-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_16230201-16459005

-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.3133-T1
Couldn't classify 133598, 133669
Couldn't classify 134456, 134815
Sorry, prediction pasa_asmbl_25367.p1 fails validation.
(AAG)	 AC	133598-133669	GT	TGG
(GAC)	 AG	134456-134815	GG	AGG
Valid prediction for CodingQuarry_transcript_28791-T1
Valid prediction for Augustus_model.g3529.t1
Valid prediction for GlimmerHMM_glimmerT_5213-T1
Valid prediction for Augustus_model.g3532.t1
Valid prediction for pasa_asmbl_25121.p1
Valid prediction for snap_scaffold_2-snap.3125-T1
Valid prediction for pasa_asmbl_25137.p1
Valid prediction for Augustus_model.g3541.t1
Couldn't classify 56065, 56419
Sorry, prediction pasa_asmbl_25110.p1 fails validation.
(ATG)	 AC	55229-55478	GT	AGG
(GTG)	 AG	55714-55924	GT	AGG
(GTA)	 AG	56065-56419	AA	CCA
-recovered pasa_asmbl_25110.p1, initial, 55229, 55478
-recovered pasa_asmbl_25110.p1, internal, 55714, 55924
Valid prediction for HiQ_model.g3539.t1
Valid prediction for snap_scaffold_2-snap.3135-T1
Valid prediction for GlimmerHMM_glimmerT_5205-T1
Valid prediction for snap_scaffold_2-snap.3130-T1
Valid prediction for GlimmerHMM_glimmerT_5225-T1
Couldn't classify 124014, 124162
Couldn't classify 124803, 124907
Sorry, prediction pasa_asmbl_25366.p1 fails validation.
(GTC)	 GG	124014-124162	GT	AGG
(GTC)	 AG	124516-124654	GT	AGG
(AGA)	 AG	124803-124907	AC	CAA
-recovered pasa_asmbl_25366.p1, internal, 124516, 124654
Valid prediction for GlimmerHMM_glimmerT_5220-T1
Valid prediction for CodingQuarry_transcript_28798-T1
Valid prediction for snap_scaffold_2-snap.3136-T1
Valid prediction for pasa_asmbl_25133.p1
Valid prediction for Augustus_model.g3534.t1
Valid prediction for HiQ_model.g3518.t1
Valid prediction for HiQ_model.g3517.t1
Valid prediction for Augustus_model.g3527.t1
Valid prediction for CodingQuarry_transcript_28790-T1
Valid prediction for Augustus_model.g3531.t1
Valid prediction for snap_scaffold_2-snap.3123-T1
Valid prediction for snap_scaffold_2-snap.3137-T1
Valid prediction for pasa_asmbl_25107.p1
Valid prediction for GlimmerHMM_glimmerT_5209-T1
Valid prediction for snap_scaffold_2-snap.3132-T1
Valid prediction for pasa_asmbl_25141.p1
Valid prediction for snap_scaffold_2-snap.3122-T1
Valid prediction for Augustus_model.g3530.t1
Couldn't classify 74639, 74896
Sorry, prediction pasa_asmbl_25120.p1 fails validation.
(AAT)	 CC	74639-74896	GT	AGG
(ACC)	 AG	75083-75254	GT	AGG
(ACA)	 AG	75372-75513	GT	AGG
(ACA)	 AG	76002-76137	CA	GAC
-recovered pasa_asmbl_25120.p1, terminal, 76002, 76137
-recovered pasa_asmbl_25120.p1, internal, 75083, 75254
-recovered pasa_asmbl_25120.p1, internal, 75372, 75513
Valid prediction for snap_scaffold_2-snap.3112-T1
Valid prediction for snap_scaffold_2-snap.3120-T1
Valid prediction for GlimmerHMM_glimmerT_5200-T1
Valid prediction for pasa_asmbl_25103.p1
Valid prediction for CodingQuarry_transcript_28794-T1
Valid prediction for snap_scaffold_2-snap.3129-T1
Valid prediction for GlimmerHMM_glimmerT_5224-T1
Valid prediction for snap_scaffold_2-snap.3115-T1
Valid prediction for snap_scaffold_2-snap.3116-T1
Valid prediction for CodingQuarry_transcript_28797-T1
Valid prediction for snap_scaffold_2-snap.3142-T1
Valid prediction for GlimmerHMM_glimmerT_5215-T1
Valid prediction for GlimmerHMM_glimmerT_5203-T1
Valid prediction for snap_scaffold_2-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_5218-T1
Valid prediction for HiQ_model.g3535.t1
Valid prediction for snap_scaffold_2-snap.3150-T1
Valid prediction for snap_scaffold_2-snap.3144-T1
Valid prediction for snap_scaffold_2-snap.3118-T1
Valid prediction for HiQ_model.g3522.t1
Valid prediction for GlimmerHMM_glimmerT_5207-T1
Valid prediction for HiQ_model.g3519.t1
Couldn't classify 139495, 139553
Couldn't classify 141059, 141108
Sorry, prediction pasa_asmbl_25127.p1 fails validation.
(ACC)	 TC	139495-139553	GT	CAG
(GTA)	 AG	140117-140367	GT	AGG
(ATG)	 AG	140689-140943	GT	CGG
(AGA)	 AG	141059-141108	AT	GCA
add_exon() Sorry, pasa_asmbl_25127.p1 140689-140943-initial-1 is invalid.
-recovered pasa_asmbl_25127.p1, initial, 140689, 140943
-recovered pasa_asmbl_25127.p1, internal, 140117, 140367
-recovered pasa_asmbl_25127.p1, internal, 140689, 140943
Valid prediction for snap_scaffold_2-snap.3108-T1
Valid prediction for Augustus_model.g3536.t1
Valid prediction for snap_scaffold_2-snap.3138-T1
Valid prediction for snap_scaffold_2-snap.3128-T1
Valid prediction for Augustus_model.g3524.t1
Valid prediction for GlimmerHMM_glimmerT_5202-T1
Valid prediction for GlimmerHMM_glimmerT_5208-T1
Valid prediction for CodingQuarry_transcript_28792-T1
Valid prediction for snap_scaffold_2-snap.3113-T1
Valid prediction for HiQ_model.g3520.t1
Valid prediction for GlimmerHMM_glimmerT_5219-T1
Valid prediction for CodingQuarry_transcript_28796-T1
Valid prediction for pasa_asmbl_25116.p1
Couldn't classify 129875, 130471
Sorry, prediction pasa_asmbl_25124.p1 fails validation.
(CAG)	 CT	129875-130471	TA	GAT
Valid prediction for GlimmerHMM_glimmerT_5214-T1
Valid prediction for snap_scaffold_2-snap.3151-T1
Valid prediction for snap_scaffold_2-snap.3152-T1
Valid prediction for Augustus_model.g3526.t1
Valid prediction for CodingQuarry_transcript_28801-T1
Couldn't classify 56438, 56500
Sorry, prediction pasa_asmbl_25111.p1 fails validation.
(CCA)	 GT	56438-56500	GT	AGG
(GAC)	 AG	56609-56728	GT	AGG
(GGA)	 AG	56865-56996	GT	AGG
(GAT)	 AG	57086-57197	GT	GGG
(GTG)	 AG	57403-57475	GT	AGG
(TCT)	 AG	57542-57678	GT	AGG
(GGC)	 AG	57867-58000	GT	GGG
(GCT)	 AG	58110-58124	GA	AGG
-recovered pasa_asmbl_25111.p1, terminal, 58110, 58124
-recovered pasa_asmbl_25111.p1, internal, 56609, 56728
-recovered pasa_asmbl_25111.p1, internal, 56865, 56996
-recovered pasa_asmbl_25111.p1, internal, 57086, 57197
-recovered pasa_asmbl_25111.p1, internal, 57403, 57475
-recovered pasa_asmbl_25111.p1, internal, 57542, 57678
-recovered pasa_asmbl_25111.p1, internal, 57867, 58000
Valid prediction for GlimmerHMM_glimmerT_5201-T1
Valid prediction for GlimmerHMM_glimmerT_5210-T1
Valid prediction for snap_scaffold_2-snap.3131-T1
Valid prediction for CodingQuarry_transcript_28799-T1
Valid prediction for GlimmerHMM_glimmerT_5212-T1
Valid prediction for CodingQuarry_transcript_28793-T1
Valid prediction for snap_scaffold_2-snap.3126-T1
Sorry, intron length (5) is less than minimum required (10)

-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: -)Couldn't classify 50472, 50534
Sorry, prediction pasa_asmbl_23686.p1 fails validation.
(GAG)	 CA	50472-50534	GT	GGG
(ATG)	 AG	50668-50784	GT	AGG
(GCT)	 AG	51036-51169	GT	AGG
(GTT)	 AG	51384-51432	GT	CTG
(AAC)	 AG	51559-51655	GT	GGG
(ACT)	 AG	51792-51902	GT	CTG
(CGC)	 AG	52191-52363	GT	GTG
(GCG)	 AG	52482-52601	GT	AGG
(TTC)	 AG	52679-52777	GT	TGG
(AAT)	 AG	52989-53062	GT	CAG
(GTA)	 AG	53156-53236	GT	AGG
(TGA)	 AG	53317-53434	GG	GAG
-recovered pasa_asmbl_23686.p1, initial, 50668, 50784
-recovered pasa_asmbl_23686.p1, terminal, 53317, 53434
-recovered pasa_asmbl_23686.p1, internal, 50668, 50784
-recovered pasa_asmbl_23686.p1, internal, 51036, 51169
-recovered pasa_asmbl_23686.p1, internal, 51384, 51432
-recovered pasa_asmbl_23686.p1, internal, 51559, 51655
-recovered pasa_asmbl_23686.p1, internal, 51792, 51902
-recovered pasa_asmbl_23686.p1, internal, 52191, 52363
-recovered pasa_asmbl_23686.p1, internal, 52482, 52601
-recovered pasa_asmbl_23686.p1, internal, 52679, 52777
-recovered pasa_asmbl_23686.p1, internal, 52989, 53062
-recovered pasa_asmbl_23686.p1, internal, 53156, 53236
Valid prediction for pasa_asmbl_23691.p1
Couldn't classify 47071, 47220
Couldn't classify 48257, 48376
Sorry, prediction pasa_asmbl_23999.p1 fails validation.
(CAG)	 GG	47071-47220	GT	AGG
(GAC)	 AG	47319-47441	GT	TGG
(GAC)	 AG	47553-47614	GT	AGG
(GTT)	 AG	47802-47916	GT	AGG
(GAG)	 AG	48007-48114	GT	AGG
(GCC)	 AG	48257-48376	GC	GAG
-recovered pasa_asmbl_23999.p1, internal, 47319, 47441
-recovered pasa_asmbl_23999.p1, internal, 47553, 47614
-recovered pasa_asmbl_23999.p1, internal, 47802, 47916
-recovered pasa_asmbl_23999.p1, internal, 48007, 48114
-recovered pasa_asmbl_23999.p1, internal, 48257, 48376
Valid prediction for snap_scaffold_2-snap.3143-T1
Couldn't classify 48786, 48833
Couldn't classify 50241, 50309
Sorry, prediction pasa_asmbl_23687.p1 fails validation.
(GCA)	 AG	48786-48833	GT	AGG
(TAC)	 AG	48955-49091	GT	GGG
(GTA)	 AG	49344-49468	GT	AGG
(CCC)	 AG	49576-49726	GT	CTG
(ATA)	 AG	49828-49924	GT	AGG
(AAC)	 AG	50032-50148	GT	AGG
(GTA)	 AG	50241-50309	GG	CGG
-recovered pasa_asmbl_23687.p1, internal, 48786, 48833
-recovered pasa_asmbl_23687.p1, internal, 48955, 49091
-recovered pasa_asmbl_23687.p1, internal, 49344, 49468
-recovered pasa_asmbl_23687.p1, internal, 49576, 49726
-recovered pasa_asmbl_23687.p1, internal, 49828, 49924
-recovered pasa_asmbl_23687.p1, internal, 50032, 50148
Valid prediction for GlimmerHMM_glimmerT_5204-T1
Valid prediction for Augustus_model.g3516.t1
Valid prediction for snap_scaffold_2-snap.3147-T1
Valid prediction for snap_scaffold_2-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_5199-T1
Valid prediction for GlimmerHMM_glimmerT_5196-T1
Valid prediction for Augustus_model.g3523.t1
Valid prediction for snap_scaffold_2-snap.3121-T1
Valid prediction for snap_scaffold_2-snap.3146-T1
Valid prediction for snap_scaffold_2-snap.3145-T1
Valid prediction for Augustus_model.g3537.t1
Valid prediction for snap_scaffold_2-snap.3141-T1
Valid prediction for snap_scaffold_2-snap.3109-T1
Valid prediction for Augustus_model.g3515.t1
Valid prediction for snap_scaffold_2-snap.3110-T1
Valid prediction for GlimmerHMM_glimmerT_5216-T1
Valid prediction for GlimmerHMM_glimmerT_5217-T1
Valid prediction for GlimmerHMM_glimmerT_5198-T1
Valid prediction for snap_scaffold_2-snap.3149-T1
Valid prediction for snap_scaffold_2-snap.3148-T1
Valid prediction for CodingQuarry_transcript_28795-T1
Valid prediction for HiQ_model.g3538.t1
Valid prediction for GlimmerHMM_glimmerT_5197-T1
Valid prediction for GlimmerHMM_glimmerT_5211-T1
Couldn't classify 200090, 200111
Couldn't classify 200906, 201058
Sorry, prediction pasa_asmbl_23679.p1 fails validation.
(CGG)	 AA	200090-200111	GT	AGG
(ACA)	 AG	200223-200338	GT	AGG
(GTG)	 AG	200485-200592	GT	CTG
(GCT)	 AG	200906-201058	AT	GAA
-recovered pasa_asmbl_23679.p1, internal, 200223, 200338
-recovered pasa_asmbl_23679.p1, internal, 200485, 200592
Valid prediction for GlimmerHMM_glimmerT_5223-T1
Valid prediction for snap_scaffold_2-snap.3139-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5226-T1
Valid prediction for GlimmerHMM_glimmerT_5221-T1
Valid prediction for snap_scaffold_2-snap.3114-T1
Valid prediction for snap_scaffold_2-snap.3127-T1
Valid prediction for pasa_asmbl_23685.p1
Valid prediction for HiQ_model.g3528.t1
Valid prediction for snap_scaffold_2-snap.3111-T1
Valid prediction for snap_scaffold_2-snap.3140-T1
Valid prediction for Augustus_model.g3540.t1
Valid prediction for Augustus_model.g3521.t1
Valid prediction for Augustus_model.g3525.t1
Valid prediction for snap_scaffold_2-snap.3134-T1
Valid prediction for snap_scaffold_2-snap.3117-T1
Valid prediction for Augustus_model.g3533.t1
Valid prediction for GlimmerHMM_glimmerT_5206-T1
Valid prediction for GlimmerHMM_glimmerT_5222-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 53524, rend_intergenic: 43503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147506, rend_intergenic: 143959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153128, rend_intergenic: 147990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177034, rend_intergenic: 175372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200956, rend_intergenic: 198700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227101, rend_intergenic: 222370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228805
-exon list size: 542


building trellis

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86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 53524, rend_intergenic: 43503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147506, rend_intergenic: 143959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153128, rend_intergenic: 147990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177034, rend_intergenic: 175372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200956, rend_intergenic: 198700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227101, rend_intergenic: 222370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16931
-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 1133 - 16931
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 2092 - 16931