-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_9296683-9478290

-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_20-snap.2069-T1
Valid prediction for snap_scaffold_20-snap.2075-T1
Valid prediction for GeneMark_model.83352_t
Valid prediction for GeneMark_model.83317_t
Valid prediction for snap_scaffold_20-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_47765-T1
Valid prediction for snap_scaffold_20-snap.2086-T1
Valid prediction for snap_scaffold_20-snap.2055-T1
Valid prediction for GeneMark_model.83332_t
Valid prediction for snap_scaffold_20-snap.2080-T1
Valid prediction for snap_scaffold_20-snap.2082-T1
Valid prediction for snap_scaffold_20-snap.2091-T1
Valid prediction for GeneMark_model.83324_t
Valid prediction for GeneMark_model.83341_t
Valid prediction for Augustus_model.g31858.t1
Valid prediction for GeneMark_model.83329_t
Valid prediction for snap_scaffold_20-snap.2073-T1
Valid prediction for GlimmerHMM_glimmerT_47754-T1
Valid prediction for GlimmerHMM_glimmerT_47767-T1
Valid prediction for GeneMark_model.83339_t
Valid prediction for snap_scaffold_20-snap.2077-T1
Valid prediction for GeneMark_model.83319_t
Valid prediction for snap_scaffold_20-snap.2064-T1
Valid prediction for GlimmerHMM_glimmerT_47753-T1
Valid prediction for GlimmerHMM_glimmerT_47760-T1
Valid prediction for GlimmerHMM_glimmerT_47771-T1
Valid prediction for GlimmerHMM_glimmerT_47764-T1
Valid prediction for GeneMark_model.83331_t
Valid prediction for GlimmerHMM_glimmerT_47755-T1
Valid prediction for snap_scaffold_20-snap.2061-T1
Valid prediction for snap_scaffold_20-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_47763-T1
Valid prediction for snap_scaffold_20-snap.2066-T1
Valid prediction for snap_scaffold_20-snap.2056-T1
Valid prediction for GeneMark_model.83315_t
Valid prediction for GeneMark_model.83307_t
Valid prediction for GeneMark_model.83335_t
Valid prediction for snap_scaffold_20-snap.2089-T1
Valid prediction for snap_scaffold_20-snap.2084-T1
Valid prediction for GeneMark_model.83349_t
Valid prediction for snap_scaffold_20-snap.2059-T1
Valid prediction for GeneMark_model.83306_t
Valid prediction for GeneMark_model.83327_t
Valid prediction for GeneMark_model.83334_t
Valid prediction for GeneMark_model.83313_t
Valid prediction for snap_scaffold_20-snap.2101-T1
Valid prediction for GeneMark_model.83304_t
Valid prediction for GeneMark_model.83321_t
Valid prediction for GlimmerHMM_glimmerT_47758-T1
Valid prediction for GeneMark_model.83323_t
Valid prediction for GlimmerHMM_glimmerT_47766-T1
Valid prediction for GeneMark_model.83322_t
Valid prediction for GeneMark_model.83326_t
Valid prediction for GeneMark_model.83354_t
Valid prediction for GlimmerHMM_glimmerT_47762-T1
Valid prediction for Augustus_model.g31857.t1
Valid prediction for snap_scaffold_20-snap.2072-T1
Valid prediction for GlimmerHMM_glimmerT_47759-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 GeneMark_model.83340_t
Valid prediction for GlimmerHMM_glimmerT_47757-T1
Valid prediction for GeneMark_model.83342_t
Valid prediction for snap_scaffold_20-snap.2074-T1
Valid prediction for snap_scaffold_20-snap.2085-T1
Valid prediction for snap_scaffold_20-snap.2070-T1
Valid prediction for snap_scaffold_20-snap.2076-T1
Valid prediction for GeneMark_model.83346_t
Valid prediction for GeneMark_model.83350_t
Couldn't classify 27983, 28079
Couldn't classify 28826, 28926
Sorry, prediction pasa_asmbl_26963.p1 fails validation.
(GGT)	 TA	27983-28079	GT	AGG
(GGA)	 AG	28235-28295	GT	GTG
(ATT)	 AG	28616-28719	GT	AAG
(CTG)	 AG	28826-28926	AG	CGA
-recovered pasa_asmbl_26963.p1, internal, 28235, 28295
-recovered pasa_asmbl_26963.p1, internal, 28616, 28719
Valid prediction for GlimmerHMM_glimmerT_47752-T1
Valid prediction for GlimmerHMM_glimmerT_47772-T1
Valid prediction for GeneMark_model.83303_t
Valid prediction for GeneMark_model.83314_t
Valid prediction for GeneMark_model.83337_t
Valid prediction for snap_scaffold_20-snap.2068-T1
Valid prediction for Augustus_model.g31864.t1
Valid prediction for snap_scaffold_20-snap.2092-T1
Valid prediction for snap_scaffold_20-snap.2058-T1
Valid prediction for GlimmerHMM_glimmerT_47777-T1
Valid prediction for Augustus_model.g31860.t1
Valid prediction for pasa_asmbl_26958.p1
Couldn't classify 66088, 66106
Couldn't classify 66774, 66788
Sorry, prediction pasa_asmbl_27232.p1 fails validation.
(CTT)	 TC	66088-66106	GT	GGG
(ACT)	 AG	66218-66582	GT	AGG
(AAC)	 AG	66774-66788	GA	GGG
-recovered pasa_asmbl_27232.p1, internal, 66218, 66582
Valid prediction for GeneMark_model.83348_t
Valid prediction for GeneMark_model.83316_t
Valid prediction for snap_scaffold_20-snap.2093-T1
Valid prediction for snap_scaffold_20-snap.2054-T1
Valid prediction for snap_scaffold_20-snap.2057-T1
Valid prediction for GeneMark_model.83338_t
Valid prediction for snap_scaffold_20-snap.2097-T1
Valid prediction for GeneMark_model.83320_t
Valid prediction for snap_scaffold_20-snap.2078-T1
Valid prediction for GeneMark_model.83336_t
Valid prediction for GeneMark_model.83333_t
Valid prediction for GlimmerHMM_glimmerT_47761-T1
Valid prediction for GeneMark_model.83330_t
Valid prediction for GeneMark_model.83310_t
Valid prediction for GeneMark_model.83353_t
Valid prediction for GeneMark_model.83344_t
Valid prediction for GlimmerHMM_glimmerT_47773-T1
Valid prediction for GlimmerHMM_glimmerT_47769-T1
Valid prediction for snap_scaffold_20-snap.2090-T1
Valid prediction for snap_scaffold_20-snap.2095-T1
Valid prediction for Augustus_model.g31861.t1
Valid prediction for GlimmerHMM_glimmerT_47768-T1
Valid prediction for Augustus_model.g31862.t1
Valid prediction for GlimmerHMM_glimmerT_47756-T1
Valid prediction for GeneMark_model.83309_t
Valid prediction for GeneMark_model.83347_t
Valid prediction for CodingQuarry_transcript_30535-T1
Valid prediction for GlimmerHMM_glimmerT_47774-T1
Valid prediction for snap_scaffold_20-snap.2063-T1
Valid prediction for GeneMark_model.83325_t
Valid prediction for CodingQuarry_transcript_30536-T1
Valid prediction for GlimmerHMM_glimmerT_47775-T1
Couldn't classify 30030, 30072
Sorry, prediction pasa_asmbl_26961.p1 fails validation.
(TGG)	 AG	30030-30072	GT	TTG
(CTC)	 AG	30516-30663	GT	ACG
(GGC)	 AG	30985-31032	GT	AGG
(TAA)	 AG	32101-32407	AA	AAA
-recovered pasa_asmbl_26961.p1, terminal, 32101, 32407
-recovered pasa_asmbl_26961.p1, internal, 30030, 30072
-recovered pasa_asmbl_26961.p1, internal, 30516, 30663
-recovered pasa_asmbl_26961.p1, internal, 30985, 31032
Valid prediction for GlimmerHMM_glimmerT_47770-T1
Valid prediction for snap_scaffold_20-snap.2081-T1
Valid prediction for snap_scaffold_20-snap.2065-T1
Valid prediction for GeneMark_model.83328_t
Valid prediction for snap_scaffold_20-snap.2094-T1
Valid prediction for snap_scaffold_20-snap.2062-T1
Valid prediction for snap_scaffold_20-snap.2096-T1
Valid prediction for snap_scaffold_20-snap.2100-T1
Valid prediction for HiQ_model.g31865.t1
Valid prediction for GeneMark_model.83312_t
Valid prediction for GeneMark_model.83311_t
Valid prediction for GeneMark_model.83318_t
Valid prediction for HiQ_model.g31859.t1
Valid prediction for snap_scaffold_20-snap.2099-T1
Valid prediction for snap_scaffold_20-snap.2071-T1
Valid prediction for snap_scaffold_20-snap.2088-T1
Valid prediction for pasa_asmbl_26965.p1
Valid prediction for CodingQuarry_transcript_30534-T1
Valid prediction for GeneMark_model.83351_t
Valid prediction for snap_scaffold_20-snap.2079-T1
Valid prediction for snap_scaffold_20-snap.2083-T1
Valid prediction for GeneMark_model.83308_t
Valid prediction for HiQ_model.g31863.t1
Valid prediction for GeneMark_model.83305_t
Valid prediction for Augustus_model.g31856.t1
Valid prediction for snap_scaffold_20-snap.2087-T1
Valid prediction for snap_scaffold_20-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_47776-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13483, rend_intergenic: 11863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31370, rend_intergenic: 28425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37274, rend_intergenic: 33040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48513, rend_intergenic: 46042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60010, rend_intergenic: 52174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64537, rend_intergenic: 60564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78272, rend_intergenic: 73522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87790, rend_intergenic: 84271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97430, rend_intergenic: 90221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99618, rend_intergenic: 98385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101553, rend_intergenic: 100826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105003, rend_intergenic: 102042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125834, rend_intergenic: 119353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175233, rend_intergenic: 173394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181608
-exon list size: 570


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 13483, rend_intergenic: 11863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31370, rend_intergenic: 28425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37274, rend_intergenic: 33040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48513, rend_intergenic: 46042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60010, rend_intergenic: 52174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64537, rend_intergenic: 60564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78272, rend_intergenic: 73522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87790, rend_intergenic: 84271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97430, rend_intergenic: 90221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99618, rend_intergenic: 98385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101553, rend_intergenic: 100826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105003, rend_intergenic: 102042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125834, rend_intergenic: 119353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175233, rend_intergenic: 173394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10436
-exon list size: 30


building trellis

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18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support