-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_1820687-2129724

-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.424-T1
Valid prediction for GeneMark_model.19696_t
Valid prediction for Augustus_model.g7751.t1
Valid prediction for GeneMark_model.19700_t
Valid prediction for GeneMark_model.19681_t
Valid prediction for GeneMark_model.19772_t
Valid prediction for GeneMark_model.19746_t
Valid prediction for snap_scaffold_5-snap.418-T1
Valid prediction for Augustus_model.g7747.t1
Valid prediction for GeneMark_model.19753_t
Valid prediction for Augustus_model.g7749.t1
Valid prediction for snap_scaffold_5-snap.410-T1
Valid prediction for GeneMark_model.19759_t
Valid prediction for GeneMark_model.19679_t
Valid prediction for GlimmerHMM_glimmerT_11788-T1
Valid prediction for GeneMark_model.19766_t
Valid prediction for snap_scaffold_5-snap.379-T1
Valid prediction for snap_scaffold_5-snap.395-T1
Valid prediction for snap_scaffold_5-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_11783-T1
Valid prediction for GlimmerHMM_glimmerT_11770-T1
Valid prediction for snap_scaffold_5-snap.421-T1
Valid prediction for snap_scaffold_5-snap.369-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.390-T1
Valid prediction for snap_scaffold_5-snap.375-T1
Couldn't classify 216305, 216754
Sorry, prediction pasa_asmbl_43819.p1 fails validation.
(AGC)	 AC	216305-216754	AT	GAA
Valid prediction for GeneMark_model.19731_t
Valid prediction for Augustus_model.g7758.t1
Valid prediction for GlimmerHMM_glimmerT_11791-T1
Valid prediction for GeneMark_model.19686_t
Valid prediction for GeneMark_model.19687_t
Valid prediction for GlimmerHMM_glimmerT_11778-T1
Valid prediction for GeneMark_model.19722_t
Valid prediction for GeneMark_model.19698_t
Valid prediction for snap_scaffold_5-snap.376-T1
Valid prediction for snap_scaffold_5-snap.423-T1
Valid prediction for GlimmerHMM_glimmerT_11781-T1
Valid prediction for GeneMark_model.19767_t
Valid prediction for GeneMark_model.19735_t
Valid prediction for Augustus_model.g7756.t1
Valid prediction for GlimmerHMM_glimmerT_11775-T1
Valid prediction for GeneMark_model.19720_t
Valid prediction for GeneMark_model.19716_t
Valid prediction for GeneMark_model.19748_t
Valid prediction for GlimmerHMM_glimmerT_11786-T1
Valid prediction for snap_scaffold_5-snap.400-T1
Valid prediction for GeneMark_model.19702_t
Valid prediction for Augustus_model.g7754.t1
Valid prediction for GeneMark_model.19729_t
Valid prediction for GeneMark_model.19714_t
Valid prediction for GlimmerHMM_glimmerT_11793-T1
Valid prediction for GlimmerHMM_glimmerT_11790-T1
Valid prediction for snap_scaffold_5-snap.404-T1
Valid prediction for snap_scaffold_5-snap.417-T1
Valid prediction for GeneMark_model.19733_t
Valid prediction for snap_scaffold_5-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_11780-T1
Valid prediction for snap_scaffold_5-snap.383-T1
Valid prediction for GeneMark_model.19769_t
Valid prediction for snap_scaffold_5-snap.386-T1
Valid prediction for snap_scaffold_5-snap.409-T1
Valid prediction for snap_scaffold_5-snap.399-T1
Valid prediction for GeneMark_model.19712_t
Valid prediction for GeneMark_model.19750_t
Valid prediction for snap_scaffold_5-snap.422-T1
Valid prediction for GeneMark_model.19706_t
Valid prediction for snap_scaffold_5-snap.408-T1
Valid prediction for snap_scaffold_5-snap.393-T1
Valid prediction for GeneMark_model.19678_t
Valid prediction for GeneMark_model.19691_t
Valid prediction for GeneMark_model.19741_t
Valid prediction for Augustus_model.g7746.t1
Valid prediction for GeneMark_model.19739_t
Valid prediction for GeneMark_model.19763_t
Valid prediction for GlimmerHMM_glimmerT_11774-T1
Valid prediction for GeneMark_model.19718_t
Valid prediction for snap_scaffold_5-snap.380-T1
Valid prediction for GeneMark_model.19670_t
Valid prediction for snap_scaffold_5-snap.368-T1
Valid prediction for Augustus_model.g7750.t1
Valid prediction for snap_scaffold_5-snap.389-T1
Valid prediction for snap_scaffold_5-snap.371-T1
Valid prediction for GeneMark_model.19675_t
Valid prediction for GeneMark_model.19689_t
Valid prediction for GeneMark_model.19760_t
Valid prediction for snap_scaffold_5-snap.416-T1
Valid prediction for GeneMark_model.19762_t
Valid prediction for GeneMark_model.19758_t
Valid prediction for GeneMark_model.19768_t
Valid prediction for GeneMark_model.19710_t
Valid prediction for GeneMark_model.19755_t
Valid prediction for GeneMark_model.19745_t
Valid prediction for GeneMark_model.19726_t
Valid prediction for snap_scaffold_5-snap.412-T1
Valid prediction for GeneMark_model.19704_t
Valid prediction for snap_scaffold_5-snap.415-T1
Valid prediction for GeneMark_model.19674_t
Valid prediction for GeneMark_model.19724_t
Valid prediction for GeneMark_model.19684_t
Valid prediction for snap_scaffold_5-snap.392-T1
Valid prediction for snap_scaffold_5-snap.402-T1
Valid prediction for snap_scaffold_5-snap.407-T1
Valid prediction for GeneMark_model.19693_t
Valid prediction for GlimmerHMM_glimmerT_11779-T1
Valid prediction for GeneMark_model.19770_t
Valid prediction for GeneMark_model.19671_t
Valid prediction for Augustus_model.g7748.t1
Valid prediction for GeneMark_model.19682_t
Valid prediction for GeneMark_model.19737_t
Valid prediction for GeneMark_model.19743_t
Valid prediction for GlimmerHMM_glimmerT_11796-T1
Valid prediction for GeneMark_model.19708_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 GeneMark_model.19695_t
Valid prediction for Augustus_model.g7761.t1
Valid prediction for GeneMark_model.19707_t
Valid prediction for GeneMark_model.19690_t
Valid prediction for snap_scaffold_5-snap.378-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.19683_t
Valid prediction for snap_scaffold_5-snap.398-T1
Valid prediction for snap_scaffold_5-snap.420-T1
Valid prediction for snap_scaffold_5-snap.405-T1
Valid prediction for GeneMark_model.19749_t
Valid prediction for GeneMark_model.19744_t
Valid prediction for GeneMark_model.19747_t
Valid prediction for snap_scaffold_5-snap.373-T1
Valid prediction for snap_scaffold_5-snap.414-T1
Valid prediction for snap_scaffold_5-snap.401-T1
Valid prediction for GeneMark_model.19761_t
Valid prediction for GeneMark_model.19752_t
Valid prediction for GeneMark_model.19738_t
Valid prediction for snap_scaffold_5-snap.406-T1
Valid prediction for Augustus_model.g7760.t1
Valid prediction for GeneMark_model.19703_t
Valid prediction for snap_scaffold_5-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_11795-T1
Valid prediction for GeneMark_model.19694_t
Valid prediction for GlimmerHMM_glimmerT_11787-T1
Valid prediction for GeneMark_model.19717_t
Valid prediction for snap_scaffold_5-snap.382-T1
Valid prediction for GeneMark_model.19672_t
Valid prediction for GeneMark_model.19705_t
Valid prediction for GeneMark_model.19676_t
Valid prediction for snap_scaffold_5-snap.374-T1
Valid prediction for Augustus_model.g7745.t1
Valid prediction for GlimmerHMM_glimmerT_11771-T1
Valid prediction for GeneMark_model.19765_t
Valid prediction for Augustus_model.g7752.t1
Valid prediction for snap_scaffold_5-snap.370-T1
Valid prediction for GeneMark_model.19699_t
Valid prediction for snap_scaffold_5-snap.413-T1
Valid prediction for snap_scaffold_5-snap.397-T1
Valid prediction for GeneMark_model.19751_t
Valid prediction for GeneMark_model.19685_t
Valid prediction for Augustus_model.g7753.t1
Valid prediction for GlimmerHMM_glimmerT_11768-T1
Valid prediction for GeneMark_model.19723_t
Valid prediction for GeneMark_model.19680_t
Valid prediction for GeneMark_model.19673_t
Valid prediction for GeneMark_model.19709_t
Valid prediction for GeneMark_model.19697_t
Valid prediction for GlimmerHMM_glimmerT_11785-T1
Valid prediction for Augustus_model.g7759.t1
Valid prediction for GeneMark_model.19721_t
Valid prediction for snap_scaffold_5-snap.388-T1
Valid prediction for snap_scaffold_5-snap.425-T1
Valid prediction for GeneMark_model.19734_t
Valid prediction for Augustus_model.g7755.t1
Valid prediction for GeneMark_model.19725_t
Valid prediction for snap_scaffold_5-snap.384-T1
Valid prediction for GeneMark_model.19771_t
Valid prediction for GeneMark_model.19740_t
Valid prediction for GeneMark_model.19742_t
Valid prediction for GlimmerHMM_glimmerT_11772-T1
Valid prediction for GeneMark_model.19756_t
Couldn't classify 76403, 76458
Couldn't classify 81166, 81260
Sorry, prediction pasa_asmbl_46345.p1 fails validation.
(AAT)	 AG	76403-76458	GT	ATG
(GGG)	 AG	77407-77494	GT	GGG
(GAT)	 AG	77629-77748	GT	AGG
(GTG)	 AG	78147-78244	GT	AGG
(GAC)	 AG	80359-80477	GT	ATG
(GTT)	 AG	81166-81260	GC	ACG
-recovered pasa_asmbl_46345.p1, internal, 76403, 76458
-recovered pasa_asmbl_46345.p1, internal, 77407, 77494
-recovered pasa_asmbl_46345.p1, internal, 77629, 77748
-recovered pasa_asmbl_46345.p1, internal, 78147, 78244
-recovered pasa_asmbl_46345.p1, internal, 80359, 80477
-recovered pasa_asmbl_46345.p1, internal, 81166, 81260
Valid prediction for GlimmerHMM_glimmerT_11782-T1
Valid prediction for GeneMark_model.19730_t
Valid prediction for GeneMark_model.19719_t
Valid prediction for GeneMark_model.19677_t
Valid prediction for GeneMark_model.19688_t
Valid prediction for snap_scaffold_5-snap.367-T1
Valid prediction for snap_scaffold_5-snap.381-T1
Valid prediction for snap_scaffold_5-snap.394-T1
Valid prediction for GeneMark_model.19757_t
Valid prediction for GeneMark_model.19764_t
Valid prediction for GeneMark_model.19701_t
Valid prediction for snap_scaffold_5-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_11792-T1
Valid prediction for snap_scaffold_5-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_11777-T1
Valid prediction for GeneMark_model.19728_t
Valid prediction for GeneMark_model.19732_t
Valid prediction for snap_scaffold_5-snap.377-T1
Valid prediction for snap_scaffold_5-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_11773-T1
Valid prediction for GlimmerHMM_glimmerT_11769-T1
Valid prediction for Augustus_model.g7757.t1
Valid prediction for GeneMark_model.19713_t
Couldn't classify 150088, 150156
Sorry, prediction GeneMark_model.19727_t fails validation.
(GGA)	 AG	150088-150156	GT	ACG
(AGG)	 AG	150177-150338	GT	GAG
(TGA)	 AG	150371-150391	GT	GTG
(AGA)	 AG	150413-150427	GT	AGG
(CGT)	 AG	150463-150469	AC	GAA
-recovered GeneMark_model.19727_t, terminal, 150463, 150469
-recovered GeneMark_model.19727_t, internal, 150088, 150156
-recovered GeneMark_model.19727_t, internal, 150177, 150338
-recovered GeneMark_model.19727_t, internal, 150371, 150391
-recovered GeneMark_model.19727_t, internal, 150413, 150427
Valid prediction for snap_scaffold_5-snap.372-T1
Couldn't classify 84953, 85057
Sorry, prediction pasa_asmbl_46353.p2 fails validation.
(GGG)	 TG	84953-85057	GT	AGG
(GAG)	 AG	85492-85573	GT	TGG
(GAC)	 AG	86142-86280	GT	AGG
(CCT)	 AG	87526-87568	AA	AGA
-recovered pasa_asmbl_46353.p2, terminal, 87526, 87568
-recovered pasa_asmbl_46353.p2, internal, 85492, 85573
-recovered pasa_asmbl_46353.p2, internal, 86142, 86280
Valid prediction for GeneMark_model.19692_t
Valid prediction for GeneMark_model.19711_t
Valid prediction for GlimmerHMM_glimmerT_11794-T1
Valid prediction for GlimmerHMM_glimmerT_11784-T1
Valid prediction for GlimmerHMM_glimmerT_11776-T1
Valid prediction for GlimmerHMM_glimmerT_11789-T1
Valid prediction for snap_scaffold_5-snap.403-T1
Valid prediction for GeneMark_model.19736_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17662, rend_intergenic: 12125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38397, rend_intergenic: 33165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51299, rend_intergenic: 47097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62030, rend_intergenic: 58140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65284, rend_intergenic: 62297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89205, rend_intergenic: 65498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94720, rend_intergenic: 91137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109772, rend_intergenic: 99936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126116, rend_intergenic: 117282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142190, rend_intergenic: 126141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155366, rend_intergenic: 149846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158771, rend_intergenic: 155589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174233, rend_intergenic: 166718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201583, rend_intergenic: 176141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209185, rend_intergenic: 208977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211908, rend_intergenic: 211448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214120, rend_intergenic: 213181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216675, rend_intergenic: 215964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235350, rend_intergenic: 220858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240151, rend_intergenic: 236503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246578, rend_intergenic: 242024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269259, rend_intergenic: 246589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283006, rend_intergenic: 275027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 303111, rend_intergenic: 285639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306688, rend_intergenic: 304753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 309038
-exon list size: 1488


building trellis

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54.0    
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64.0    
64.0    
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65.0    
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68.1    
68.1    
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69.0    
69.1    
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72.1    
72.1    
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72.6    
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72.9    
73.0    
73.0    
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76.9    
77.0    
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77.1    
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77.2    
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99.0    
99.1    
99.1    
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99.3    
99.4    
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99.9    
99.9    
-found 65 predictions from path traversal
Error with prediction: snap lend_intergenic: 17662, rend_intergenic: 12125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38397, rend_intergenic: 33165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51299, rend_intergenic: 47097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62030, rend_intergenic: 58140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65284, rend_intergenic: 62297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89205, rend_intergenic: 65498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94720, rend_intergenic: 91137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109772, rend_intergenic: 99936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126116, rend_intergenic: 117282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142190, rend_intergenic: 126141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155366, rend_intergenic: 149846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158771, rend_intergenic: 155589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174233, rend_intergenic: 166718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201583, rend_intergenic: 176141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209185, rend_intergenic: 208977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211908, rend_intergenic: 211448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214120, rend_intergenic: 213181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216675, rend_intergenic: 215964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235350, rend_intergenic: 220858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240151, rend_intergenic: 236503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246578, rend_intergenic: 242024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269259, rend_intergenic: 246589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283006, rend_intergenic: 275027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 303111, rend_intergenic: 285639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306688, rend_intergenic: 304753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12390
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 - 12189
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 - 11981
-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
	-no exons in range 1730 - 11981