-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_18964006-19195790

-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_5-snap.3570-T1
Couldn't classify 26526, 26950
Sorry, prediction pasa_asmbl_46299.p1 fails validation.
(ATG)	 AG	24867-25064	GT	TGG
(GTT)	 AG	25360-25633	GT	TGG
(GCT)	 AG	26308-26385	GT	TGG
(GGG)	 AG	26526-26950	AG	ACA
-recovered pasa_asmbl_46299.p1, initial, 24867, 25064
-recovered pasa_asmbl_46299.p1, internal, 24867, 25064
-recovered pasa_asmbl_46299.p1, internal, 25360, 25633
-recovered pasa_asmbl_46299.p1, internal, 26308, 26385
Valid prediction for GlimmerHMM_glimmerT_13751-T1
Valid prediction for snap_scaffold_5-snap.3578-T1
Couldn't classify 195511, 195682
Couldn't classify 195919, 196073
Sorry, prediction pasa_asmbl_46336.p1 fails validation.
(CTC)	 CC	195511-195682	GT	TGG
(GTC)	 AG	195919-196073	AC	CCA
Valid prediction for snap_scaffold_5-snap.3548-T1
Valid prediction for snap_scaffold_5-snap.3563-T1
Valid prediction for Augustus_model.g9144.t1
Valid prediction for CodingQuarry_transcript_52479-T1
Valid prediction for GlimmerHMM_glimmerT_13764-T1
Valid prediction for HiQ_model.g9136.t1
Valid prediction for snap_scaffold_5-snap.3545-T1
Valid prediction for snap_scaffold_5-snap.3567-T1
Valid prediction for Augustus_model.g9148.t1
Valid prediction for GlimmerHMM_glimmerT_13763-T1
Valid prediction for snap_scaffold_5-snap.3580-T1
Valid prediction for GlimmerHMM_glimmerT_13753-T1
Valid prediction for Augustus_model.g9138.t1
Valid prediction for snap_scaffold_5-snap.3556-T1
Valid prediction for snap_scaffold_5-snap.3576-T1
Valid prediction for snap_scaffold_5-snap.3568-T1
Valid prediction for GlimmerHMM_glimmerT_13757-T1
Valid prediction for pasa_asmbl_46297.p1
Valid prediction for pasa_asmbl_46303.p1
Valid prediction for GlimmerHMM_glimmerT_13766-T1
Valid prediction for GlimmerHMM_glimmerT_13760-T1
Valid prediction for snap_scaffold_5-snap.3572-T1
Valid prediction for GlimmerHMM_glimmerT_13767-T1
Valid prediction for Augustus_model.g9142.t1
Valid prediction for GlimmerHMM_glimmerT_13771-T1
Valid prediction for snap_scaffold_5-snap.3577-T1
Valid prediction for snap_scaffold_5-snap.3559-T1
Valid prediction for HiQ_model.g9134.t1
Valid prediction for Augustus_model.g9145.t1
Valid prediction for snap_scaffold_5-snap.3565-T1
Valid prediction for GlimmerHMM_glimmerT_13772-T1
Valid prediction for GlimmerHMM_glimmerT_13761-T1
Valid prediction for Augustus_model.g9147.t1
Valid prediction for Augustus_model.g9143.t1
Valid prediction for GlimmerHMM_glimmerT_13758-T1
Valid prediction for snap_scaffold_5-snap.3547-T1
Valid prediction for GlimmerHMM_glimmerT_13770-T1
Valid prediction for GlimmerHMM_glimmerT_13759-T1
Valid prediction for Augustus_model.g9153.t1
Valid prediction for snap_scaffold_5-snap.3562-T1
Valid prediction for snap_scaffold_5-snap.3550-T1
Valid prediction for GlimmerHMM_glimmerT_13749-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_5-snap.3573-T1
Valid prediction for Augustus_model.g9151.t1
Couldn't classify 188999, 189107
Couldn't classify 189849, 189946
Sorry, prediction pasa_asmbl_45015.p1 fails validation.
(CAC)	 GC	188999-189107	GT	AGG
(GTC)	 AG	189659-189769	GT	TGG
(TTA)	 AG	189849-189946	AC	CAA
-recovered pasa_asmbl_45015.p1, internal, 189659, 189769
Valid prediction for Augustus_model.g9152.t1
Valid prediction for snap_scaffold_5-snap.3561-T1
Valid prediction for GlimmerHMM_glimmerT_13769-T1
Valid prediction for Augustus_model.g9150.t1
Valid prediction for GlimmerHMM_glimmerT_13752-T1
Valid prediction for CodingQuarry_transcript_52483-T1
Valid prediction for snap_scaffold_5-snap.3553-T1
Couldn't classify 160932, 161094
Sorry, prediction pasa_asmbl_44892.p1 fails validation.
(GGG)	 AC	160932-161094	GT	TGG
(GGC)	 AG	163831-163895	GT	AGG
(GTC)	 AG	164225-164287	GT	AGG
(GCC)	 AG	166280-166291	GT	TGG
(GAC)	 AG	166684-166794	GT	GGG
(TTT)	 AG	166888-166931	GT	GAG
(CAT)	 AG	167054-167115	GT	TAG
(GTT)	 AG	167225-167361	GT	CGG
(TTC)	 AG	167554-167727	GT	GGG
(GCG)	 AG	168904-169044	GT	AGG
(ACG)	 AG	169194-169346	GT	AGG
(GTG)	 AG	169907-170020	CG	AAC
-recovered pasa_asmbl_44892.p1, terminal, 169907, 170020
-recovered pasa_asmbl_44892.p1, internal, 163831, 163895
-recovered pasa_asmbl_44892.p1, internal, 164225, 164287
-recovered pasa_asmbl_44892.p1, internal, 166280, 166291
-recovered pasa_asmbl_44892.p1, internal, 166684, 166794
-recovered pasa_asmbl_44892.p1, internal, 166888, 166931
-recovered pasa_asmbl_44892.p1, internal, 167054, 167115
-recovered pasa_asmbl_44892.p1, internal, 167225, 167361
-recovered pasa_asmbl_44892.p1, internal, 167554, 167727
-recovered pasa_asmbl_44892.p1, internal, 168904, 169044
-recovered pasa_asmbl_44892.p1, internal, 169194, 169346
Valid prediction for snap_scaffold_5-snap.3574-T1
Valid prediction for Augustus_model.g9140.t1
Valid prediction for HiQ_model.g9139.t1
Valid prediction for CodingQuarry_transcript_52480-T1
Valid prediction for snap_scaffold_5-snap.3579-T1
Valid prediction for snap_scaffold_5-snap.3560-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3555-T1
Valid prediction for snap_scaffold_5-snap.3566-T1
Valid prediction for snap_scaffold_5-snap.3549-T1
Valid prediction for GlimmerHMM_glimmerT_13765-T1
Valid prediction for Augustus_model.g9135.t1
Valid prediction for GlimmerHMM_glimmerT_13754-T1
Valid prediction for CodingQuarry_transcript_52485-T1
Couldn't classify 48401, 48579
Sorry, prediction pasa_asmbl_44895.p1 fails validation.
(CTT)	 AC	48401-48579	GT	AGG
(GTT)	 AG	48831-48970	GT	GCG
(AGA)	 AG	49071-49140	GT	AGG
(GTA)	 AG	49252-49357	GT	AGG
(GGT)	 AG	50062-50160	GT	TAG
(TCA)	 AG	50246-50329	GT	CTG
(GGA)	 AG	50560-50682	AT	AGA
-recovered pasa_asmbl_44895.p1, terminal, 50560, 50682
-recovered pasa_asmbl_44895.p1, internal, 48831, 48970
-recovered pasa_asmbl_44895.p1, internal, 49071, 49140
-recovered pasa_asmbl_44895.p1, internal, 49252, 49357
-recovered pasa_asmbl_44895.p1, internal, 50062, 50160
-recovered pasa_asmbl_44895.p1, internal, 50246, 50329
Valid prediction for GlimmerHMM_glimmerT_13756-T1
Valid prediction for snap_scaffold_5-snap.3554-T1
Valid prediction for snap_scaffold_5-snap.3546-T1
Valid prediction for GlimmerHMM_glimmerT_13750-T1
Valid prediction for snap_scaffold_5-snap.3551-T1
Valid prediction for CodingQuarry_transcript_52482-T1
Couldn't classify 190222, 190266
Sorry, prediction pasa_asmbl_44882.p1 fails validation.
(GTG)	 GG	190222-190266	GT	AGG
(AAC)	 AG	190342-190442	GT	AGG
(GTT)	 AG	191618-191828	CG	AGC
-recovered pasa_asmbl_44882.p1, terminal, 191618, 191828
-recovered pasa_asmbl_44882.p1, internal, 190342, 190442
Couldn't classify 167182, 167361
Sorry, prediction pasa_asmbl_44894.p1 fails validation.
(GTC)	 GT	167182-167361	GT	CGG
(TTC)	 AG	167554-167727	GT	GGG
(GCG)	 AG	168904-169044	GT	AGG
(ACG)	 AG	169194-169346	GT	AGG
(GTG)	 AG	169907-170020	CG	AAC
-recovered pasa_asmbl_44894.p1, terminal, 169907, 170020
-recovered pasa_asmbl_44894.p1, internal, 167554, 167727
-recovered pasa_asmbl_44894.p1, internal, 168904, 169044
-recovered pasa_asmbl_44894.p1, internal, 169194, 169346
Valid prediction for GlimmerHMM_glimmerT_13762-T1
Valid prediction for snap_scaffold_5-snap.3575-T1
Valid prediction for Augustus_model.g9149.t1
Valid prediction for snap_scaffold_5-snap.3564-T1
Valid prediction for Augustus_model.g9154.t1
Valid prediction for Augustus_model.g9146.t1
Valid prediction for snap_scaffold_5-snap.3558-T1
Valid prediction for snap_scaffold_5-snap.3557-T1
Valid prediction for GlimmerHMM_glimmerT_13755-T1
Valid prediction for Augustus_model.g9137.t1
Valid prediction for GlimmerHMM_glimmerT_13768-T1
Valid prediction for snap_scaffold_5-snap.3552-T1
Valid prediction for Augustus_model.g9141.t1
Valid prediction for GlimmerHMM_glimmerT_13748-T1
Valid prediction for CodingQuarry_transcript_52481-T1
Valid prediction for snap_scaffold_5-snap.3571-T1
Valid prediction for GlimmerHMM_glimmerT_13773-T1
Valid prediction for snap_scaffold_5-snap.3569-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 93429, rend_intergenic: 86394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123068, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135863, rend_intergenic: 129308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167034, rend_intergenic: 162949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196091, rend_intergenic: 193497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227314, rend_intergenic: 224665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231785
-exon list size: 385


building trellis

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27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
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29.7    
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31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
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47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
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59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
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62.3    
62.5    
62.8    
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63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
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66.4    
66.7    
66.9    
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67.4    
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68.0    
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69.5    
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73.1    
73.4    
73.6    
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74.9    
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75.5    
75.7    
76.0    
76.2    
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76.7    
77.0    
77.3    
77.5    
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78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
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80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 93429, rend_intergenic: 86394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123068, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135863, rend_intergenic: 129308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167034, rend_intergenic: 162949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196091, rend_intergenic: 193497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227314, rend_intergenic: 224665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13634
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 12836
-exon list size: 1


building trellis

33.3    
66.7    
-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