-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_5229678-5436269

-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 GlimmerHMM_glimmerT_625-T1
Valid prediction for Augustus_model.g495.t1
Valid prediction for pasa_asmbl_1721.p1
Valid prediction for GlimmerHMM_glimmerT_646-T1
Valid prediction for Augustus_model.g488.t1
Valid prediction for GlimmerHMM_glimmerT_641-T1
Valid prediction for snap_scaffold_1-snap.795-T1
Valid prediction for snap_scaffold_1-snap.809-T1
Valid prediction for snap_scaffold_1-snap.798-T1
Valid prediction for HiQ_model.g493.t1
Valid prediction for GlimmerHMM_glimmerT_627-T1
Valid prediction for GlimmerHMM_glimmerT_643-T1
Couldn't classify 81736, 81835
Sorry, prediction pasa_asmbl_2749.p1 fails validation.
(GTC)	 CT	81736-81835	GT	CAG
(CTC)	 AG	82653-82903	AG	GAA
-recovered pasa_asmbl_2749.p1, terminal, 82653, 82903
Valid prediction for Augustus_model.g490.t1
Valid prediction for GlimmerHMM_glimmerT_633-T1
Valid prediction for snap_scaffold_1-snap.814-T1
Valid prediction for snap_scaffold_1-snap.812-T1
Valid prediction for snap_scaffold_1-snap.807-T1
Valid prediction for snap_scaffold_1-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_637-T1
Valid prediction for GlimmerHMM_glimmerT_632-T1
Valid prediction for CodingQuarry_transcript_2607-T1
Valid prediction for snap_scaffold_1-snap.805-T1
Valid prediction for Augustus_model.g491.t1
Couldn't classify 27911, 28006
Couldn't classify 28885, 28923
Sorry, prediction pasa_asmbl_2795.p1 fails validation.
(ATC)	 TG	27911-28006	GT	AGG
(ATG)	 AG	28251-28365	GT	AGG
(GAA)	 AG	28502-28626	GT	GAG
(ATC)	 AG	28885-28923	GA	GGG
-recovered pasa_asmbl_2795.p1, initial, 28251, 28365
-recovered pasa_asmbl_2795.p1, internal, 28251, 28365
-recovered pasa_asmbl_2795.p1, internal, 28502, 28626
Valid prediction for GlimmerHMM_glimmerT_642-T1
Valid prediction for Augustus_model.g496.t1
Valid prediction for snap_scaffold_1-snap.808-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.826-T1
Valid prediction for snap_scaffold_1-snap.803-T1
Valid prediction for GlimmerHMM_glimmerT_621-T1
Valid prediction for GlimmerHMM_glimmerT_626-T1
Valid prediction for GlimmerHMM_glimmerT_620-T1
Valid prediction for snap_scaffold_1-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_628-T1
Valid prediction for snap_scaffold_1-snap.806-T1
Valid prediction for GlimmerHMM_glimmerT_623-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_1-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_630-T1
Valid prediction for snap_scaffold_1-snap.792-T1
Valid prediction for Augustus_model.g505.t1
Valid prediction for snap_scaffold_1-snap.821-T1
Valid prediction for snap_scaffold_1-snap.824-T1
Valid prediction for snap_scaffold_1-snap.811-T1
Valid prediction for GlimmerHMM_glimmerT_622-T1
Valid prediction for snap_scaffold_1-snap.822-T1
Valid prediction for Augustus_model.g494.t1
Valid prediction for GlimmerHMM_glimmerT_635-T1
Valid prediction for GlimmerHMM_glimmerT_645-T1
Valid prediction for snap_scaffold_1-snap.796-T1
Valid prediction for snap_scaffold_1-snap.819-T1
Valid prediction for GlimmerHMM_glimmerT_624-T1
Valid prediction for Augustus_model.g501.t1
Valid prediction for Augustus_model.g504.t1
Valid prediction for Augustus_model.g486.t1
Valid prediction for Augustus_model.g487.t1
Valid prediction for snap_scaffold_1-snap.820-T1
Valid prediction for Augustus_model.g489.t1
Couldn't classify 103441, 103521
Sorry, prediction pasa_asmbl_260.p1 fails validation.
(ATG)	 CG	90208-90373	GT	TGG
(GCG)	 AG	91163-91217	GT	GTG
(AGA)	 AG	91311-91428	GT	AGG
(ATA)	 AG	91815-91892	GT	CGG
(GAT)	 AG	91978-92094	GT	AGG
(ATC)	 AG	92789-92935	GT	AGG
(GTG)	 AG	93065-93153	GT	TGG
(GGG)	 AG	93474-93595	GT	AGG
(GAT)	 AG	94081-94171	GT	AGG
(ACT)	 AG	94295-94439	GT	TGG
(GGC)	 AG	94663-94821	GT	TGG
(AAC)	 AG	97183-97377	GT	AGG
(CTG)	 AG	97767-98003	GT	ATG
(TCC)	 AG	98631-98746	GT	GGG
(AGG)	 AG	100581-100656	GT	AGG
(ATC)	 AG	103441-103521	GT	CCG
-recovered pasa_asmbl_260.p1, initial, 90208, 90373
-recovered pasa_asmbl_260.p1, internal, 91163, 91217
-recovered pasa_asmbl_260.p1, internal, 91311, 91428
-recovered pasa_asmbl_260.p1, internal, 91815, 91892
-recovered pasa_asmbl_260.p1, internal, 91978, 92094
-recovered pasa_asmbl_260.p1, internal, 92789, 92935
-recovered pasa_asmbl_260.p1, internal, 93065, 93153
-recovered pasa_asmbl_260.p1, internal, 93474, 93595
-recovered pasa_asmbl_260.p1, internal, 94081, 94171
-recovered pasa_asmbl_260.p1, internal, 94295, 94439
-recovered pasa_asmbl_260.p1, internal, 94663, 94821
-recovered pasa_asmbl_260.p1, internal, 97183, 97377
-recovered pasa_asmbl_260.p1, internal, 97767, 98003
-recovered pasa_asmbl_260.p1, internal, 98631, 98746
-recovered pasa_asmbl_260.p1, internal, 100581, 100656
-recovered pasa_asmbl_260.p1, internal, 103441, 103521
Valid prediction for snap_scaffold_1-snap.791-T1
Valid prediction for Augustus_model.g498.t1
Valid prediction for GlimmerHMM_glimmerT_639-T1
Valid prediction for Augustus_model.g506.t1
Valid prediction for GlimmerHMM_glimmerT_619-T1
Valid prediction for snap_scaffold_1-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_644-T1
Valid prediction for GlimmerHMM_glimmerT_640-T1
Valid prediction for Augustus_model.g500.t1
Valid prediction for GlimmerHMM_glimmerT_636-T1
Valid prediction for snap_scaffold_1-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_634-T1
Valid prediction for snap_scaffold_1-snap.801-T1
Valid prediction for Augustus_model.g497.t1
Valid prediction for snap_scaffold_1-snap.825-T1
Valid prediction for GlimmerHMM_glimmerT_631-T1
Valid prediction for snap_scaffold_1-snap.813-T1
Valid prediction for Augustus_model.g499.t1
Valid prediction for snap_scaffold_1-snap.793-T1
Valid prediction for snap_scaffold_1-snap.823-T1
Valid prediction for Augustus_model.g507.t1
Valid prediction for Augustus_model.g502.t1
Valid prediction for snap_scaffold_1-snap.794-T1
Valid prediction for snap_scaffold_1-snap.797-T1
Valid prediction for Augustus_model.g508.t1
Valid prediction for GlimmerHMM_glimmerT_629-T1
Valid prediction for snap_scaffold_1-snap.789-T1
Valid prediction for snap_scaffold_1-snap.818-T1
Valid prediction for snap_scaffold_1-snap.800-T1
Valid prediction for snap_scaffold_1-snap.815-T1
Valid prediction for Augustus_model.g503.t1
Valid prediction for Augustus_model.g492.t1
Valid prediction for snap_scaffold_1-snap.790-T1
Valid prediction for GlimmerHMM_glimmerT_638-T1
Valid prediction for snap_scaffold_1-snap.816-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24900, rend_intergenic: 20547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59382, rend_intergenic: 56698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99855, rend_intergenic: 89594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101375, rend_intergenic: 100257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104852, rend_intergenic: 101743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109486, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206592
-exon list size: 345


building trellis

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25.9    
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30.0    
30.3    
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30.8    
31.1    
31.4    
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32.0    
32.3    
32.6    
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33.4    
33.7    
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34.6    
34.9    
35.2    
35.4    
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36.6    
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38.6    
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39.2    
39.5    
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40.3    
40.6    
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42.4    
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43.2    
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44.4    
44.7    
45.0    
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45.8    
46.1    
46.4    
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47.0    
47.3    
47.6    
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48.1    
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50.7    
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52.7    
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64.0    
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84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
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86.2    
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87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
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91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
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93.9    
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95.1    
95.4    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 24900, rend_intergenic: 20547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59382, rend_intergenic: 56698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99855, rend_intergenic: 89594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101375, rend_intergenic: 100257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104852, rend_intergenic: 101743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109486, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 193520 - 206592
-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

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