-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_3574483-3722921

-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.15298_t
Valid prediction for Augustus_model.g6017.t1
Valid prediction for snap_scaffold_4-snap.840-T1
Valid prediction for GeneMark_model.15297_t
Valid prediction for GlimmerHMM_glimmerT_9300-T1
Valid prediction for GlimmerHMM_glimmerT_9291-T1
Valid prediction for snap_scaffold_4-snap.834-T1
Valid prediction for Augustus_model.g6029.t1
Valid prediction for snap_scaffold_4-snap.823-T1
Valid prediction for GlimmerHMM_glimmerT_9285-T1
Valid prediction for snap_scaffold_4-snap.837-T1
Valid prediction for GlimmerHMM_glimmerT_9288-T1
Valid prediction for snap_scaffold_4-snap.826-T1
Valid prediction for Augustus_model.g6024.t1
Valid prediction for Augustus_model.g6027.t1
Valid prediction for GeneMark_model.15315_t
Valid prediction for Augustus_model.g6020.t1
Valid prediction for snap_scaffold_4-snap.812-T1
Valid prediction for GlimmerHMM_glimmerT_9280-T1
Valid prediction for snap_scaffold_4-snap.836-T1
Valid prediction for Augustus_model.g6022.t1
Valid prediction for snap_scaffold_4-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_9296-T1
Valid prediction for snap_scaffold_4-snap.838-T1
Valid prediction for GeneMark_model.15311_t
Valid prediction for GeneMark_model.15319_t
Valid prediction for GeneMark_model.15324_t
Valid prediction for GeneMark_model.15301_t
Valid prediction for GeneMark_model.15320_t
Valid prediction for snap_scaffold_4-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_9283-T1
Valid prediction for GlimmerHMM_glimmerT_9295-T1
Valid prediction for Augustus_model.g6023.t1
Valid prediction for GeneMark_model.15309_t
Valid prediction for GlimmerHMM_glimmerT_9293-T1
Valid prediction for snap_scaffold_4-snap.831-T1
Valid prediction for snap_scaffold_4-snap.811-T1
Valid prediction for GeneMark_model.15305_t
Valid prediction for snap_scaffold_4-snap.829-T1
Valid prediction for GeneMark_model.15304_t
Valid prediction for GeneMark_model.15317_t
Valid prediction for GeneMark_model.15322_t
Valid prediction for GeneMark_model.15307_t
Valid prediction for GeneMark_model.15313_t
Valid prediction for snap_scaffold_4-snap.822-T1
Valid prediction for GeneMark_model.15306_t
Valid prediction for GlimmerHMM_glimmerT_9275-T1
Valid prediction for GlimmerHMM_glimmerT_9292-T1
Valid prediction for GeneMark_model.15303_t
Valid prediction for GeneMark_model.15295_t
Valid prediction for snap_scaffold_4-snap.817-T1
Valid prediction for snap_scaffold_4-snap.814-T1
Valid prediction for snap_scaffold_4-snap.821-T1
Valid prediction for Augustus_model.g6031.t1
Valid prediction for snap_scaffold_4-snap.830-T1
Valid prediction for snap_scaffold_4-snap.835-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 GlimmerHMM_glimmerT_9282-T1
Valid prediction for GlimmerHMM_glimmerT_9281-T1
Valid prediction for GeneMark_model.15314_t
Valid prediction for snap_scaffold_4-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_9301-T1
Valid prediction for snap_scaffold_4-snap.847-T1
Valid prediction for snap_scaffold_4-snap.839-T1
Valid prediction for snap_scaffold_4-snap.842-T1
Valid prediction for GeneMark_model.15299_t
Valid prediction for GeneMark_model.15300_t
Valid prediction for GeneMark_model.15321_t
Valid prediction for GeneMark_model.15308_t
Valid prediction for snap_scaffold_4-snap.825-T1
Valid prediction for GlimmerHMM_glimmerT_9297-T1
Valid prediction for snap_scaffold_4-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_9286-T1
Valid prediction for GeneMark_model.15296_t
Valid prediction for snap_scaffold_4-snap.819-T1
Valid prediction for snap_scaffold_4-snap.820-T1
Valid prediction for GlimmerHMM_glimmerT_9276-T1
Valid prediction for GlimmerHMM_glimmerT_9290-T1
Valid prediction for snap_scaffold_4-snap.828-T1
Valid prediction for snap_scaffold_4-snap.827-T1
Valid prediction for snap_scaffold_4-snap.841-T1
Valid prediction for GlimmerHMM_glimmerT_9287-T1
Valid prediction for GlimmerHMM_glimmerT_9277-T1
Valid prediction for snap_scaffold_4-snap.845-T1
Valid prediction for GlimmerHMM_glimmerT_9278-T1
Valid prediction for snap_scaffold_4-snap.844-T1
Couldn't classify 36816, 36846
Couldn't classify 41802, 41913
Sorry, prediction pasa_asmbl_41195.p1 fails validation.
(CAT)	 AC	36816-36846	GT	GGG
(GTC)	 AG	38465-38562	GT	GGG
(GTC)	 AG	39827-39943	GT	GGG
(AGA)	 AG	40842-40996	GT	AGG
(CGT)	 AG	41802-41913	CG	GAC
-recovered pasa_asmbl_41195.p1, internal, 38465, 38562
-recovered pasa_asmbl_41195.p1, internal, 39827, 39943
-recovered pasa_asmbl_41195.p1, internal, 40842, 40996
Valid prediction for Augustus_model.g6026.t1
Valid prediction for GeneMark_model.15318_t
Valid prediction for Augustus_model.g6025.t1
Couldn't classify 11364, 11385
Couldn't classify 14474, 14750
Sorry, prediction pasa_asmbl_42269.p2 fails validation.
(GAA)	 CT	11364-11385	GT	CGG
(CCC)	 AG	14093-14195	GT	AGG
(TAC)	 AG	14474-14750	GT	GGG
-recovered pasa_asmbl_42269.p2, internal, 14093, 14195
-recovered pasa_asmbl_42269.p2, internal, 14474, 14750
Valid prediction for GeneMark_model.15316_t
Valid prediction for snap_scaffold_4-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_9284-T1
Valid prediction for snap_scaffold_4-snap.843-T1
Valid prediction for snap_scaffold_4-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_9299-T1
Valid prediction for GeneMark_model.15294_t
Valid prediction for snap_scaffold_4-snap.813-T1
Valid prediction for GeneMark_model.15310_t
Valid prediction for snap_scaffold_4-snap.833-T1
Valid prediction for Augustus_model.g6016.t1
Valid prediction for Augustus_model.g6021.t1
Valid prediction for Augustus_model.g6030.t1
Valid prediction for GeneMark_model.15312_t
Valid prediction for Augustus_model.g6028.t1
Valid prediction for Augustus_model.g6019.t1
Valid prediction for GeneMark_model.15323_t
Valid prediction for GeneMark_model.15302_t
Valid prediction for GlimmerHMM_glimmerT_9298-T1
Valid prediction for Augustus_model.g6018.t1
Valid prediction for GlimmerHMM_glimmerT_9294-T1
Valid prediction for GlimmerHMM_glimmerT_9279-T1
Valid prediction for GlimmerHMM_glimmerT_9289-T1
Valid prediction for GeneMark_model.15325_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 63673, rend_intergenic: 60007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87381, rend_intergenic: 83405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91149, rend_intergenic: 88009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111993, rend_intergenic: 94758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120016, rend_intergenic: 116775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148439
-exon list size: 598


building trellis

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91.8    
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92.3    
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92.7    
92.8    
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93.5    
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93.8    
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96.8    
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98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 63673, rend_intergenic: 60007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87381, rend_intergenic: 83405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91149, rend_intergenic: 88009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111993, rend_intergenic: 94758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120016, rend_intergenic: 116775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support