-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_3675818-3833290

-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 GeneMark_model.96433_t
Valid prediction for snap_scaffold_25-snap.784-T1
Valid prediction for GlimmerHMM_glimmerT_55215-T1
Valid prediction for GeneMark_model.96414_t
Valid prediction for GeneMark_model.96416_t
Valid prediction for GlimmerHMM_glimmerT_55200-T1
Valid prediction for GeneMark_model.96428_t
Valid prediction for GeneMark_model.96431_t
Valid prediction for Augustus_model.g36832.t1
Valid prediction for GlimmerHMM_glimmerT_55211-T1
Valid prediction for GeneMark_model.96426_t
Valid prediction for GeneMark_model.96435_t
Valid prediction for HiQ_model.g36816.t1
Valid prediction for HiQ_model.g36817.t1
Valid prediction for GeneMark_model.96413_t
Valid prediction for pasa_asmbl_33444.p1
Couldn't classify 79665, 79820
Sorry, prediction pasa_asmbl_33459.p1 fails validation.
(ATG)	 CC	72107-72120	GT	TGG
(GTT)	 AG	73832-74012	GT	AGG
(GAC)	 AG	75406-75630	GT	AGG
(GCC)	 AG	75897-75971	GT	AGG
(ATG)	 AG	76098-76223	GT	AGG
(GAG)	 AG	76702-76845	GT	AGG
(GGT)	 AG	77164-77253	GT	AGG
(CAC)	 AG	77385-77482	GT	AAG
(GCT)	 AG	77614-77674	GT	AGG
(AGG)	 AG	77789-77842	GT	AAG
(GAA)	 AG	79155-79187	GT	AGG
(GGA)	 AG	79665-79820	GT	CGG
-recovered pasa_asmbl_33459.p1, initial, 72107, 72120
-recovered pasa_asmbl_33459.p1, initial, 76098, 76223
-recovered pasa_asmbl_33459.p1, internal, 73832, 74012
-recovered pasa_asmbl_33459.p1, internal, 75406, 75630
-recovered pasa_asmbl_33459.p1, internal, 75897, 75971
-recovered pasa_asmbl_33459.p1, internal, 76098, 76223
-recovered pasa_asmbl_33459.p1, internal, 76702, 76845
-recovered pasa_asmbl_33459.p1, internal, 77164, 77253
-recovered pasa_asmbl_33459.p1, internal, 77385, 77482
-recovered pasa_asmbl_33459.p1, internal, 77614, 77674
-recovered pasa_asmbl_33459.p1, internal, 77789, 77842
-recovered pasa_asmbl_33459.p1, internal, 79155, 79187
-recovered pasa_asmbl_33459.p1, internal, 79665, 79820
Valid prediction for snap_scaffold_25-snap.814-T1
Couldn't classify 86983, 87084
Sorry, prediction pasa_asmbl_33462.p1 fails validation.
(TTT)	 TC	86983-87084	GT	AGG
(ATC)	 AG	88453-88719	CC	GAC
-recovered pasa_asmbl_33462.p1, terminal, 88453, 88719
Valid prediction for snap_scaffold_25-snap.798-T1
Valid prediction for GeneMark_model.96422_t
Valid prediction for CodingQuarry_transcript_38603-T1
Valid prediction for pasa_asmbl_33454.p1
Valid prediction for snap_scaffold_25-snap.808-T1
Valid prediction for snap_scaffold_25-snap.800-T1
Couldn't classify 82164, 82325
Couldn't classify 83329, 83424
Sorry, prediction pasa_asmbl_33940.p1 fails validation.
(CAG)	 CA	82164-82325	GT	AGG
(AAC)	 AG	82612-82758	GT	AGG
(AGC)	 AG	83329-83424	GT	AGG
-recovered pasa_asmbl_33940.p1, internal, 82612, 82758
-recovered pasa_asmbl_33940.p1, internal, 83329, 83424
Valid prediction for snap_scaffold_25-snap.778-T1
Valid prediction for CodingQuarry_transcript_38596-T1
Valid prediction for CodingQuarry_transcript_38598-T1
Valid prediction for GeneMark_model.96438_t
Valid prediction for snap_scaffold_25-snap.789-T1
Valid prediction for snap_scaffold_25-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_55197-T1
Valid prediction for snap_scaffold_25-snap.803-T1
Valid prediction for snap_scaffold_25-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_55201-T1
Valid prediction for GlimmerHMM_glimmerT_55204-T1
Valid prediction for Augustus_model.g36829.t1
Valid prediction for GlimmerHMM_glimmerT_55194-T1
Valid prediction for snap_scaffold_25-snap.796-T1
Valid prediction for snap_scaffold_25-snap.788-T1
Valid prediction for GeneMark_model.96424_t
Valid prediction for GlimmerHMM_glimmerT_55198-T1
Valid prediction for pasa_asmbl_33446.p1
Valid prediction for snap_scaffold_25-snap.799-T1
Valid prediction for GeneMark_model.96430_t
Valid prediction for GlimmerHMM_glimmerT_55195-T1
Valid prediction for Augustus_model.g36818.t1
Valid prediction for pasa_asmbl_33448.p1
Valid prediction for GeneMark_model.96412_t
Valid prediction for snap_scaffold_25-snap.777-T1
Valid prediction for Augustus_model.g36820.t1
Valid prediction for Augustus_model.g36831.t1
Valid prediction for GeneMark_model.96440_t
Valid prediction for GlimmerHMM_glimmerT_55210-T1
Valid prediction for CodingQuarry_transcript_38597-T1
Valid prediction for GlimmerHMM_glimmerT_55214-T1
Valid prediction for CodingQuarry_transcript_38601-T1
Valid prediction for Augustus_model.g36830.t1
Valid prediction for GeneMark_model.96417_t
Valid prediction for snap_scaffold_25-snap.806-T1
Valid prediction for snap_scaffold_25-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_55196-T1
Valid prediction for snap_scaffold_25-snap.807-T1
Valid prediction for snap_scaffold_25-snap.811-T1
Valid prediction for GeneMark_model.96429_t
Valid prediction for GlimmerHMM_glimmerT_55206-T1
Valid prediction for GlimmerHMM_glimmerT_55213-T1
Valid prediction for snap_scaffold_25-snap.805-T1
Valid prediction for snap_scaffold_25-snap.779-T1
Valid prediction for snap_scaffold_25-snap.780-T1
Valid prediction for HiQ_model.g36825.t1
Valid prediction for CodingQuarry_transcript_38602-T1
Valid prediction for snap_scaffold_25-snap.795-T1
Valid prediction for HiQ_model.g36823.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.96437_t
Valid prediction for snap_scaffold_25-snap.818-T1
Valid prediction for Augustus_model.g36836.t1
Valid prediction for GlimmerHMM_glimmerT_55199-T1
Valid prediction for HiQ_model.g36828.t1
Valid prediction for snap_scaffold_25-snap.810-T1
Valid prediction for Augustus_model.g36834.t1
Valid prediction for GeneMark_model.96415_t
Valid prediction for GlimmerHMM_glimmerT_55205-T1
Valid prediction for GeneMark_model.96420_t
Valid prediction for Augustus_model.g36819.t1
Valid prediction for GlimmerHMM_glimmerT_55212-T1
Couldn't classify 127153, 127281
Sorry, prediction pasa_asmbl_34129.p2 fails validation.
(AAA)	 GG	127153-127281	GT	AGG
(CCT)	 AG	127425-127583	GT	AGG
(GGC)	 AG	127679-127794	GT	AGG
(GTT)	 AG	127900-128002	GT	AGG
(CTA)	 AG	128132-128290	CG	GAC
-recovered pasa_asmbl_34129.p2, terminal, 128132, 128290
-recovered pasa_asmbl_34129.p2, internal, 127425, 127583
-recovered pasa_asmbl_34129.p2, internal, 127679, 127794
-recovered pasa_asmbl_34129.p2, internal, 127900, 128002
Valid prediction for snap_scaffold_25-snap.790-T1
Valid prediction for snap_scaffold_25-snap.801-T1
Valid prediction for pasa_asmbl_34134.p1
Valid prediction for Augustus_model.g36827.t1
Valid prediction for GeneMark_model.96439_t
Valid prediction for snap_scaffold_25-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_55216-T1
Valid prediction for snap_scaffold_25-snap.791-T1
Valid prediction for Augustus_model.g36822.t1
Valid prediction for GlimmerHMM_glimmerT_55217-T1
Valid prediction for Augustus_model.g36833.t1
Valid prediction for snap_scaffold_25-snap.817-T1
Valid prediction for CodingQuarry_transcript_38604-T1
Valid prediction for snap_scaffold_25-snap.793-T1
Valid prediction for GeneMark_model.96436_t
Couldn't classify 126216, 126446
Couldn't classify 126767, 126885
Sorry, prediction pasa_asmbl_34130.p1 fails validation.
(GGA)	 GA	126216-126446	GT	TTG
(CCT)	 AG	126601-126676	GT	GGG
(AGA)	 AG	126767-126885	GC	TGG
-recovered pasa_asmbl_34130.p1, internal, 126601, 126676
-recovered pasa_asmbl_34130.p1, internal, 126767, 126885
Valid prediction for snap_scaffold_25-snap.809-T1
Valid prediction for snap_scaffold_25-snap.813-T1
Valid prediction for snap_scaffold_25-snap.816-T1
Valid prediction for snap_scaffold_25-snap.782-T1
Valid prediction for GeneMark_model.96434_t
Valid prediction for GeneMark_model.96432_t
Valid prediction for GeneMark_model.96423_t
Valid prediction for CodingQuarry_transcript_38607-T1
Valid prediction for GlimmerHMM_glimmerT_55208-T1
Valid prediction for snap_scaffold_25-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_55209-T1
Couldn't classify 9897, 9961
Sorry, prediction pasa_asmbl_34144.p1 fails validation.
(ATG)	 CC	6811-7005	GT	CAG
(GAT)	 AG	7157-7294	GT	GGG
(CCA)	 AG	7413-7551	GT	AGG
(GTG)	 AG	7640-7764	GT	AGG
(ATC)	 AG	7871-8227	GT	GGG
(AAA)	 AG	8345-8473	GT	AGG
(GAT)	 AG	8574-8801	GT	AGG
(CTG)	 AG	8906-9090	GT	ACG
(GCC)	 AG	9182-9468	GT	CCG
(AGG)	 AG	9567-9677	GT	AAG
(GTC)	 AG	9897-9961	AG	ACA
-recovered pasa_asmbl_34144.p1, initial, 6811, 7005
-recovered pasa_asmbl_34144.p1, internal, 7157, 7294
-recovered pasa_asmbl_34144.p1, internal, 7413, 7551
-recovered pasa_asmbl_34144.p1, internal, 7640, 7764
-recovered pasa_asmbl_34144.p1, internal, 7871, 8227
-recovered pasa_asmbl_34144.p1, internal, 8345, 8473
-recovered pasa_asmbl_34144.p1, internal, 8574, 8801
-recovered pasa_asmbl_34144.p1, internal, 8906, 9090
-recovered pasa_asmbl_34144.p1, internal, 9182, 9468
-recovered pasa_asmbl_34144.p1, internal, 9567, 9677
Valid prediction for GeneMark_model.96419_t
Valid prediction for Augustus_model.g36821.t1
Valid prediction for GeneMark_model.96425_t
Valid prediction for CodingQuarry_transcript_38608-T1
Valid prediction for GeneMark_model.96421_t
Valid prediction for Augustus_model.g36837.t1
Couldn't classify 11620, 11746
Sorry, prediction pasa_asmbl_34140.p1 fails validation.
(CAA)	 AC	11620-11746	GT	AGG
(CCT)	 AG	11915-12256	GT	AGG
(GGT)	 AG	12460-12533	GT	AGG
(CAG)	 AG	12807-12888	GT	GAG
(CTA)	 AG	12992-13107	GT	AGG
(GAT)	 AG	13225-13421	GT	AGG
(TCT)	 AG	13533-13746	GT	CAG
(ATG)	 AG	13872-13940	AG	AAA
-recovered pasa_asmbl_34140.p1, terminal, 13872, 13940
-recovered pasa_asmbl_34140.p1, internal, 11915, 12256
-recovered pasa_asmbl_34140.p1, internal, 12460, 12533
-recovered pasa_asmbl_34140.p1, internal, 12807, 12888
-recovered pasa_asmbl_34140.p1, internal, 12992, 13107
-recovered pasa_asmbl_34140.p1, internal, 13225, 13421
-recovered pasa_asmbl_34140.p1, internal, 13533, 13746
Valid prediction for GlimmerHMM_glimmerT_55207-T1
Valid prediction for HiQ_model.g36824.t1
Valid prediction for GlimmerHMM_glimmerT_55202-T1
Valid prediction for GlimmerHMM_glimmerT_55218-T1
Valid prediction for snap_scaffold_25-snap.804-T1
Valid prediction for GeneMark_model.96441_t
Valid prediction for snap_scaffold_25-snap.786-T1
Valid prediction for Augustus_model.g36826.t1
Valid prediction for GlimmerHMM_glimmerT_55203-T1
Valid prediction for snap_scaffold_25-snap.812-T1
Valid prediction for GeneMark_model.96418_t
Valid prediction for pasa_asmbl_34132.p1
Valid prediction for GeneMark_model.96427_t
Valid prediction for Augustus_model.g36835.t1
Valid prediction for snap_scaffold_25-snap.787-T1
Valid prediction for snap_scaffold_25-snap.781-T1
Valid prediction for snap_scaffold_25-snap.785-T1
Valid prediction for CodingQuarry_transcript_38600-T1
Valid prediction for snap_scaffold_25-snap.794-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56206, rend_intergenic: 54860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60610, rend_intergenic: 58900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83685, rend_intergenic: 80822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124665, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127024, rend_intergenic: 124975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131705, rend_intergenic: 129056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157473
-exon list size: 562


building trellis

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94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 56206, rend_intergenic: 54860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60610, rend_intergenic: 58900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83685, rend_intergenic: 80822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124665, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127024, rend_intergenic: 124975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131705, rend_intergenic: 129056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support