-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_6261085-6484393

-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_1-snap.1056-T1
Couldn't classify 61009, 61098
Sorry, prediction pasa_asmbl_1827.p1 fails validation.
(AAG)	 AA	61009-61098	GT	AGG
(GCC)	 AG	62045-62235	GT	AGG
(CAT)	 AG	62324-62450	GT	AGG
(GTG)	 AG	62595-62752	GT	AGG
(ACA)	 AG	62865-63025	GT	TGG
(GAA)	 AG	63153-63253	GT	AGG
(TTT)	 AG	63339-63443	AC	AAA
-recovered pasa_asmbl_1827.p1, terminal, 63339, 63443
-recovered pasa_asmbl_1827.p1, internal, 62045, 62235
-recovered pasa_asmbl_1827.p1, internal, 62324, 62450
-recovered pasa_asmbl_1827.p1, internal, 62595, 62752
-recovered pasa_asmbl_1827.p1, internal, 62865, 63025
-recovered pasa_asmbl_1827.p1, internal, 63153, 63253
Valid prediction for snap_scaffold_1-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_853-T1
Valid prediction for snap_scaffold_1-snap.1065-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1061-T1
Valid prediction for Augustus_model.g648.t1
Couldn't classify 158406, 158440
Sorry, prediction pasa_asmbl_2722.p2 fails validation.
(ATG)	 GA	157213-157297	GT	AGG
(ACG)	 AG	158096-158281	GT	TGG
(GTG)	 AG	158406-158440	CG	AAC
-recovered pasa_asmbl_2722.p2, initial, 157213, 157297
-recovered pasa_asmbl_2722.p2, internal, 158096, 158281
Valid prediction for Augustus_model.g646.t1
Valid prediction for snap_scaffold_1-snap.1033-T1
Valid prediction for snap_scaffold_1-snap.1063-T1
Valid prediction for CodingQuarry_transcript_2655-T1
Valid prediction for CodingQuarry_transcript_2657-T1
Valid prediction for HiQ_model.g629.t1
Valid prediction for snap_scaffold_1-snap.1044-T1
Valid prediction for snap_scaffold_1-snap.1040-T1
Valid prediction for snap_scaffold_1-snap.1046-T1
Valid prediction for HiQ_model.g633.t1
Valid prediction for Augustus_model.g644.t1
Valid prediction for Augustus_model.g637.t1
Valid prediction for snap_scaffold_1-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_815-T1
Valid prediction for pasa_asmbl_1826.p1
Valid prediction for GlimmerHMM_glimmerT_827-T1
Valid prediction for snap_scaffold_1-snap.1037-T1
Valid prediction for snap_scaffold_1-snap.1038-T1
Valid prediction for GlimmerHMM_glimmerT_832-T1
Valid prediction for Augustus_model.g635.t1
Valid prediction for snap_scaffold_1-snap.1025-T1
Valid prediction for HiQ_model.g624.t1
Valid prediction for GlimmerHMM_glimmerT_819-T1
Valid prediction for GlimmerHMM_glimmerT_858-T1
Valid prediction for GlimmerHMM_glimmerT_834-T1
Valid prediction for Augustus_model.g642.t1
Valid prediction for Augustus_model.g639.t1
Valid prediction for snap_scaffold_1-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_833-T1
Valid prediction for snap_scaffold_1-snap.1064-T1
Couldn't classify 159224, 159233
Sorry, prediction pasa_asmbl_1838.p1 fails validation.
(ATC)	 CC	159224-159233	GT	TGG
(GTG)	 AG	159332-159440	GT	AGG
(TGT)	 AG	159596-159664	GT	ATG
(CTT)	 AG	159775-159931	GG	AGG
-recovered pasa_asmbl_1838.p1, terminal, 159775, 159931
-recovered pasa_asmbl_1838.p1, internal, 159332, 159440
-recovered pasa_asmbl_1838.p1, internal, 159596, 159664
Valid prediction for GlimmerHMM_glimmerT_859-T1
Valid prediction for GlimmerHMM_glimmerT_841-T1
Valid prediction for Augustus_model.g632.t1
Valid prediction for snap_scaffold_1-snap.1021-T1
Valid prediction for snap_scaffold_1-snap.1058-T1
Valid prediction for GlimmerHMM_glimmerT_835-T1
Valid prediction for HiQ_model.g630.t1
Valid prediction for GlimmerHMM_glimmerT_823-T1
Valid prediction for GlimmerHMM_glimmerT_838-T1
Couldn't classify 69978, 70046
Sorry, prediction pasa_asmbl_1830.p1 fails validation.
(ATG)	 CG	64203-64290	GT	CGG
(TCA)	 AG	64752-64822	GT	AGG
(GTC)	 AG	65385-65472	GT	CTG
(ACC)	 AG	65578-65697	GT	CGG
(AGA)	 AG	65856-65949	GT	AAG
(GTG)	 AG	66165-66330	GT	AGG
(GTG)	 AG	66427-66484	GT	TGG
(TTC)	 AG	67876-67907	GT	ATG
(ATC)	 AG	68020-68116	GT	AGG
(CAT)	 AG	69821-69885	GT	AGG
(GTG)	 AG	69978-70046	GG	AGG
-recovered pasa_asmbl_1830.p1, initial, 64203, 64290
-recovered pasa_asmbl_1830.p1, internal, 64752, 64822
-recovered pasa_asmbl_1830.p1, internal, 65385, 65472
-recovered pasa_asmbl_1830.p1, internal, 65578, 65697
-recovered pasa_asmbl_1830.p1, internal, 65856, 65949
-recovered pasa_asmbl_1830.p1, internal, 66165, 66330
-recovered pasa_asmbl_1830.p1, internal, 66427, 66484
-recovered pasa_asmbl_1830.p1, internal, 67876, 67907
-recovered pasa_asmbl_1830.p1, internal, 68020, 68116
-recovered pasa_asmbl_1830.p1, internal, 69821, 69885
Valid prediction for CodingQuarry_transcript_2650-T1
Valid prediction for Augustus_model.g645.t1
Valid prediction for GlimmerHMM_glimmerT_829-T1
Valid prediction for snap_scaffold_1-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_828-T1
Valid prediction for pasa_asmbl_1832.p1
Valid prediction for Augustus_model.g638.t1
Valid prediction for GlimmerHMM_glimmerT_848-T1
Valid prediction for GlimmerHMM_glimmerT_831-T1
Valid prediction for Augustus_model.g634.t1
Valid prediction for snap_scaffold_1-snap.1026-T1
Valid prediction for snap_scaffold_1-snap.1045-T1
Valid prediction for snap_scaffold_1-snap.1043-T1
Valid prediction for pasa_asmbl_1824.p1
Valid prediction for GlimmerHMM_glimmerT_855-T1
Valid prediction for GlimmerHMM_glimmerT_852-T1
Valid prediction for GlimmerHMM_glimmerT_850-T1
Valid prediction for snap_scaffold_1-snap.1055-T1
Valid prediction for snap_scaffold_1-snap.1030-T1
Valid prediction for Augustus_model.g636.t1
Valid prediction for snap_scaffold_1-snap.1051-T1
Valid prediction for snap_scaffold_1-snap.1054-T1
Valid prediction for Augustus_model.g650.t1
Valid prediction for HiQ_model.g627.t1
Valid prediction for GlimmerHMM_glimmerT_824-T1
Valid prediction for snap_scaffold_1-snap.1041-T1
Valid prediction for snap_scaffold_1-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_851-T1
Valid prediction for snap_scaffold_1-snap.1053-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 pasa_asmbl_340.p1
Valid prediction for GlimmerHMM_glimmerT_825-T1
Valid prediction for snap_scaffold_1-snap.1022-T1
Valid prediction for snap_scaffold_1-snap.1028-T1
Valid prediction for snap_scaffold_1-snap.1035-T1
Valid prediction for Augustus_model.g622.t1
Valid prediction for pasa_asmbl_359.p1
Valid prediction for GlimmerHMM_glimmerT_856-T1
Valid prediction for GlimmerHMM_glimmerT_826-T1
Valid prediction for HiQ_model.g625.t1
Valid prediction for GlimmerHMM_glimmerT_817-T1
Valid prediction for GlimmerHMM_glimmerT_822-T1
Valid prediction for snap_scaffold_1-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_840-T1
Valid prediction for GlimmerHMM_glimmerT_814-T1
Valid prediction for CodingQuarry_transcript_2651-T1
Couldn't classify 186885, 186932
Sorry, prediction CodingQuarry_transcript_2652-T1 fails validation.
(ATG)	 AG	185362-185372	GT	AGG
(TTA)	 AG	185746-185842	GT	GAG
(TTC)	 AG	186086-186184	GT	ATG
(GCC)	 AG	186290-186355	GT	AAG
(CGT)	 AG	186485-186541	GT	AGG
(AGG)	 GT	186885-186932	GT	AGG
(TGG)	 AG	187041-187099	GT	AAG
(GGC)	 AG	187621-187681	GT	AGG
(TAT)	 AG	187795-187866	GT	TGG
(GCC)	 AG	187946-188001	GT	AAG
(AGA)	 AG	188161-188269	AT	AGA
-recovered CodingQuarry_transcript_2652-T1, initial, 185362, 185372
-recovered CodingQuarry_transcript_2652-T1, terminal, 188161, 188269
-recovered CodingQuarry_transcript_2652-T1, internal, 185362, 185372
-recovered CodingQuarry_transcript_2652-T1, internal, 185746, 185842
-recovered CodingQuarry_transcript_2652-T1, internal, 186086, 186184
-recovered CodingQuarry_transcript_2652-T1, internal, 186290, 186355
-recovered CodingQuarry_transcript_2652-T1, internal, 186485, 186541
-recovered CodingQuarry_transcript_2652-T1, internal, 187041, 187099
-recovered CodingQuarry_transcript_2652-T1, internal, 187621, 187681
-recovered CodingQuarry_transcript_2652-T1, internal, 187795, 187866
-recovered CodingQuarry_transcript_2652-T1, internal, 187946, 188001
Valid prediction for snap_scaffold_1-snap.1039-T1
Valid prediction for pasa_asmbl_335.p1
Valid prediction for snap_scaffold_1-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_830-T1
Valid prediction for snap_scaffold_1-snap.1031-T1
Valid prediction for Augustus_model.g649.t1
Valid prediction for GlimmerHMM_glimmerT_854-T1
Valid prediction for pasa_asmbl_355.p1
Valid prediction for CodingQuarry_transcript_2654-T1
Valid prediction for Augustus_model.g643.t1
Valid prediction for GlimmerHMM_glimmerT_837-T1
Valid prediction for CodingQuarry_transcript_2645-T1
Valid prediction for Augustus_model.g647.t1
Valid prediction for snap_scaffold_1-snap.1047-T1
Valid prediction for CodingQuarry_transcript_2646-T1
Valid prediction for CodingQuarry_transcript_2653-T1
Valid prediction for snap_scaffold_1-snap.1027-T1
Valid prediction for HiQ_model.g640.t1
Valid prediction for snap_scaffold_1-snap.1050-T1
Valid prediction for CodingQuarry_transcript_2649-T1
Valid prediction for GlimmerHMM_glimmerT_813-T1
Valid prediction for CodingQuarry_transcript_2648-T1
Valid prediction for GlimmerHMM_glimmerT_836-T1
Valid prediction for GlimmerHMM_glimmerT_821-T1
Valid prediction for GlimmerHMM_glimmerT_849-T1
Valid prediction for snap_scaffold_1-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_844-T1
Valid prediction for snap_scaffold_1-snap.1049-T1
Valid prediction for snap_scaffold_1-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_816-T1
Valid prediction for GlimmerHMM_glimmerT_846-T1
Valid prediction for GlimmerHMM_glimmerT_843-T1
Valid prediction for GlimmerHMM_glimmerT_857-T1
Valid prediction for HiQ_model.g631.t1
Valid prediction for snap_scaffold_1-snap.1059-T1
Valid prediction for snap_scaffold_1-snap.1052-T1
Valid prediction for CodingQuarry_transcript_2647-T1
Valid prediction for Augustus_model.g626.t1
Valid prediction for GlimmerHMM_glimmerT_845-T1
Valid prediction for GlimmerHMM_glimmerT_818-T1
Valid prediction for GlimmerHMM_glimmerT_820-T1
Valid prediction for GlimmerHMM_glimmerT_847-T1
Valid prediction for HiQ_model.g623.t1
Valid prediction for pasa_asmbl_348.p1
Valid prediction for Augustus_model.g641.t1
Valid prediction for snap_scaffold_1-snap.1060-T1
Valid prediction for snap_scaffold_1-snap.1048-T1
Valid prediction for CodingQuarry_transcript_2656-T1
Valid prediction for Augustus_model.g621.t1
Couldn't classify 181500, 181609
Sorry, prediction pasa_asmbl_353.p1 fails validation.
(CCG)	 CC	181500-181609	GT	AAG
(GGA)	 AG	181715-182054	GA	AGG
-recovered pasa_asmbl_353.p1, terminal, 181715, 182054
Valid prediction for HiQ_model.g628.t1
Valid prediction for GlimmerHMM_glimmerT_842-T1
Couldn't classify 178983, 179008
Couldn't classify 180014, 180180
Sorry, prediction pasa_asmbl_354.p1 fails validation.
(GCG)	 AA	178983-179008	GT	AGG
(AAA)	 AG	179354-179453	GT	TGG
(GAC)	 AG	179645-179807	GT	AGG
(AGG)	 AG	180014-180180	GT	TGG
-recovered pasa_asmbl_354.p1, internal, 179354, 179453
-recovered pasa_asmbl_354.p1, internal, 179645, 179807
-recovered pasa_asmbl_354.p1, internal, 180014, 180180
Valid prediction for GlimmerHMM_glimmerT_839-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20077, rend_intergenic: 17125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85871, rend_intergenic: 85477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99651, rend_intergenic: 86371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113039, rend_intergenic: 101903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205423, rend_intergenic: 197299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210153, rend_intergenic: 205689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215890, rend_intergenic: 211053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223309
-exon list size: 577


building trellis

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84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
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 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 20077, rend_intergenic: 17125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85871, rend_intergenic: 85477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99651, rend_intergenic: 86371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113039, rend_intergenic: 101903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205423, rend_intergenic: 197299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210153, rend_intergenic: 205689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215890, rend_intergenic: 211053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support