-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_11060370-11291334

-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_9-snap.2193-T1
Valid prediction for HiQ_model.g15227.t1
Valid prediction for GlimmerHMM_glimmerT_22852-T1
Valid prediction for pasa_asmbl_54340.p2
Valid prediction for snap_scaffold_9-snap.2178-T1
Valid prediction for CodingQuarry_transcript_62307-T1
Valid prediction for snap_scaffold_9-snap.2214-T1
Couldn't classify 62440, 62522
Couldn't classify 65978, 66154
Sorry, prediction pasa_asmbl_54333.p1 fails validation.
(CAC)	 AC	62440-62522	GT	GGG
(ATA)	 AG	62813-63115	GT	AGG
(TTT)	 AG	63693-63888	GT	GGG
(TTG)	 AG	64098-64233	GT	TGG
(GTA)	 AG	64782-64928	GT	AGG
(TGG)	 AG	65221-65319	GT	GAG
(TGG)	 AG	65454-65518	GT	AGG
(GAC)	 AG	65672-65803	GT	AGG
(GTC)	 AG	65978-66154	CG	AAC
-recovered pasa_asmbl_54333.p1, internal, 62813, 63115
-recovered pasa_asmbl_54333.p1, internal, 63693, 63888
-recovered pasa_asmbl_54333.p1, internal, 64098, 64233
-recovered pasa_asmbl_54333.p1, internal, 64782, 64928
-recovered pasa_asmbl_54333.p1, internal, 65221, 65319
-recovered pasa_asmbl_54333.p1, internal, 65454, 65518
-recovered pasa_asmbl_54333.p1, internal, 65672, 65803
Valid prediction for GlimmerHMM_glimmerT_22874-T1
Valid prediction for snap_scaffold_9-snap.2190-T1
Couldn't classify 54879, 55075
Couldn't classify 55548, 55656
Sorry, prediction pasa_asmbl_54774.p1 fails validation.
(TAC)	 TC	54879-55075	GT	AAG
(GTT)	 AG	55548-55656	AA	ACA
Valid prediction for snap_scaffold_9-snap.2181-T1
Valid prediction for Augustus_model.g15218.t1
Valid prediction for snap_scaffold_9-snap.2195-T1
Valid prediction for HiQ_model.g15223.t1
Valid prediction for snap_scaffold_9-snap.2176-T1
Valid prediction for snap_scaffold_9-snap.2180-T1
Valid prediction for snap_scaffold_9-snap.2203-T1
Valid prediction for GlimmerHMM_glimmerT_22862-T1
Valid prediction for snap_scaffold_9-snap.2205-T1
Couldn't classify 71079, 71171
Sorry, prediction pasa_asmbl_54335.p1 fails validation.
(ATG)	 AG	69530-69560	GT	AGG
(ATC)	 AG	70181-70292	GT	AGG
(CAG)	 AG	70519-70609	GT	AGG
(CTT)	 AG	70761-70868	GT	AGG
(GAC)	 AG	71079-71171	TG	AGT
-recovered pasa_asmbl_54335.p1, initial, 69530, 69560
-recovered pasa_asmbl_54335.p1, internal, 69530, 69560
-recovered pasa_asmbl_54335.p1, internal, 70181, 70292
-recovered pasa_asmbl_54335.p1, internal, 70519, 70609
-recovered pasa_asmbl_54335.p1, internal, 70761, 70868
Valid prediction for snap_scaffold_9-snap.2209-T1
Valid prediction for Augustus_model.g15225.t1
Valid prediction for snap_scaffold_9-snap.2212-T1
Valid prediction for HiQ_model.g15226.t1
Valid prediction for GlimmerHMM_glimmerT_22879-T1
Valid prediction for snap_scaffold_9-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_22863-T1
Valid prediction for snap_scaffold_9-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_22858-T1
Valid prediction for GlimmerHMM_glimmerT_22880-T1
Valid prediction for GlimmerHMM_glimmerT_22864-T1
Valid prediction for snap_scaffold_9-snap.2200-T1
Valid prediction for GlimmerHMM_glimmerT_22856-T1
Valid prediction for HiQ_model.g15215.t1
Valid prediction for snap_scaffold_9-snap.2215-T1
Valid prediction for Augustus_model.g15224.t1
Valid prediction for Augustus_model.g15219.t1
Valid prediction for snap_scaffold_9-snap.2186-T1
Valid prediction for snap_scaffold_9-snap.2211-T1
Valid prediction for snap_scaffold_9-snap.2188-T1
Valid prediction for GlimmerHMM_glimmerT_22868-T1
Valid prediction for snap_scaffold_9-snap.2210-T1
Valid prediction for Augustus_model.g15237.t1
Valid prediction for GlimmerHMM_glimmerT_22859-T1
Valid prediction for snap_scaffold_9-snap.2187-T1
Valid prediction for GlimmerHMM_glimmerT_22857-T1
Valid prediction for Augustus_model.g15238.t1
Valid prediction for HiQ_model.g15236.t1
Valid prediction for GlimmerHMM_glimmerT_22851-T1
Valid prediction for Augustus_model.g15220.t1
Valid prediction for snap_scaffold_9-snap.2175-T1
Valid prediction for snap_scaffold_9-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_22865-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_22878-T1
Valid prediction for GlimmerHMM_glimmerT_22875-T1
Valid prediction for GlimmerHMM_glimmerT_22876-T1
Valid prediction for snap_scaffold_9-snap.2197-T1
Valid prediction for HiQ_model.g15232.t1
Valid prediction for Augustus_model.g15221.t1
Couldn't classify 221276, 221387
Sorry, prediction pasa_asmbl_55273.p1 fails validation.
(ATG)	 TT	220248-220562	GT	AGG
(GAA)	 AG	220788-221179	GT	GGG
(GTA)	 AG	221276-221387	CC	CCC
-recovered pasa_asmbl_55273.p1, initial, 220248, 220562
-recovered pasa_asmbl_55273.p1, internal, 220788, 221179
Valid prediction for snap_scaffold_9-snap.2198-T1
Valid prediction for HiQ_model.g15216.t1
Valid prediction for Augustus_model.g15229.t1
Couldn't classify 83677, 84003
Sorry, prediction pasa_asmbl_55821.p1 fails validation.
(GTG)	 AG	83677-84003	GC	CGG
-recovered pasa_asmbl_55821.p1, internal, 83677, 84003
Valid prediction for Augustus_model.g15217.t1
Valid prediction for snap_scaffold_9-snap.2204-T1
Valid prediction for snap_scaffold_9-snap.2196-T1
Valid prediction for pasa_asmbl_55281.p1
Valid prediction for GlimmerHMM_glimmerT_22867-T1
Valid prediction for GlimmerHMM_glimmerT_22869-T1
Valid prediction for snap_scaffold_9-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_22860-T1
Valid prediction for Augustus_model.g15233.t1
Valid prediction for snap_scaffold_9-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_22866-T1
Valid prediction for GlimmerHMM_glimmerT_22855-T1
Valid prediction for CodingQuarry_transcript_62308-T1
Valid prediction for Augustus_model.g15231.t1
Valid prediction for GlimmerHMM_glimmerT_22872-T1
Valid prediction for GlimmerHMM_glimmerT_22853-T1
Valid prediction for snap_scaffold_9-snap.2213-T1
Valid prediction for snap_scaffold_9-snap.2183-T1
Valid prediction for snap_scaffold_9-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_22854-T1
Valid prediction for snap_scaffold_9-snap.2206-T1
Valid prediction for snap_scaffold_9-snap.2184-T1
Valid prediction for Augustus_model.g15228.t1
Valid prediction for Augustus_model.g15230.t1
Valid prediction for Augustus_model.g15222.t1
Couldn't classify 49143, 49185
Sorry, prediction pasa_asmbl_55280.p1 fails validation.
(ATG)	 AC	42064-42098	GT	AGG
(AGT)	 AG	43621-43699	GT	AGG
(AGG)	 AG	43912-44055	GT	ACG
(GTG)	 AG	44337-44479	GT	AGG
(GAT)	 AG	44735-44876	GT	GGG
(AAG)	 AG	45236-45331	GT	GGG
(CCA)	 AG	45518-45612	GT	AAG
(GAA)	 AG	46588-46830	GT	AAG
(GAC)	 AG	47709-47856	GT	AGG
(TTG)	 AG	48311-48393	GT	ACG
(TGT)	 AG	48490-48568	GT	AGG
(ATG)	 AG	48911-49059	GT	AAG
(TTC)	 AG	49143-49185	CC	AGC
-recovered pasa_asmbl_55280.p1, initial, 42064, 42098
-recovered pasa_asmbl_55280.p1, initial, 48911, 49059
-recovered pasa_asmbl_55280.p1, terminal, 45518, 45612
-recovered pasa_asmbl_55280.p1, internal, 43621, 43699
-recovered pasa_asmbl_55280.p1, internal, 43912, 44055
-recovered pasa_asmbl_55280.p1, internal, 44337, 44479
-recovered pasa_asmbl_55280.p1, internal, 44735, 44876
-recovered pasa_asmbl_55280.p1, internal, 45236, 45331
-recovered pasa_asmbl_55280.p1, internal, 45518, 45612
-recovered pasa_asmbl_55280.p1, internal, 46588, 46830
-recovered pasa_asmbl_55280.p1, internal, 47709, 47856
-recovered pasa_asmbl_55280.p1, internal, 48311, 48393
-recovered pasa_asmbl_55280.p1, internal, 48490, 48568
-recovered pasa_asmbl_55280.p1, internal, 48911, 49059
Couldn't classify 221481, 221754
Sorry, prediction pasa_asmbl_55271.p1 fails validation.
(TAC)	 TC	221481-221754	GT	AGG
(GGT)	 AG	222072-222155	GT	AGG
(GGG)	 AG	222408-222564	GT	GGG
(GAT)	 AG	222738-222795	TG	GAT
-recovered pasa_asmbl_55271.p1, terminal, 222738, 222795
-recovered pasa_asmbl_55271.p1, internal, 222072, 222155
-recovered pasa_asmbl_55271.p1, internal, 222408, 222564
Valid prediction for GlimmerHMM_glimmerT_22877-T1
Valid prediction for GlimmerHMM_glimmerT_22861-T1
Valid prediction for GlimmerHMM_glimmerT_22870-T1
Valid prediction for snap_scaffold_9-snap.2177-T1
Valid prediction for GlimmerHMM_glimmerT_22871-T1
Valid prediction for snap_scaffold_9-snap.2207-T1
Valid prediction for snap_scaffold_9-snap.2194-T1
Valid prediction for snap_scaffold_9-snap.2189-T1
Valid prediction for pasa_asmbl_55278.p1
Valid prediction for CodingQuarry_transcript_62309-T1
Valid prediction for snap_scaffold_9-snap.2192-T1
Valid prediction for snap_scaffold_9-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_22873-T1
Valid prediction for Augustus_model.g15234.t1
Valid prediction for Augustus_model.g15235.t1
Valid prediction for snap_scaffold_9-snap.2179-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15125, rend_intergenic: 13981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66839, rend_intergenic: 62892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115985, rend_intergenic: 113209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196432, rend_intergenic: 181919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230965
-exon list size: 350


building trellis

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45.5    
45.7    
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47.7    
48.0    
48.3    
48.6    
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50.9    
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51.4    
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53.4    
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55.4    
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56.0    
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92.3    
92.6    
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93.2    
93.5    
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96.0    
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97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 15125, rend_intergenic: 13981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66839, rend_intergenic: 62892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115985, rend_intergenic: 113209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196432, rend_intergenic: 181919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support