-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_8554410-8758040

-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_15-snap.1804-T1
Valid prediction for Augustus_model.g25069.t1
Valid prediction for GeneMark_model.64341_t
Valid prediction for GeneMark_model.64351_t
Valid prediction for snap_scaffold_15-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_37390-T1
Valid prediction for pasa_asmbl_14290.p1
Valid prediction for GlimmerHMM_glimmerT_37403-T1
Valid prediction for GlimmerHMM_glimmerT_37408-T1
Valid prediction for snap_scaffold_15-snap.1812-T1
Valid prediction for HiQ_model.g25067.t1
Valid prediction for GeneMark_model.64357_t
Valid prediction for GlimmerHMM_glimmerT_37394-T1
Valid prediction for snap_scaffold_15-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_37389-T1
Valid prediction for CodingQuarry_transcript_18030-T1
Couldn't classify 142240, 142961
Sorry, prediction pasa_asmbl_14291.p1 fails validation.
(CCC)	 AA	142240-142961	GT	AAG
(AAT)	 AG	143745-143886	GG	AAG
-recovered pasa_asmbl_14291.p1, terminal, 143745, 143886
Valid prediction for snap_scaffold_15-snap.1789-T1
Valid prediction for snap_scaffold_15-snap.1805-T1
Valid prediction for snap_scaffold_15-snap.1811-T1
Valid prediction for Augustus_model.g25071.t1
Valid prediction for snap_scaffold_15-snap.1806-T1
Valid prediction for pasa_asmbl_14288.p1
Valid prediction for snap_scaffold_15-snap.1791-T1
Valid prediction for snap_scaffold_15-snap.1793-T1
Valid prediction for CodingQuarry_transcript_18034-T1
Valid prediction for snap_scaffold_15-snap.1802-T1
Valid prediction for GeneMark_model.64338_t
Valid prediction for GlimmerHMM_glimmerT_37404-T1
Valid prediction for snap_scaffold_15-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_37410-T1
Valid prediction for GeneMark_model.64358_t
Valid prediction for snap_scaffold_15-snap.1813-T1
Valid prediction for snap_scaffold_15-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_37402-T1
Valid prediction for GlimmerHMM_glimmerT_37386-T1
Valid prediction for GeneMark_model.64354_t
Valid prediction for GeneMark_model.64340_t
Valid prediction for GlimmerHMM_glimmerT_37391-T1
Valid prediction for GlimmerHMM_glimmerT_37409-T1
Valid prediction for snap_scaffold_15-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_37401-T1
Valid prediction for GlimmerHMM_glimmerT_37396-T1
Valid prediction for GeneMark_model.64349_t
Valid prediction for GeneMark_model.64353_t
Valid prediction for snap_scaffold_15-snap.1787-T1
Valid prediction for CodingQuarry_transcript_18032-T1
Valid prediction for snap_scaffold_15-snap.1792-T1
Valid prediction for Augustus_model.g25074.t1
Valid prediction for GeneMark_model.64347_t
Valid prediction for Augustus_model.g25072.t1
Valid prediction for HiQ_model.g25065.t1
Valid prediction for GeneMark_model.64350_t
Valid prediction for GeneMark_model.64336_t
Couldn't classify 37565, 37727
Sorry, prediction pasa_asmbl_14284.p1 fails validation.
(TGT)	 CT	37565-37727	GT	CGG
(ATC)	 AG	37861-38070	GT	AGG
(AAG)	 AG	38165-39081	GA	GAG
-recovered pasa_asmbl_14284.p1, terminal, 38165, 39081
-recovered pasa_asmbl_14284.p1, internal, 37861, 38070
Valid prediction for CodingQuarry_transcript_18035-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_15-snap.1788-T1
Valid prediction for snap_scaffold_15-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_37405-T1
Valid prediction for Augustus_model.g25070.t1
Valid prediction for GeneMark_model.64339_t
Valid prediction for GlimmerHMM_glimmerT_37399-T1
Valid prediction for GeneMark_model.64337_t
Valid prediction for HiQ_model.g25068.t1
Valid prediction for Augustus_model.g25066.t1
Valid prediction for HiQ_model.g25073.t1
Valid prediction for GeneMark_model.64345_t
Valid prediction for GlimmerHMM_glimmerT_37397-T1
Valid prediction for snap_scaffold_15-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_37392-T1
Valid prediction for snap_scaffold_15-snap.1809-T1
Valid prediction for GeneMark_model.64342_t
Valid prediction for GlimmerHMM_glimmerT_37388-T1
Valid prediction for snap_scaffold_15-snap.1807-T1
Valid prediction for snap_scaffold_15-snap.1796-T1
Valid prediction for GeneMark_model.64346_t
Valid prediction for snap_scaffold_15-snap.1801-T1
Couldn't classify 44398, 44419
Couldn't classify 47094, 47142
Sorry, prediction pasa_asmbl_15374.p1 fails validation.
(TTC)	 CG	44398-44419	GT	AGG
(ATA)	 AG	44615-44651	GT	ACG
(AAA)	 AG	44836-44867	GT	GGG
(GAT)	 AG	45029-45073	GT	TGG
(TTG)	 AG	45189-45286	GC	AGG
(AAC)	 AG	45626-45707	GT	AGG
(TGA)	 AG	45821-45921	GT	AGG
(CTG)	 AG	46062-46177	GT	AGG
(AGA)	 AG	46319-46419	GT	AGG
(CTT)	 AG	46539-46628	GT	TGG
(CGG)	 AG	46736-46940	GT	AGG
(TGA)	 AG	47094-47142	AG	ACA
-recovered pasa_asmbl_15374.p1, internal, 44615, 44651
-recovered pasa_asmbl_15374.p1, internal, 44836, 44867
-recovered pasa_asmbl_15374.p1, internal, 45029, 45073
-recovered pasa_asmbl_15374.p1, internal, 45189, 45286
-recovered pasa_asmbl_15374.p1, internal, 45626, 45707
-recovered pasa_asmbl_15374.p1, internal, 45821, 45921
-recovered pasa_asmbl_15374.p1, internal, 46062, 46177
-recovered pasa_asmbl_15374.p1, internal, 46319, 46419
-recovered pasa_asmbl_15374.p1, internal, 46539, 46628
-recovered pasa_asmbl_15374.p1, internal, 46736, 46940
Valid prediction for GeneMark_model.64356_t
Valid prediction for snap_scaffold_15-snap.1808-T1
Valid prediction for snap_scaffold_15-snap.1794-T1
Valid prediction for GeneMark_model.64344_t
Valid prediction for GlimmerHMM_glimmerT_37398-T1
Valid prediction for GeneMark_model.64348_t
Valid prediction for GlimmerHMM_glimmerT_37407-T1
Couldn't classify 40798, 40998
Couldn't classify 44080, 44118
Sorry, prediction pasa_asmbl_15375.p1 fails validation.
(TAC)	 TG	40798-40998	GT	GGG
(GCT)	 AG	41777-41955	GT	AGG
(GTA)	 AG	42387-42474	GT	AGG
(GTG)	 AG	42851-42930	GT	AGG
(AAG)	 AG	43116-43178	GT	GAG
(GAA)	 AG	43306-43360	GT	AGG
(CCC)	 AG	43520-43660	GT	TGG
(CAA)	 AG	43800-43874	GT	CAG
(CCT)	 AG	44080-44118	AA	TCA
-recovered pasa_asmbl_15375.p1, internal, 41777, 41955
-recovered pasa_asmbl_15375.p1, internal, 42387, 42474
-recovered pasa_asmbl_15375.p1, internal, 42851, 42930
-recovered pasa_asmbl_15375.p1, internal, 43116, 43178
-recovered pasa_asmbl_15375.p1, internal, 43306, 43360
-recovered pasa_asmbl_15375.p1, internal, 43520, 43660
-recovered pasa_asmbl_15375.p1, internal, 43800, 43874
Couldn't classify 147221, 147242
Sorry, prediction pasa_asmbl_15365.p1 fails validation.
(CTG)	 AG	147221-147242	GT	TGG
(TGC)	 AG	148765-148829	GT	AGG
(GAG)	 AG	150742-150852	GT	AGG
(GCT)	 AG	151573-151663	GT	ATG
(TTG)	 AG	153140-153227	GT	AGG
(CTA)	 AG	154942-155011	GT	AGG
(ACG)	 AG	155788-155880	GT	AGG
(TTT)	 AG	156251-156454	GT	CGG
(CAG)	 AG	158377-158505	GT	AGG
(GCT)	 AG	158853-158930	GT	AGG
(ATG)	 AG	159399-159473	GT	TGG
(GAC)	 AG	159575-159616	GT	CAG
(ACA)	 AG	159830-159949	TC	AAT
-recovered pasa_asmbl_15365.p1, initial, 159399, 159473
-recovered pasa_asmbl_15365.p1, terminal, 159830, 159949
-recovered pasa_asmbl_15365.p1, internal, 147221, 147242
-recovered pasa_asmbl_15365.p1, internal, 148765, 148829
-recovered pasa_asmbl_15365.p1, internal, 150742, 150852
-recovered pasa_asmbl_15365.p1, internal, 151573, 151663
-recovered pasa_asmbl_15365.p1, internal, 153140, 153227
-recovered pasa_asmbl_15365.p1, internal, 154942, 155011
-recovered pasa_asmbl_15365.p1, internal, 155788, 155880
-recovered pasa_asmbl_15365.p1, internal, 156251, 156454
-recovered pasa_asmbl_15365.p1, internal, 158377, 158505
-recovered pasa_asmbl_15365.p1, internal, 158853, 158930
-recovered pasa_asmbl_15365.p1, internal, 159399, 159473
-recovered pasa_asmbl_15365.p1, internal, 159575, 159616
Valid prediction for pasa_asmbl_15957.p1
Valid prediction for pasa_asmbl_15368.p1
Valid prediction for GlimmerHMM_glimmerT_37406-T1
Valid prediction for GlimmerHMM_glimmerT_37395-T1
Valid prediction for snap_scaffold_15-snap.1798-T1
Valid prediction for GeneMark_model.64343_t
Valid prediction for GeneMark_model.64355_t
Valid prediction for Augustus_model.g25064.t1
Valid prediction for snap_scaffold_15-snap.1814-T1
Valid prediction for GlimmerHMM_glimmerT_37400-T1
Valid prediction for GlimmerHMM_glimmerT_37387-T1
Valid prediction for GlimmerHMM_glimmerT_37393-T1
Valid prediction for GeneMark_model.64352_t
Valid prediction for CodingQuarry_transcript_18031-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30992, rend_intergenic: 18873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55069, rend_intergenic: 43845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157830, rend_intergenic: 154089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197799, rend_intergenic: 188568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203631
-exon list size: 376


building trellis

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18.0    
18.3    
18.5    
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27.0    
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28.6    
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29.1    
29.4    
29.6    
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31.0    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 30992, rend_intergenic: 18873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55069, rend_intergenic: 43845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157830, rend_intergenic: 154089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197799, rend_intergenic: 188568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16783
-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
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15518
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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