469, rend_intergenic: 129843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144080, rend_intergenic: 141228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156445, rend_intergenic: 151231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166878, rend_intergenic: 165110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181431, rend_intergenic: 174168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support