-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_14594812-14777895

-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 GeneMark_model.65661_t
Valid prediction for snap_scaffold_15-snap.2920-T1
Valid prediction for pasa_asmbl_14646.p1
Valid prediction for snap_scaffold_15-snap.2943-T1
Couldn't classify 55727, 55945
Couldn't classify 56012, 56017
Sorry, prediction CodingQuarry_transcript_18188-T1 fails validation.
(ATG)	 TA	54989-55231	GT	AGG
(GTA)	 AG	55421-55528	GT	AGG
(GAG)	 AG	55727-55945	CT	ACC
(CTG)	 AC	56012-56017	TC	GAT
-recovered CodingQuarry_transcript_18188-T1, initial, 54989, 55231
-recovered CodingQuarry_transcript_18188-T1, internal, 55421, 55528
Valid prediction for Augustus_model.g25646.t1
Valid prediction for CodingQuarry_transcript_18187-T1
Valid prediction for snap_scaffold_15-snap.2933-T1
Valid prediction for CodingQuarry_transcript_18194-T1
Valid prediction for snap_scaffold_15-snap.2929-T1
Valid prediction for GlimmerHMM_glimmerT_38224-T1
Valid prediction for snap_scaffold_15-snap.2936-T1
Couldn't classify 89081, 89169
Couldn't classify 95565, 95684
Sorry, prediction pasa_asmbl_14845.p1 fails validation.
(CAT)	 AG	89081-89169	GT	CAG
(ATA)	 AG	89980-90036	GT	GGG
(GTT)	 AG	90809-90883	GT	ATG
(CTA)	 AG	93080-93317	GT	AGG
(GTG)	 AG	93666-93809	GT	AGG
(ATC)	 AG	95565-95684	TC	AGT
-recovered pasa_asmbl_14845.p1, internal, 89081, 89169
-recovered pasa_asmbl_14845.p1, internal, 89980, 90036
-recovered pasa_asmbl_14845.p1, internal, 90809, 90883
-recovered pasa_asmbl_14845.p1, internal, 93080, 93317
-recovered pasa_asmbl_14845.p1, internal, 93666, 93809
Valid prediction for snap_scaffold_15-snap.2928-T1
Valid prediction for GeneMark_model.65668_t
Valid prediction for snap_scaffold_15-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_38214-T1
Valid prediction for Augustus_model.g25627.t1
Valid prediction for snap_scaffold_15-snap.2947-T1
Valid prediction for snap_scaffold_15-snap.2916-T1
Valid prediction for GlimmerHMM_glimmerT_38209-T1
Valid prediction for snap_scaffold_15-snap.2938-T1
Valid prediction for HiQ_model.g25632.t1
Valid prediction for snap_scaffold_15-snap.2942-T1
Valid prediction for CodingQuarry_transcript_18190-T1
Valid prediction for GeneMark_model.65681_t
Valid prediction for GeneMark_model.65669_t
Valid prediction for CodingQuarry_transcript_18192-T1
Valid prediction for GlimmerHMM_glimmerT_38211-T1
Valid prediction for GeneMark_model.65649_t
Valid prediction for GeneMark_model.65663_t
Valid prediction for snap_scaffold_15-snap.2911-T1
Valid prediction for snap_scaffold_15-snap.2918-T1
Valid prediction for GlimmerHMM_glimmerT_38210-T1
Valid prediction for GlimmerHMM_glimmerT_38220-T1
Valid prediction for Augustus_model.g25628.t1
Valid prediction for snap_scaffold_15-snap.2921-T1
Valid prediction for snap_scaffold_15-snap.2950-T1
Valid prediction for Augustus_model.g25639.t1
Valid prediction for GeneMark_model.65658_t
Valid prediction for GeneMark_model.65666_t
Valid prediction for GlimmerHMM_glimmerT_38217-T1
Valid prediction for GlimmerHMM_glimmerT_38221-T1
Valid prediction for GeneMark_model.65670_t
Valid prediction for Augustus_model.g25642.t1
Valid prediction for pasa_asmbl_14638.p1
Valid prediction for GlimmerHMM_glimmerT_38222-T1
Valid prediction for GlimmerHMM_glimmerT_38223-T1
Valid prediction for CodingQuarry_transcript_18193-T1
Valid prediction for GeneMark_model.65667_t
Valid prediction for snap_scaffold_15-snap.2934-T1
Valid prediction for snap_scaffold_15-snap.2930-T1
Valid prediction for snap_scaffold_15-snap.2944-T1
Valid prediction for GeneMark_model.65652_t
Valid prediction for GeneMark_model.65682_t
Valid prediction for snap_scaffold_15-snap.2932-T1
Valid prediction for GeneMark_model.65656_t
Valid prediction for GeneMark_model.65653_t
Valid prediction for Augustus_model.g25638.t1
Valid prediction for HiQ_model.g25635.t1
Valid prediction for snap_scaffold_15-snap.2913-T1
Valid prediction for GeneMark_model.65674_t
Valid prediction for pasa_asmbl_14635.p1
Valid prediction for GlimmerHMM_glimmerT_38229-T1
Valid prediction for Augustus_model.g25629.t1
Valid prediction for snap_scaffold_15-snap.2917-T1
Valid prediction for Augustus_model.g25640.t1
Valid prediction for Augustus_model.g25644.t1
Valid prediction for GeneMark_model.65677_t
Valid prediction for snap_scaffold_15-snap.2931-T1
Valid prediction for pasa_asmbl_14642.p1
Valid prediction for snap_scaffold_15-snap.2945-T1
Valid prediction for GeneMark_model.65650_t

-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_38226-T1
Valid prediction for GeneMark_model.65684_t
Valid prediction for GlimmerHMM_glimmerT_38218-T1
Valid prediction for GlimmerHMM_glimmerT_38216-T1
Valid prediction for GlimmerHMM_glimmerT_38225-T1
Valid prediction for GeneMark_model.65679_t
Valid prediction for GlimmerHMM_glimmerT_38231-T1
Valid prediction for HiQ_model.g25637.t1
Valid prediction for HiQ_model.g25631.t1
Valid prediction for snap_scaffold_15-snap.2935-T1
Valid prediction for GlimmerHMM_glimmerT_38228-T1
Valid prediction for CodingQuarry_transcript_18189-T1
Valid prediction for GeneMark_model.65651_t
Valid prediction for GlimmerHMM_glimmerT_38230-T1
Valid prediction for snap_scaffold_15-snap.2941-T1
Valid prediction for snap_scaffold_15-snap.2951-T1
Couldn't classify 29073, 29217
Sorry, prediction pasa_asmbl_15762.p1 fails validation.
(ATG)	 AC	20661-20706	GT	CGG
(GGT)	 AG	22391-22475	GT	AAG
(AAC)	 AG	24498-24601	GT	CGG
(AGA)	 AG	24964-25090	GT	AAG
(GAA)	 AG	27533-27625	GT	GAG
(TAT)	 AG	27926-28009	GT	AAG
(GGT)	 AG	29073-29217	GT	AGG
-recovered pasa_asmbl_15762.p1, initial, 20661, 20706
-recovered pasa_asmbl_15762.p1, internal, 22391, 22475
-recovered pasa_asmbl_15762.p1, internal, 24498, 24601
-recovered pasa_asmbl_15762.p1, internal, 24964, 25090
-recovered pasa_asmbl_15762.p1, internal, 27533, 27625
-recovered pasa_asmbl_15762.p1, internal, 27926, 28009
-recovered pasa_asmbl_15762.p1, internal, 29073, 29217
Valid prediction for GeneMark_model.65673_t
Valid prediction for snap_scaffold_15-snap.2922-T1
Valid prediction for CodingQuarry_transcript_18195-T1
Valid prediction for CodingQuarry_transcript_18186-T1
Valid prediction for snap_scaffold_15-snap.2924-T1
Valid prediction for pasa_asmbl_15758.p1
Valid prediction for GeneMark_model.65660_t
Valid prediction for GeneMark_model.65655_t
Valid prediction for snap_scaffold_15-snap.2948-T1
Valid prediction for pasa_asmbl_15756.p1
Valid prediction for GeneMark_model.65683_t
Valid prediction for GeneMark_model.65675_t
Valid prediction for Augustus_model.g25636.t1
Valid prediction for Augustus_model.g25643.t1
Valid prediction for GeneMark_model.65678_t
Valid prediction for GeneMark_model.65671_t
Valid prediction for snap_scaffold_15-snap.2937-T1
Valid prediction for GeneMark_model.65657_t
Valid prediction for snap_scaffold_15-snap.2919-T1
Valid prediction for snap_scaffold_15-snap.2926-T1
Valid prediction for snap_scaffold_15-snap.2923-T1
Valid prediction for snap_scaffold_15-snap.2949-T1
Valid prediction for GeneMark_model.65664_t
Valid prediction for snap_scaffold_15-snap.2914-T1
Valid prediction for Augustus_model.g25647.t1
Valid prediction for Augustus_model.g25645.t1
Valid prediction for GeneMark_model.65680_t
Valid prediction for GeneMark_model.65672_t
Valid prediction for snap_scaffold_15-snap.2946-T1
Valid prediction for GlimmerHMM_glimmerT_38227-T1
Valid prediction for pasa_asmbl_15749.p1
Valid prediction for Augustus_model.g25634.t1
Valid prediction for snap_scaffold_15-snap.2939-T1
Valid prediction for snap_scaffold_15-snap.2915-T1
Valid prediction for Augustus_model.g25649.t1
Valid prediction for Augustus_model.g25633.t1
Valid prediction for GeneMark_model.65662_t
Valid prediction for HiQ_model.g25641.t1
Valid prediction for GlimmerHMM_glimmerT_38215-T1
Valid prediction for GlimmerHMM_glimmerT_38212-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_18184-T1
Valid prediction for snap_scaffold_15-snap.2912-T1
Valid prediction for CodingQuarry_transcript_18185-T1
Valid prediction for GlimmerHMM_glimmerT_38213-T1
Valid prediction for GlimmerHMM_glimmerT_38219-T1
Valid prediction for Augustus_model.g25630.t1
Valid prediction for GeneMark_model.65676_t
Valid prediction for GeneMark_model.65665_t
Valid prediction for GeneMark_model.65659_t
Valid prediction for snap_scaffold_15-snap.2927-T1
Valid prediction for GeneMark_model.65654_t
Valid prediction for CodingQuarry_transcript_18198-T1
Valid prediction for CodingQuarry_transcript_18197-T1
Valid prediction for snap_scaffold_15-snap.2940-T1
Valid prediction for Augustus_model.g25648.t1
Valid prediction for GeneMark_model.65648_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18035, rend_intergenic: 13015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27518, rend_intergenic: 19430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30754, rend_intergenic: 27919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44698, rend_intergenic: 41634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95690, rend_intergenic: 87261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151222, rend_intergenic: 149298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158702, rend_intergenic: 153459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174150, rend_intergenic: 168097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177794, rend_intergenic: 174787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183084
-exon list size: 523


building trellis

0.2    
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1.0    
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1.9    
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2.9    
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6.9    
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8.0    
8.2    
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8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
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9.9    
10.1    
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10.9    
11.0    
11.2    
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11.6    
11.8    
12.0    
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12.4    
12.6    
12.8    
13.0    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.6    
15.8    
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16.2    
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16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
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    
26.9    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
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    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.1    
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    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 18035, rend_intergenic: 13015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27518, rend_intergenic: 19430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30754, rend_intergenic: 27919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44698, rend_intergenic: 41634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95690, rend_intergenic: 87261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151222, rend_intergenic: 149298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158702, rend_intergenic: 153459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174150, rend_intergenic: 168097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177794, rend_intergenic: 174787  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

-building DP trellis

-building trellis in range 1 - 12679
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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