-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_5992548-6205920

-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 HiQ_model.g13569.t1
Valid prediction for GeneMark_model.34699_t
Couldn't classify 30321, 30881
Sorry, prediction pasa_asmbl_51912.p1 fails validation.
(CAC)	 CA	30321-30881	GT	AGG
(GTT)	 AG	32804-34961	GT	AGG
(CTC)	 AG	35272-35419	GT	AGG
(TGC)	 AG	35515-35642	GT	TAG
(TTC)	 AG	35732-35767	GT	GGG
(TGG)	 AG	35868-36142	GT	TGG
(GAA)	 AG	36278-36366	GT	GAG
(AGT)	 AG	36468-36685	GT	AGG
(GTG)	 AG	36789-36837	GT	GGG
(GTA)	 AG	36984-37293	AA	AGA
-recovered pasa_asmbl_51912.p1, terminal, 36984, 37293
-recovered pasa_asmbl_51912.p1, internal, 32804, 34961
-recovered pasa_asmbl_51912.p1, internal, 35272, 35419
-recovered pasa_asmbl_51912.p1, internal, 35515, 35642
-recovered pasa_asmbl_51912.p1, internal, 35732, 35767
-recovered pasa_asmbl_51912.p1, internal, 35868, 36142
-recovered pasa_asmbl_51912.p1, internal, 36278, 36366
-recovered pasa_asmbl_51912.p1, internal, 36468, 36685
-recovered pasa_asmbl_51912.p1, internal, 36789, 36837
Valid prediction for GlimmerHMM_glimmerT_20289-T1
Valid prediction for GlimmerHMM_glimmerT_20292-T1
Valid prediction for snap_scaffold_8-snap.1210-T1
Valid prediction for CodingQuarry_transcript_59527-T1
Valid prediction for HiQ_model.g13562.t1
Valid prediction for GeneMark_model.34714_t
Valid prediction for snap_scaffold_8-snap.1207-T1
Valid prediction for Augustus_model.g13560.t1
Valid prediction for snap_scaffold_8-snap.1238-T1
Valid prediction for GeneMark_model.34700_t
Valid prediction for GeneMark_model.34708_t
Valid prediction for GeneMark_model.34719_t
Valid prediction for snap_scaffold_8-snap.1244-T1
Valid prediction for snap_scaffold_8-snap.1218-T1
Valid prediction for snap_scaffold_8-snap.1208-T1
Valid prediction for GeneMark_model.34705_t
Valid prediction for snap_scaffold_8-snap.1205-T1
Valid prediction for CodingQuarry_transcript_59524-T1
Valid prediction for GlimmerHMM_glimmerT_20278-T1
Couldn't classify 120621, 120731
Couldn't classify 124075, 124184
Sorry, prediction pasa_asmbl_51928.p1 fails validation.
(CGA)	 GA	120621-120731	GT	TGG
(CAC)	 AG	121500-121649	GT	AGG
(GTA)	 AG	121749-121830	GT	AGG
(AGG)	 AG	121938-122020	GT	AGG
(AAT)	 AG	122665-122764	GT	TGG
(GAA)	 AG	123449-123556	GT	GGG
(TGA)	 AG	123682-123783	GT	GGG
(GAC)	 AG	123868-123936	GT	AGG
(TTG)	 AG	124075-124184	CA	CAC
-recovered pasa_asmbl_51928.p1, internal, 121500, 121649
-recovered pasa_asmbl_51928.p1, internal, 121749, 121830
-recovered pasa_asmbl_51928.p1, internal, 121938, 122020
-recovered pasa_asmbl_51928.p1, internal, 122665, 122764
-recovered pasa_asmbl_51928.p1, internal, 123449, 123556
-recovered pasa_asmbl_51928.p1, internal, 123682, 123783
-recovered pasa_asmbl_51928.p1, internal, 123868, 123936
Valid prediction for snap_scaffold_8-snap.1216-T1
Valid prediction for snap_scaffold_8-snap.1228-T1
Valid prediction for GeneMark_model.34710_t
Valid prediction for pasa_asmbl_51916.p1
Valid prediction for snap_scaffold_8-snap.1246-T1
Valid prediction for Augustus_model.g13574.t1
Valid prediction for GlimmerHMM_glimmerT_20279-T1
Valid prediction for GeneMark_model.34715_t
Valid prediction for snap_scaffold_8-snap.1209-T1
Valid prediction for CodingQuarry_transcript_59523-T1
Valid prediction for snap_scaffold_8-snap.1219-T1
Valid prediction for snap_scaffold_8-snap.1214-T1
Valid prediction for GeneMark_model.34718_t
Valid prediction for GeneMark_model.34724_t
Valid prediction for CodingQuarry_transcript_59520-T1
Valid prediction for GeneMark_model.34716_t
Valid prediction for snap_scaffold_8-snap.1227-T1
Valid prediction for GeneMark_model.34728_t
Valid prediction for GeneMark_model.34731_t
Valid prediction for GeneMark_model.34722_t
Couldn't classify 29996, 30123
Couldn't classify 30313, 30619
Sorry, prediction CodingQuarry_transcript_59521-T1 fails validation.
(ATG)	 CA	29996-30123	AA	AGA
(AAC)	 AA	30313-30619	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_20276-T1
Valid prediction for HiQ_model.g13561.t1
Valid prediction for CodingQuarry_transcript_59522-T1
Valid prediction for GeneMark_model.34712_t
Valid prediction for GlimmerHMM_glimmerT_20283-T1
Valid prediction for Augustus_model.g13567.t1
Valid prediction for snap_scaffold_8-snap.1224-T1
Valid prediction for pasa_asmbl_51914.p1
Valid prediction for GlimmerHMM_glimmerT_20286-T1
Valid prediction for GlimmerHMM_glimmerT_20277-T1
Valid prediction for GeneMark_model.34701_t
Valid prediction for CodingQuarry_transcript_59526-T1
Valid prediction for pasa_asmbl_51921.p1
Couldn't classify 120621, 120731
Sorry, prediction pasa_asmbl_51923.p1 fails validation.
(CGA)	 GA	120621-120731	GT	TGG
(CAC)	 AG	121500-121649	GT	AGG
(GTA)	 AG	121749-121830	GT	AGG
(AGG)	 AG	121938-122020	GT	AGG
(AAT)	 AG	122665-122764	GT	TGG
(GAA)	 AG	123449-123556	GT	GGG
(TGA)	 AG	123682-123783	GT	GGG
(GAC)	 AG	123868-123936	GT	AGG
(TTG)	 AG	124075-124157	GT	CGG
(GAG)	 AG	126902-126967	GT	AGG
(ACA)	 AG	128425-128505	GT	AGG
(GCT)	 AG	129668-129706	AT	AGA
-recovered pasa_asmbl_51923.p1, terminal, 129668, 129706
-recovered pasa_asmbl_51923.p1, internal, 121500, 121649
-recovered pasa_asmbl_51923.p1, internal, 121749, 121830
-recovered pasa_asmbl_51923.p1, internal, 121938, 122020
-recovered pasa_asmbl_51923.p1, internal, 122665, 122764
-recovered pasa_asmbl_51923.p1, internal, 123449, 123556
-recovered pasa_asmbl_51923.p1, internal, 123682, 123783
-recovered pasa_asmbl_51923.p1, internal, 123868, 123936
-recovered pasa_asmbl_51923.p1, internal, 124075, 124157
-recovered pasa_asmbl_51923.p1, internal, 126902, 126967
-recovered pasa_asmbl_51923.p1, internal, 128425, 128505
Valid prediction for snap_scaffold_8-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_20294-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.34698_t
Valid prediction for GeneMark_model.34733_t
Valid prediction for GlimmerHMM_glimmerT_20280-T1
Valid prediction for snap_scaffold_8-snap.1239-T1
Valid prediction for Augustus_model.g13573.t1
Valid prediction for GeneMark_model.34720_t
Valid prediction for GlimmerHMM_glimmerT_20295-T1
Valid prediction for snap_scaffold_8-snap.1242-T1
Valid prediction for GeneMark_model.34709_t
Valid prediction for Augustus_model.g13565.t1
Couldn't classify 48762, 48883
Sorry, prediction pasa_asmbl_52852.p1 fails validation.
(GAT)	 AT	48762-48883	GT	AGG
(TGT)	 AG	49260-49392	GT	AGG
(AAT)	 AG	49577-49664	GT	AGG
(CAC)	 AG	49909-50007	GT	TTG
(TAA)	 AG	50929-51081	GT	AGG
(GAT)	 AG	51234-51399	GT	TGG
(CTG)	 AG	51574-51967	GC	GAG
-recovered pasa_asmbl_52852.p1, terminal, 51574, 51967
-recovered pasa_asmbl_52852.p1, internal, 49260, 49392
-recovered pasa_asmbl_52852.p1, internal, 49577, 49664
-recovered pasa_asmbl_52852.p1, internal, 49909, 50007
-recovered pasa_asmbl_52852.p1, internal, 50929, 51081
-recovered pasa_asmbl_52852.p1, internal, 51234, 51399
-recovered pasa_asmbl_52852.p1, internal, 51574, 51967
Valid prediction for snap_scaffold_8-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_20290-T1
Valid prediction for GeneMark_model.34713_t
Valid prediction for CodingQuarry_transcript_59528-T1
Valid prediction for GlimmerHMM_glimmerT_20281-T1
Valid prediction for GlimmerHMM_glimmerT_20298-T1
Valid prediction for snap_scaffold_8-snap.1237-T1
Valid prediction for Augustus_model.g13566.t1
Valid prediction for HiQ_model.g13576.t1
Valid prediction for GlimmerHMM_glimmerT_20291-T1
Valid prediction for snap_scaffold_8-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_20297-T1
Valid prediction for snap_scaffold_8-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_20296-T1
Valid prediction for Augustus_model.g13564.t1
Valid prediction for GeneMark_model.34723_t
Valid prediction for snap_scaffold_8-snap.1223-T1
Valid prediction for GeneMark_model.34707_t
Valid prediction for snap_scaffold_8-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_20284-T1
Valid prediction for snap_scaffold_8-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_20282-T1
Valid prediction for Augustus_model.g13559.t1
Valid prediction for Augustus_model.g13571.t1
Valid prediction for GeneMark_model.34732_t
Valid prediction for CodingQuarry_transcript_59529-T1
Valid prediction for GeneMark_model.34726_t
Valid prediction for snap_scaffold_8-snap.1231-T1
Valid prediction for GeneMark_model.34706_t
Valid prediction for snap_scaffold_8-snap.1235-T1
Valid prediction for HiQ_model.g13568.t1
Valid prediction for GeneMark_model.34711_t
Valid prediction for GeneMark_model.34730_t
Valid prediction for snap_scaffold_8-snap.1234-T1
Valid prediction for snap_scaffold_8-snap.1221-T1
Valid prediction for snap_scaffold_8-snap.1241-T1
Valid prediction for pasa_asmbl_52859.p1
Valid prediction for snap_scaffold_8-snap.1236-T1
Valid prediction for snap_scaffold_8-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_20288-T1
Valid prediction for GeneMark_model.34702_t
Valid prediction for Augustus_model.g13572.t1
Valid prediction for snap_scaffold_8-snap.1240-T1
Couldn't classify 28832, 28972
Sorry, prediction pasa_asmbl_52861.p1 fails validation.
(AAG)	 CC	28832-28972	GT	AGG
(GTG)	 AG	29260-29385	GT	AGG
(GTG)	 AG	30325-30441	GT	CGG
(GTG)	 AG	30560-30745	GT	AGG
(CAA)	 AG	30852-30959	GT	TGG
(GTC)	 AG	31205-31310	GT	AGG
(GCA)	 AG	32059-32183	GT	AGG
(CAA)	 AG	33758-33946	GT	CGG
(GCA)	 AG	34121-34303	GT	AGG
(TCT)	 AG	34453-34578	GT	AGG
(ATC)	 AG	34769-34897	CA	AAC
-recovered pasa_asmbl_52861.p1, terminal, 34769, 34897
-recovered pasa_asmbl_52861.p1, internal, 29260, 29385
-recovered pasa_asmbl_52861.p1, internal, 30325, 30441
-recovered pasa_asmbl_52861.p1, internal, 30560, 30745
-recovered pasa_asmbl_52861.p1, internal, 30852, 30959
-recovered pasa_asmbl_52861.p1, internal, 31205, 31310
-recovered pasa_asmbl_52861.p1, internal, 32059, 32183
-recovered pasa_asmbl_52861.p1, internal, 33758, 33946
-recovered pasa_asmbl_52861.p1, internal, 34121, 34303
-recovered pasa_asmbl_52861.p1, internal, 34453, 34578
Valid prediction for snap_scaffold_8-snap.1230-T1
Valid prediction for snap_scaffold_8-snap.1215-T1
Valid prediction for snap_scaffold_8-snap.1211-T1
Valid prediction for snap_scaffold_8-snap.1222-T1
Valid prediction for snap_scaffold_8-snap.1213-T1
Valid prediction for GeneMark_model.34721_t
Valid prediction for GeneMark_model.34717_t
Valid prediction for GeneMark_model.34703_t
Valid prediction for GeneMark_model.34704_t
Valid prediction for GlimmerHMM_glimmerT_20287-T1
Valid prediction for GlimmerHMM_glimmerT_20285-T1
Valid prediction for snap_scaffold_8-snap.1217-T1
Valid prediction for GeneMark_model.34727_t
Valid prediction for Augustus_model.g13570.t1
Valid prediction for Augustus_model.g13563.t1
Valid prediction for GlimmerHMM_glimmerT_20293-T1
Valid prediction for HiQ_model.g13575.t1
Valid prediction for snap_scaffold_8-snap.1232-T1
Valid prediction for snap_scaffold_8-snap.1206-T1
Valid prediction for GeneMark_model.34725_t
Valid prediction for GeneMark_model.34729_t
Valid prediction for snap_scaffold_8-snap.1229-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 62875, rend_intergenic: 61130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64857, rend_intergenic: 63088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206744, rend_intergenic: 195609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213373
-exon list size: 539


building trellis

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97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 62875, rend_intergenic: 61130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64857, rend_intergenic: 63088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206744, rend_intergenic: 195609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 28514
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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 - 11005
-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
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 - 10475
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 11105 - 28514
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 11464 - 28514
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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