-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_12354131-12494296

-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_2-snap.2391-T1
Couldn't classify 17895, 18064
Couldn't classify 24238, 24445
Sorry, prediction pasa_asmbl_24824.p1 fails validation.
(GGG)	 CA	17895-18064	GT	AGG
(GTA)	 AG	18468-18607	GT	AGG
(CCG)	 AG	18832-18930	GT	AGG
(ACG)	 AG	20601-21227	GT	AGG
(CTC)	 AG	23521-23598	GT	AAG
(ATT)	 AG	23835-23913	GT	AGG
(CTT)	 AG	24238-24445	GC	TGG
-recovered pasa_asmbl_24824.p1, internal, 18468, 18607
-recovered pasa_asmbl_24824.p1, internal, 18832, 18930
-recovered pasa_asmbl_24824.p1, internal, 20601, 21227
-recovered pasa_asmbl_24824.p1, internal, 23521, 23598
-recovered pasa_asmbl_24824.p1, internal, 23835, 23913
-recovered pasa_asmbl_24824.p1, internal, 24238, 24445
Valid prediction for GeneMark_model.7610_t
Valid prediction for GeneMark_model.7592_t
Valid prediction for GlimmerHMM_glimmerT_4736-T1
Valid prediction for Augustus_model.g3192.t1
Valid prediction for GeneMark_model.7608_t
Valid prediction for GeneMark_model.7624_t
Valid prediction for snap_scaffold_2-snap.2382-T1
Valid prediction for GeneMark_model.7605_t
Valid prediction for Augustus_model.g3185.t1
Valid prediction for snap_scaffold_2-snap.2400-T1
Valid prediction for GeneMark_model.7585_t
Valid prediction for GlimmerHMM_glimmerT_4754-T1
Valid prediction for snap_scaffold_2-snap.2387-T1
Valid prediction for GeneMark_model.7590_t
Valid prediction for snap_scaffold_2-snap.2386-T1
Valid prediction for GeneMark_model.7619_t
Valid prediction for Augustus_model.g3193.t1
Valid prediction for GlimmerHMM_glimmerT_4750-T1
Valid prediction for GlimmerHMM_glimmerT_4752-T1
Valid prediction for GeneMark_model.7595_t
Valid prediction for snap_scaffold_2-snap.2401-T1
Valid prediction for Augustus_model.g3189.t1
Valid prediction for snap_scaffold_2-snap.2406-T1
Valid prediction for GlimmerHMM_glimmerT_4753-T1
Valid prediction for GeneMark_model.7620_t
Valid prediction for snap_scaffold_2-snap.2374-T1
Valid prediction for GeneMark_model.7587_t
Valid prediction for snap_scaffold_2-snap.2379-T1
Valid prediction for Augustus_model.g3195.t1
Valid prediction for GeneMark_model.7615_t
Valid prediction for GeneMark_model.7600_t
Valid prediction for snap_scaffold_2-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_4738-T1
Valid prediction for snap_scaffold_2-snap.2398-T1
Valid prediction for Augustus_model.g3194.t1
Valid prediction for snap_scaffold_2-snap.2396-T1
Valid prediction for Augustus_model.g3197.t1
Valid prediction for snap_scaffold_2-snap.2402-T1
Valid prediction for snap_scaffold_2-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_4748-T1
Valid prediction for GlimmerHMM_glimmerT_4756-T1
Valid prediction for snap_scaffold_2-snap.2399-T1
Valid prediction for GeneMark_model.7612_t
Valid prediction for snap_scaffold_2-snap.2377-T1
Valid prediction for GeneMark_model.7603_t
Valid prediction for GeneMark_model.7622_t
Valid prediction for snap_scaffold_2-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_4739-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 GlimmerHMM_glimmerT_4758-T1
Valid prediction for Augustus_model.g3187.t1
Valid prediction for GlimmerHMM_glimmerT_4740-T1
Valid prediction for GlimmerHMM_glimmerT_4749-T1
Valid prediction for Augustus_model.g3198.t1
Valid prediction for snap_scaffold_2-snap.2390-T1
Valid prediction for GeneMark_model.7591_t
Valid prediction for GeneMark_model.7623_t
Valid prediction for snap_scaffold_2-snap.2388-T1
Couldn't classify 2064, 2366
Sorry, prediction pasa_asmbl_24830.p1 fails validation.
(CAT)	 AC	2064-2366	GG	GAG
Valid prediction for snap_scaffold_2-snap.2389-T1
Valid prediction for snap_scaffold_2-snap.2378-T1
Valid prediction for GeneMark_model.7609_t
Valid prediction for Augustus_model.g3184.t1
Valid prediction for Augustus_model.g3196.t1
Valid prediction for GeneMark_model.7617_t
Valid prediction for GeneMark_model.7598_t
Valid prediction for snap_scaffold_2-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_4755-T1
Valid prediction for snap_scaffold_2-snap.2375-T1
Valid prediction for GlimmerHMM_glimmerT_4751-T1
Valid prediction for GeneMark_model.7621_t
Valid prediction for Augustus_model.g3191.t1
Valid prediction for snap_scaffold_2-snap.2392-T1
Valid prediction for snap_scaffold_2-snap.2381-T1
Valid prediction for pasa_asmbl_24825.p1
Valid prediction for snap_scaffold_2-snap.2384-T1
Valid prediction for snap_scaffold_2-snap.2403-T1
Valid prediction for snap_scaffold_2-snap.2373-T1
Valid prediction for GeneMark_model.7613_t
Valid prediction for GlimmerHMM_glimmerT_4747-T1
Valid prediction for GeneMark_model.7616_t
Valid prediction for GlimmerHMM_glimmerT_4746-T1
Valid prediction for GeneMark_model.7601_t
Valid prediction for GeneMark_model.7593_t
Valid prediction for GlimmerHMM_glimmerT_4737-T1
Valid prediction for snap_scaffold_2-snap.2407-T1
Valid prediction for snap_scaffold_2-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_4744-T1
Valid prediction for GeneMark_model.7606_t
Valid prediction for snap_scaffold_2-snap.2404-T1
Couldn't classify 66004, 66175
Sorry, prediction pasa_asmbl_23480.p1 fails validation.
(GTG)	 CA	66004-66175	GT	CGG
(TGC)	 AG	66500-66691	GT	AGG
(TTA)	 AG	66931-67845	GT	TGG
(ATA)	 AG	68031-68207	GT	AGG
(CCT)	 AG	68492-68558	GT	AGG
(GAA)	 AG	68988-69217	GT	AGG
(TAT)	 AG	69481-69860	GT	GGG
(GTG)	 AG	70572-71147	GA	GAG
-recovered pasa_asmbl_23480.p1, terminal, 70572, 71147
-recovered pasa_asmbl_23480.p1, internal, 66500, 66691
-recovered pasa_asmbl_23480.p1, internal, 66931, 67845
-recovered pasa_asmbl_23480.p1, internal, 68031, 68207
-recovered pasa_asmbl_23480.p1, internal, 68492, 68558
-recovered pasa_asmbl_23480.p1, internal, 68988, 69217
-recovered pasa_asmbl_23480.p1, internal, 69481, 69860
Valid prediction for GeneMark_model.7607_t
Valid prediction for snap_scaffold_2-snap.2397-T1
Valid prediction for GeneMark_model.7614_t
Valid prediction for GeneMark_model.7588_t
Valid prediction for GeneMark_model.7596_t
Valid prediction for GlimmerHMM_glimmerT_4741-T1
Couldn't classify 56761, 56935
Couldn't classify 59070, 59164
Sorry, prediction pasa_asmbl_23481.p1 fails validation.
(GAC)	 CA	56761-56935	GT	AGG
(GTT)	 AG	58386-58511	GT	AAG
(AAT)	 AG	59070-59164	CT	AAC
-recovered pasa_asmbl_23481.p1, terminal, 58386, 58511
-recovered pasa_asmbl_23481.p1, internal, 58386, 58511
Valid prediction for GlimmerHMM_glimmerT_4745-T1
Valid prediction for GeneMark_model.7586_t
Valid prediction for snap_scaffold_2-snap.2405-T1
Valid prediction for GeneMark_model.7599_t
Valid prediction for GlimmerHMM_glimmerT_4743-T1
Valid prediction for snap_scaffold_2-snap.2395-T1
Valid prediction for Augustus_model.g3186.t1
Valid prediction for Augustus_model.g3188.t1
Valid prediction for GeneMark_model.7594_t
Valid prediction for GeneMark_model.7602_t
Valid prediction for GlimmerHMM_glimmerT_4742-T1
Valid prediction for GlimmerHMM_glimmerT_4757-T1
Valid prediction for GeneMark_model.7604_t
Valid prediction for snap_scaffold_2-snap.2380-T1
Valid prediction for Augustus_model.g3190.t1
Valid prediction for GlimmerHMM_glimmerT_4735-T1
Couldn't classify 112370, 112753
Sorry, prediction pasa_asmbl_23479.p1 fails validation.
(AAC)	 CA	112370-112753	GG	TCG
Valid prediction for GeneMark_model.7611_t
Valid prediction for GeneMark_model.7618_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6052, rend_intergenic: 4133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14943, rend_intergenic: 9210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17678, rend_intergenic: 16374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25274, rend_intergenic: 24509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46089, rend_intergenic: 44649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53877, rend_intergenic: 49921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58145, rend_intergenic: 55398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77882, rend_intergenic: 70966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96827, rend_intergenic: 96152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99466, rend_intergenic: 96986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106401, rend_intergenic: 102009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130632, rend_intergenic: 114132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137067, rend_intergenic: 133072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140166
-exon list size: 571


building trellis

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28.3    
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29.5    
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29.8    
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33.2    
33.3    
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48.7    
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72.3    
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77.1    
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78.2    
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78.9    
79.1    
79.2    
79.4    
79.6    
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80.3    
80.5    
80.6    
80.8    
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81.2    
81.3    
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81.8    
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82.9    
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83.2    
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85.2    
85.3    
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85.9    
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86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
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89.4    
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89.7    
89.9    
90.1    
90.2    
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90.8    
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91.3    
91.4    
91.6    
91.8    
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92.5    
92.7    
92.8    
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93.2    
93.4    
93.5    
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93.9    
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94.4    
94.6    
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96.3    
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96.7    
96.9    
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97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6052, rend_intergenic: 4133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14943, rend_intergenic: 9210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17678, rend_intergenic: 16374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25274, rend_intergenic: 24509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46089, rend_intergenic: 44649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53877, rend_intergenic: 49921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58145, rend_intergenic: 55398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77882, rend_intergenic: 70966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96827, rend_intergenic: 96152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99466, rend_intergenic: 96986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106401, rend_intergenic: 102009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130632, rend_intergenic: 114132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137067, rend_intergenic: 133072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support