-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_16296723-16450992

-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.8556_t
Valid prediction for CodingQuarry_transcript_28749-T1
Valid prediction for HiQ_model.g3631.t1
Valid prediction for snap_scaffold_2-snap.3167-T1
Valid prediction for GlimmerHMM_glimmerT_5345-T1
Valid prediction for snap_scaffold_2-snap.3170-T1
Valid prediction for GlimmerHMM_glimmerT_5340-T1
Couldn't classify 67076, 67147
Couldn't classify 67934, 68293
Sorry, prediction pasa_asmbl_25398.p1 fails validation.
(AAG)	 AC	67076-67147	GT	TGG
(GAC)	 AG	67934-68293	GG	AGG
Valid prediction for GeneMark_model.8540_t
Valid prediction for GeneMark_model.8555_t
Valid prediction for snap_scaffold_2-snap.3156-T1
Valid prediction for snap_scaffold_2-snap.3165-T1
Valid prediction for pasa_asmbl_25171.p1
Valid prediction for GlimmerHMM_glimmerT_5339-T1
Valid prediction for snap_scaffold_2-snap.3180-T1
Valid prediction for snap_scaffold_2-snap.3161-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3158-T1
Valid prediction for GlimmerHMM_glimmerT_5341-T1
Valid prediction for CodingQuarry_transcript_28747-T1
Valid prediction for GeneMark_model.8547_t
Valid prediction for GeneMark_model.8542_t
Couldn't classify 8117, 8374
Sorry, prediction pasa_asmbl_25149.p1 fails validation.
(AAT)	 CC	8117-8374	GT	AGG
(ACC)	 AG	8561-8732	GT	AGG
(ACA)	 AG	8850-8991	GT	AGG
(ACA)	 AG	9480-9615	CA	GAC
-recovered pasa_asmbl_25149.p1, terminal, 9480, 9615
-recovered pasa_asmbl_25149.p1, internal, 8561, 8732
-recovered pasa_asmbl_25149.p1, internal, 8850, 8991
Valid prediction for Augustus_model.g3626.t1
Valid prediction for snap_scaffold_2-snap.3153-T1
Valid prediction for GeneMark_model.8546_t
Valid prediction for Augustus_model.g3616.t1
Valid prediction for snap_scaffold_2-snap.3171-T1
Valid prediction for Augustus_model.g3624.t1
Valid prediction for GeneMark_model.8533_t
Valid prediction for HiQ_model.g3614.t1
Valid prediction for GeneMark_model.8552_t
Valid prediction for snap_scaffold_2-snap.3178-T1
Valid prediction for CodingQuarry_transcript_28748-T1
Valid prediction for Augustus_model.g3623.t1
Valid prediction for snap_scaffold_2-snap.3168-T1
Valid prediction for GeneMark_model.8541_t
Valid prediction for snap_scaffold_2-snap.3155-T1
Valid prediction for CodingQuarry_transcript_28746-T1
Valid prediction for GlimmerHMM_glimmerT_5354-T1
Valid prediction for pasa_asmbl_25175.p1
Valid prediction for pasa_asmbl_25167.p1
Valid prediction for snap_scaffold_2-snap.3172-T1
Valid prediction for GeneMark_model.8537_t
Valid prediction for GlimmerHMM_glimmerT_5348-T1
Valid prediction for GeneMark_model.8536_t
Valid prediction for Augustus_model.g3628.t1
Valid prediction for GlimmerHMM_glimmerT_5349-T1
Valid prediction for GlimmerHMM_glimmerT_5355-T1
Valid prediction for CodingQuarry_transcript_28745-T1
Valid prediction for Augustus_model.g3618.t1
Valid prediction for GlimmerHMM_glimmerT_5350-T1
Valid prediction for HiQ_model.g3627.t1
Valid prediction for GeneMark_model.8544_t
Valid prediction for snap_scaffold_2-snap.3174-T1
Valid prediction for snap_scaffold_2-snap.3166-T1
Couldn't classify 63353, 63949
Sorry, prediction pasa_asmbl_25155.p1 fails validation.
(CAG)	 CT	63353-63949	TA	GAT
Valid prediction for GlimmerHMM_glimmerT_5334-T1
Valid prediction for CodingQuarry_transcript_28752-T1
Valid prediction for snap_scaffold_2-snap.3157-T1
Valid prediction for snap_scaffold_2-snap.3151-T1
Valid prediction for snap_scaffold_2-snap.3173-T1
Valid prediction for Augustus_model.g3619.t1
Valid prediction for snap_scaffold_2-snap.3160-T1
Valid prediction for GlimmerHMM_glimmerT_5338-T1
Valid prediction for GeneMark_model.8551_t
Valid prediction for GlimmerHMM_glimmerT_5346-T1
Valid prediction for snap_scaffold_2-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_5343-T1
Valid prediction for Augustus_model.g3622.t1
Valid prediction for snap_scaffold_2-snap.3164-T1
Valid prediction for snap_scaffold_2-snap.3159-T1
Valid prediction for GlimmerHMM_glimmerT_5344-T1
Couldn't classify 72973, 73031
Couldn't classify 74537, 74586
Sorry, prediction pasa_asmbl_25161.p1 fails validation.
(ACC)	 TC	72973-73031	GT	CAG
(GTA)	 AG	73595-73845	GT	AGG
(ATG)	 AG	74167-74421	GT	CGG
(AGA)	 AG	74537-74586	AT	GCA
add_exon() Sorry, pasa_asmbl_25161.p1 74167-74421-initial-1 is invalid.
-recovered pasa_asmbl_25161.p1, initial, 74167, 74421
-recovered pasa_asmbl_25161.p1, internal, 73595, 73845
-recovered pasa_asmbl_25161.p1, internal, 74167, 74421
Valid prediction for GeneMark_model.8538_t
Valid prediction for GeneMark_model.8550_t
Valid prediction for Augustus_model.g3621.t1
Valid prediction for CodingQuarry_transcript_28743-T1
Valid prediction for GlimmerHMM_glimmerT_5336-T1
Valid prediction for pasa_asmbl_25151.p1
Valid prediction for CodingQuarry_transcript_28750-T1
Couldn't classify 57492, 57640
Couldn't classify 58281, 58385
Sorry, prediction pasa_asmbl_25423.p1 fails validation.
(GTC)	 GG	57492-57640	GT	AGG
(GTC)	 AG	57994-58132	GT	AGG
(AGA)	 AG	58281-58385	AC	CAA
-recovered pasa_asmbl_25423.p1, internal, 57994, 58132

-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.8543_t
Valid prediction for Augustus_model.g3629.t1
Valid prediction for Augustus_model.g3613.t1
Valid prediction for GeneMark_model.8549_t
Valid prediction for snap_scaffold_2-snap.3169-T1
Valid prediction for GlimmerHMM_glimmerT_5337-T1
Valid prediction for GeneMark_model.8539_t
Valid prediction for GlimmerHMM_glimmerT_5347-T1
Valid prediction for GlimmerHMM_glimmerT_5333-T1
Valid prediction for snap_scaffold_2-snap.3177-T1
Valid prediction for GlimmerHMM_glimmerT_5342-T1
Valid prediction for HiQ_model.g3630.t1
Valid prediction for GeneMark_model.8535_t
Valid prediction for HiQ_model.g3620.t1
Valid prediction for snap_scaffold_2-snap.3175-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3152-T1
Valid prediction for GlimmerHMM_glimmerT_5353-T1
Valid prediction for Augustus_model.g3632.t1
Valid prediction for GlimmerHMM_glimmerT_5351-T1
Valid prediction for snap_scaffold_2-snap.3183-T1
Valid prediction for CodingQuarry_transcript_28744-T1
Valid prediction for snap_scaffold_2-snap.3176-T1
Valid prediction for GeneMark_model.8548_t
Valid prediction for Augustus_model.g3625.t1
Valid prediction for GeneMark_model.8554_t
Valid prediction for Augustus_model.g3617.t1
Valid prediction for snap_scaffold_2-snap.3179-T1
Couldn't classify 40773, 40820
Couldn't classify 42228, 42296
Sorry, prediction pasa_asmbl_23701.p1 fails validation.
(GCA)	 AG	40773-40820	GT	AGG
(TAC)	 AG	40942-41078	GT	GGG
(GTA)	 AG	41331-41455	GT	AGG
(CCC)	 AG	41563-41713	GT	CTG
(ATA)	 AG	41815-41911	GT	AGG
(AAC)	 AG	42019-42135	GT	AGG
(GTA)	 AG	42228-42296	GG	CGG
-recovered pasa_asmbl_23701.p1, internal, 40773, 40820
-recovered pasa_asmbl_23701.p1, internal, 40942, 41078
-recovered pasa_asmbl_23701.p1, internal, 41331, 41455
-recovered pasa_asmbl_23701.p1, internal, 41563, 41713
-recovered pasa_asmbl_23701.p1, internal, 41815, 41911
-recovered pasa_asmbl_23701.p1, internal, 42019, 42135
Valid prediction for snap_scaffold_2-snap.3162-T1
Valid prediction for pasa_asmbl_23704.p1
Valid prediction for GeneMark_model.8553_t
Valid prediction for GeneMark_model.8534_t
Couldn't classify 42459, 42521
Sorry, prediction pasa_asmbl_23699.p1 fails validation.
(GAG)	 CA	42459-42521	GT	GGG
(ATG)	 AG	42655-42771	GT	AGG
(GCT)	 AG	43023-43156	GT	AGG
(GTT)	 AG	43371-43419	GT	CTG
(AAC)	 AG	43546-43642	GT	GGG
(ACT)	 AG	43779-43889	GT	CTG
(CGC)	 AG	44178-44350	GT	GTG
(GCG)	 AG	44469-44588	GT	AGG
(TTC)	 AG	44666-44764	GT	TGG
(AAT)	 AG	44976-45049	GT	CAG
(GTA)	 AG	45143-45223	GT	AGG
(TGA)	 AG	45304-45421	GG	GAG
-recovered pasa_asmbl_23699.p1, initial, 42655, 42771
-recovered pasa_asmbl_23699.p1, terminal, 45304, 45421
-recovered pasa_asmbl_23699.p1, internal, 42655, 42771
-recovered pasa_asmbl_23699.p1, internal, 43023, 43156
-recovered pasa_asmbl_23699.p1, internal, 43371, 43419
-recovered pasa_asmbl_23699.p1, internal, 43546, 43642
-recovered pasa_asmbl_23699.p1, internal, 43779, 43889
-recovered pasa_asmbl_23699.p1, internal, 44178, 44350
-recovered pasa_asmbl_23699.p1, internal, 44469, 44588
-recovered pasa_asmbl_23699.p1, internal, 44666, 44764
-recovered pasa_asmbl_23699.p1, internal, 44976, 45049
-recovered pasa_asmbl_23699.p1, internal, 45143, 45223
Valid prediction for GeneMark_model.8545_t
Couldn't classify 39058, 39207
Couldn't classify 40244, 40363
Sorry, prediction pasa_asmbl_24066.p1 fails validation.
(CAG)	 GG	39058-39207	GT	AGG
(GAC)	 AG	39306-39428	GT	TGG
(GAC)	 AG	39540-39601	GT	AGG
(GTT)	 AG	39789-39903	GT	AGG
(GAG)	 AG	39994-40101	GT	AGG
(GCC)	 AG	40244-40363	GC	GAG
-recovered pasa_asmbl_24066.p1, internal, 39306, 39428
-recovered pasa_asmbl_24066.p1, internal, 39540, 39601
-recovered pasa_asmbl_24066.p1, internal, 39789, 39903
-recovered pasa_asmbl_24066.p1, internal, 39994, 40101
-recovered pasa_asmbl_24066.p1, internal, 40244, 40363
Valid prediction for snap_scaffold_2-snap.3154-T1
Valid prediction for GeneMark_model.8532_t
Valid prediction for snap_scaffold_2-snap.3184-T1
Valid prediction for snap_scaffold_2-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_5352-T1
Valid prediction for pasa_asmbl_23698.p1
Valid prediction for snap_scaffold_2-snap.3181-T1
Valid prediction for GlimmerHMM_glimmerT_5356-T1
Valid prediction for Augustus_model.g3615.t1
Valid prediction for snap_scaffold_2-snap.3182-T1
Valid prediction for GlimmerHMM_glimmerT_5335-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 80984, rend_intergenic: 77437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86606, rend_intergenic: 81468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110512, rend_intergenic: 108850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134434, rend_intergenic: 132178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154270
-exon list size: 473


building trellis

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99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 80984, rend_intergenic: 77437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86606, rend_intergenic: 81468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110512, rend_intergenic: 108850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134434, rend_intergenic: 132178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 143978 - 154270
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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