-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_18147558-18354933

-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 Augustus_model.g7283.t1
Couldn't classify 135270, 135716
Sorry, prediction pasa_asmbl_42087.p1 fails validation.
(ACC)	 GG	135270-135716	GC	CGG
Valid prediction for snap_scaffold_4-snap.3725-T1
Valid prediction for GlimmerHMM_glimmerT_11110-T1
Couldn't classify 87466, 87520
Couldn't classify 90153, 90359
Sorry, prediction pasa_asmbl_42080.p1 fails validation.
(GAA)	 GA	87466-87520	GT	AGG
(GCT)	 AG	88781-88929	GT	AGG
(ATA)	 AG	89319-89462	GT	CAG
(GGG)	 AG	90153-90359	GT	AGG
-recovered pasa_asmbl_42080.p1, internal, 88781, 88929
-recovered pasa_asmbl_42080.p1, internal, 89319, 89462
-recovered pasa_asmbl_42080.p1, internal, 90153, 90359
Valid prediction for snap_scaffold_4-snap.3755-T1
Valid prediction for snap_scaffold_4-snap.3732-T1
Valid prediction for Augustus_model.g7285.t1
Valid prediction for snap_scaffold_4-snap.3751-T1
Couldn't classify 109370, 109539
Couldn't classify 111109, 111181
Sorry, prediction pasa_asmbl_42083.p1 fails validation.
(GGA)	 TG	109370-109539	GT	GGG
(GAT)	 AG	110328-110396	GT	TGG
(GAC)	 AG	111109-111181	GT	AGG
-recovered pasa_asmbl_42083.p1, internal, 110328, 110396
-recovered pasa_asmbl_42083.p1, internal, 111109, 111181
Couldn't classify 45194, 45373
Sorry, prediction pasa_asmbl_42268.p1 fails validation.
(GGT)	 CA	45194-45373	GT	CGG
(AGT)	 AG	48172-48288	GT	TGG
(ACC)	 AG	48767-48817	CC	AAC
-recovered pasa_asmbl_42268.p1, terminal, 48767, 48817
-recovered pasa_asmbl_42268.p1, internal, 48172, 48288
Valid prediction for GlimmerHMM_glimmerT_11091-T1
Valid prediction for GlimmerHMM_glimmerT_11096-T1
Valid prediction for snap_scaffold_4-snap.3739-T1
Valid prediction for snap_scaffold_4-snap.3753-T1
Valid prediction for GlimmerHMM_glimmerT_11097-T1
Valid prediction for Augustus_model.g7287.t1
Valid prediction for CodingQuarry_transcript_49367-T1
Valid prediction for Augustus_model.g7281.t1
Valid prediction for snap_scaffold_4-snap.3736-T1
Valid prediction for snap_scaffold_4-snap.3746-T1
Valid prediction for pasa_asmbl_42096.p1
Couldn't classify 136344, 137207
Sorry, prediction pasa_asmbl_42089.p1 fails validation.
(TCC)	 CC	136344-137207	CA	CGC
Valid prediction for GlimmerHMM_glimmerT_11098-T1
Couldn't classify 137442, 138198
Couldn't classify 141896, 141977
Sorry, prediction pasa_asmbl_42091.p1 fails validation.
(CCC)	 AC	137442-138198	GT	AGG
(GAC)	 AG	140820-141144	GT	AGG
(TTC)	 AG	141369-141542	GT	GAG
(ACC)	 AG	141896-141977	GG	TGG
-recovered pasa_asmbl_42091.p1, terminal, 140820, 141144
-recovered pasa_asmbl_42091.p1, internal, 140820, 141144
-recovered pasa_asmbl_42091.p1, internal, 141369, 141542
Valid prediction for HiQ_model.g7282.t1
Valid prediction for GlimmerHMM_glimmerT_11090-T1
Valid prediction for snap_scaffold_4-snap.3754-T1
Couldn't classify 144010, 144220
Sorry, prediction pasa_asmbl_42092.p2 fails validation.
(GAG)	 GC	144010-144220	GT	AGG
(GTC)	 AG	144794-144876	GT	ATG
(AGC)	 AG	145182-145301	GA	GAG
-recovered pasa_asmbl_42092.p2, terminal, 145182, 145301
-recovered pasa_asmbl_42092.p2, internal, 144794, 144876
Couldn't classify 106003, 106170
Couldn't classify 109217, 109297
Sorry, prediction pasa_asmbl_42082.p1 fails validation.
(CGG)	 AC	106003-106170	GT	CGG
(GAG)	 AG	108066-108124	GT	AGG
(TCT)	 AG	108581-108635	GT	AGG
(CTG)	 AG	109217-109297	GG	GGG
-recovered pasa_asmbl_42082.p1, internal, 108066, 108124
-recovered pasa_asmbl_42082.p1, internal, 108581, 108635
Valid prediction for GlimmerHMM_glimmerT_11106-T1
Valid prediction for snap_scaffold_4-snap.3765-T1
Couldn't classify 135720, 136247
Sorry, prediction pasa_asmbl_42088.p1 fails validation.
(CCC)	 CC	135720-136247	CA	CCC
Valid prediction for snap_scaffold_4-snap.3734-T1
Valid prediction for GlimmerHMM_glimmerT_11100-T1
Valid prediction for snap_scaffold_4-snap.3724-T1
Valid prediction for Augustus_model.g7286.t1
Valid prediction for snap_scaffold_4-snap.3738-T1
Valid prediction for GlimmerHMM_glimmerT_11108-T1
Valid prediction for GlimmerHMM_glimmerT_11101-T1
Valid prediction for snap_scaffold_4-snap.3758-T1
Couldn't classify 131854, 132456
Couldn't classify 134154, 134225
Sorry, prediction pasa_asmbl_42084.p1 fails validation.
(GCT)	 AC	131854-132456	GT	AGG
(GTT)	 AG	134154-134225	AT	GCA
Valid prediction for HiQ_model.g7298.t1
Valid prediction for snap_scaffold_4-snap.3745-T1
Valid prediction for snap_scaffold_4-snap.3762-T1
Valid prediction for snap_scaffold_4-snap.3741-T1
Valid prediction for snap_scaffold_4-snap.3731-T1
Valid prediction for Augustus_model.g7284.t1
Valid prediction for Augustus_model.g7289.t1
Valid prediction for snap_scaffold_4-snap.3761-T1
Couldn't classify 96327, 96419
Couldn't classify 98096, 98167
Sorry, prediction pasa_asmbl_42081.p1 fails validation.
(TGC)	 AC	96327-96419	GT	TGG
(AAC)	 AG	96876-96989	GT	AGG
(GCT)	 AG	97680-97775	GT	AGG
(ACG)	 AG	98096-98167	GG	GAG
-recovered pasa_asmbl_42081.p1, internal, 96876, 96989
-recovered pasa_asmbl_42081.p1, internal, 97680, 97775
Valid prediction for snap_scaffold_4-snap.3767-T1
Valid prediction for GlimmerHMM_glimmerT_11092-T1
Valid prediction for GlimmerHMM_glimmerT_11099-T1
Valid prediction for GlimmerHMM_glimmerT_11094-T1
Valid prediction for GlimmerHMM_glimmerT_11089-T1
Valid prediction for Augustus_model.g7280.t1
Valid prediction for snap_scaffold_4-snap.3764-T1
Valid prediction for Augustus_model.g7292.t1
Valid prediction for GlimmerHMM_glimmerT_11104-T1
Valid prediction for snap_scaffold_4-snap.3730-T1
Couldn't classify 134310, 134834
Couldn't classify 134895, 135119
Sorry, prediction pasa_asmbl_42086.p1 fails validation.
(CCC)	 CC	134310-134834	GT	AGG
(GAG)	 AG	134895-135119	GA	CCG
Valid prediction for snap_scaffold_4-snap.3726-T1
Valid prediction for CodingQuarry_transcript_49365-T1
Valid prediction for snap_scaffold_4-snap.3748-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 Augustus_model.g7293.t1
Valid prediction for snap_scaffold_4-snap.3727-T1
Couldn't classify 14263, 14298
Couldn't classify 14453, 14581
Sorry, prediction CodingQuarry_transcript_49369-T1 fails validation.
(ATG)	 AT	14263-14298	GA	CAG
(CAC)	 CA	14453-14581	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_11107-T1
Valid prediction for GlimmerHMM_glimmerT_11116-T1
Valid prediction for CodingQuarry_transcript_49366-T1
Valid prediction for GlimmerHMM_glimmerT_11105-T1
Couldn't classify 85760, 85841
Sorry, prediction pasa_asmbl_43354.p1 fails validation.
(TTT)	 AG	85760-85841	GT	AGG
(CTC)	 AG	86183-86329	GT	GGG
(GTA)	 AG	86864-86997	GT	AGG
(ATC)	 AG	87245-87417	GT	AGG
(GTT)	 AG	87614-87703	GT	AGG
(TTT)	 AG	88863-89010	GT	TGG
(GTG)	 AG	89349-89573	GT	AGG
(GAC)	 AG	90443-90606	GT	AGG
(CAA)	 AG	90722-90838	GT	AGG
(GTC)	 AG	90919-91024	TG	GAT
-recovered pasa_asmbl_43354.p1, terminal, 90919, 91024
-recovered pasa_asmbl_43354.p1, internal, 85760, 85841
-recovered pasa_asmbl_43354.p1, internal, 86183, 86329
-recovered pasa_asmbl_43354.p1, internal, 86864, 86997
-recovered pasa_asmbl_43354.p1, internal, 87245, 87417
-recovered pasa_asmbl_43354.p1, internal, 87614, 87703
-recovered pasa_asmbl_43354.p1, internal, 88863, 89010
-recovered pasa_asmbl_43354.p1, internal, 89349, 89573
-recovered pasa_asmbl_43354.p1, internal, 90443, 90606
-recovered pasa_asmbl_43354.p1, internal, 90722, 90838
Valid prediction for GlimmerHMM_glimmerT_11109-T1
Valid prediction for HiQ_model.g7290.t1
Valid prediction for snap_scaffold_4-snap.3757-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3733-T1
Valid prediction for snap_scaffold_4-snap.3749-T1
Valid prediction for snap_scaffold_4-snap.3750-T1
Valid prediction for snap_scaffold_4-snap.3747-T1
Couldn't classify 11757, 11822
Sorry, prediction pasa_asmbl_43364.p1 fails validation.
(ATG)	 TT	7727-7850	GT	TGG
(GAA)	 AG	9215-9275	GT	TGG
(GGA)	 AG	9855-9915	GT	TGG
(GGA)	 AG	10053-10130	GT	AGG
(AAC)	 AG	10826-10915	GT	AGG
(CTG)	 AG	11757-11822	GT	AGG
-recovered pasa_asmbl_43364.p1, initial, 7727, 7850
-recovered pasa_asmbl_43364.p1, internal, 9215, 9275
-recovered pasa_asmbl_43364.p1, internal, 9855, 9915
-recovered pasa_asmbl_43364.p1, internal, 10053, 10130
-recovered pasa_asmbl_43364.p1, internal, 10826, 10915
-recovered pasa_asmbl_43364.p1, internal, 11757, 11822
Valid prediction for snap_scaffold_4-snap.3729-T1
Valid prediction for snap_scaffold_4-snap.3743-T1
Valid prediction for snap_scaffold_4-snap.3728-T1
Valid prediction for GlimmerHMM_glimmerT_11093-T1
Valid prediction for snap_scaffold_4-snap.3763-T1
Valid prediction for snap_scaffold_4-snap.3742-T1
Valid prediction for snap_scaffold_4-snap.3737-T1
Valid prediction for HiQ_model.g7294.t1
Valid prediction for snap_scaffold_4-snap.3723-T1
Valid prediction for GlimmerHMM_glimmerT_11095-T1
Valid prediction for snap_scaffold_4-snap.3744-T1
Valid prediction for GlimmerHMM_glimmerT_11115-T1
Valid prediction for snap_scaffold_4-snap.3759-T1
Valid prediction for GlimmerHMM_glimmerT_11111-T1
Valid prediction for snap_scaffold_4-snap.3756-T1
Valid prediction for pasa_asmbl_43357.p1
Valid prediction for snap_scaffold_4-snap.3760-T1
Valid prediction for Augustus_model.g7296.t1
Valid prediction for GlimmerHMM_glimmerT_11102-T1
Valid prediction for CodingQuarry_transcript_49368-T1
Valid prediction for snap_scaffold_4-snap.3740-T1
Valid prediction for HiQ_model.g7288.t1
Valid prediction for HiQ_model.g7291.t1
Valid prediction for snap_scaffold_4-snap.3722-T1
Valid prediction for pasa_asmbl_43359.p1
Valid prediction for snap_scaffold_4-snap.3752-T1
Valid prediction for pasa_asmbl_43352.p1
Valid prediction for GlimmerHMM_glimmerT_11112-T1
Valid prediction for Augustus_model.g7295.t1
Valid prediction for GlimmerHMM_glimmerT_11113-T1
Valid prediction for Augustus_model.g7297.t1
Valid prediction for pasa_asmbl_43360.p1
Valid prediction for GlimmerHMM_glimmerT_11114-T1
Valid prediction for snap_scaffold_4-snap.3735-T1
Valid prediction for GlimmerHMM_glimmerT_11103-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30547, rend_intergenic: 15240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37826, rend_intergenic: 30660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59729, rend_intergenic: 38706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66739, rend_intergenic: 61430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71273, rend_intergenic: 66832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74040, rend_intergenic: 71655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79248, rend_intergenic: 74569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83687, rend_intergenic: 79329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98190, rend_intergenic: 86799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104880, rend_intergenic: 99307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115360, rend_intergenic: 107558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126787, rend_intergenic: 116087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132388, rend_intergenic: 130876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145301, rend_intergenic: 132413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149090, rend_intergenic: 145332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166159, rend_intergenic: 157237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168000, rend_intergenic: 166392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177152, rend_intergenic: 173099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189651, rend_intergenic: 180219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199650, rend_intergenic: 191966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207376
-exon list size: 453


building trellis

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96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 30547, rend_intergenic: 15240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37826, rend_intergenic: 30660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59729, rend_intergenic: 38706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66739, rend_intergenic: 61430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71273, rend_intergenic: 66832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74040, rend_intergenic: 71655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79248, rend_intergenic: 74569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83687, rend_intergenic: 79329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98190, rend_intergenic: 86799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104880, rend_intergenic: 99307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115360, rend_intergenic: 107558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126787, rend_intergenic: 116087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132388, rend_intergenic: 130876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145301, rend_intergenic: 132413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149090, rend_intergenic: 145332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166159, rend_intergenic: 157237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168000, rend_intergenic: 166392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177152, rend_intergenic: 173099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189651, rend_intergenic: 180219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199650, rend_intergenic: 191966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14063
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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

-building DP trellis

-building trellis in range 1 - 12207
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support