-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_18907758-19195790

-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 GlimmerHMM_glimmerT_14087-T1
Valid prediction for snap_scaffold_5-snap.3585-T1
Valid prediction for GlimmerHMM_glimmerT_14088-T1
Valid prediction for snap_scaffold_5-snap.3568-T1
Valid prediction for GlimmerHMM_glimmerT_14092-T1
Valid prediction for GlimmerHMM_glimmerT_14065-T1
Valid prediction for Augustus_model.g9387.t1
Valid prediction for snap_scaffold_5-snap.3592-T1
Valid prediction for snap_scaffold_5-snap.3571-T1
Valid prediction for Augustus_model.g9406.t1
Valid prediction for snap_scaffold_5-snap.3579-T1
Valid prediction for GlimmerHMM_glimmerT_14085-T1
Valid prediction for snap_scaffold_5-snap.3610-T1
Valid prediction for GeneMark_model.23598_t
Valid prediction for pasa_asmbl_44949.p1
Valid prediction for GlimmerHMM_glimmerT_14059-T1
Valid prediction for snap_scaffold_5-snap.3612-T1
Valid prediction for Augustus_model.g9405.t1
Valid prediction for snap_scaffold_5-snap.3602-T1
Valid prediction for GeneMark_model.23566_t
Valid prediction for GlimmerHMM_glimmerT_14068-T1
Valid prediction for GeneMark_model.23590_t
Valid prediction for pasa_asmbl_44955.p1
Valid prediction for Augustus_model.g9390.t1
Valid prediction for snap_scaffold_5-snap.3569-T1
Valid prediction for snap_scaffold_5-snap.3577-T1
Valid prediction for snap_scaffold_5-snap.3605-T1
Valid prediction for GeneMark_model.23569_t
Valid prediction for GlimmerHMM_glimmerT_14056-T1
Valid prediction for snap_scaffold_5-snap.3611-T1
Valid prediction for snap_scaffold_5-snap.3570-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g9407.t1
Valid prediction for snap_scaffold_5-snap.3603-T1
Valid prediction for GlimmerHMM_glimmerT_14081-T1
Valid prediction for GeneMark_model.23597_t
Couldn't classify 251759, 251930
Couldn't classify 252167, 252321
Sorry, prediction pasa_asmbl_44986.p1 fails validation.
(CTC)	 CC	251759-251930	GT	TGG
(GTC)	 AG	252167-252321	AC	CCA
Valid prediction for GeneMark_model.23567_t
Valid prediction for snap_scaffold_5-snap.3582-T1
Valid prediction for GlimmerHMM_glimmerT_14074-T1
Valid prediction for GlimmerHMM_glimmerT_14083-T1
Valid prediction for GeneMark_model.23603_t
Valid prediction for GeneMark_model.23588_t
Valid prediction for GeneMark_model.23589_t
Valid prediction for snap_scaffold_5-snap.3598-T1
Valid prediction for GeneMark_model.23565_t
Valid prediction for Augustus_model.g9399.t1
Valid prediction for snap_scaffold_5-snap.3595-T1
Valid prediction for HiQ_model.g9395.t1
Valid prediction for snap_scaffold_5-snap.3578-T1
Valid prediction for GlimmerHMM_glimmerT_14058-T1
Valid prediction for Augustus_model.g9409.t1
Valid prediction for snap_scaffold_5-snap.3597-T1
Valid prediction for snap_scaffold_5-snap.3567-T1
Valid prediction for GlimmerHMM_glimmerT_14094-T1
Valid prediction for GeneMark_model.23587_t
Valid prediction for GlimmerHMM_glimmerT_14076-T1
Valid prediction for GlimmerHMM_glimmerT_14062-T1
Valid prediction for GeneMark_model.23579_t
Valid prediction for GeneMark_model.23595_t
Valid prediction for snap_scaffold_5-snap.3583-T1
Valid prediction for GeneMark_model.23574_t
Valid prediction for CodingQuarry_transcript_52345-T1
Valid prediction for Augustus_model.g9404.t1
Valid prediction for Augustus_model.g9394.t1
Valid prediction for GlimmerHMM_glimmerT_14054-T1
Valid prediction for GeneMark_model.23577_t
Valid prediction for GeneMark_model.23582_t
Valid prediction for HiQ_model.g9397.t1
Valid prediction for GlimmerHMM_glimmerT_14082-T1
Valid prediction for Augustus_model.g9410.t1
Valid prediction for snap_scaffold_5-snap.3572-T1
Valid prediction for GlimmerHMM_glimmerT_14093-T1
Couldn't classify 79736, 79837
Couldn't classify 82774, 83198
Sorry, prediction pasa_asmbl_44951.p1 fails validation.
(CAC)	 GA	79736-79837	GT	CGG
(ATG)	 AG	81115-81312	GT	TGG
(GTT)	 AG	81608-81881	GT	TGG
(GCT)	 AG	82556-82633	GT	TGG
(GGG)	 AG	82774-83198	AG	ACA
-recovered pasa_asmbl_44951.p1, initial, 81115, 81312
-recovered pasa_asmbl_44951.p1, internal, 81115, 81312
-recovered pasa_asmbl_44951.p1, internal, 81608, 81881
-recovered pasa_asmbl_44951.p1, internal, 82556, 82633
Valid prediction for GlimmerHMM_glimmerT_14066-T1
Valid prediction for snap_scaffold_5-snap.3600-T1
Valid prediction for Augustus_model.g9389.t1
Valid prediction for GlimmerHMM_glimmerT_14079-T1
Valid prediction for GlimmerHMM_glimmerT_14072-T1
Valid prediction for snap_scaffold_5-snap.3609-T1
Valid prediction for GeneMark_model.23602_t
Valid prediction for Augustus_model.g9415.t1
Valid prediction for snap_scaffold_5-snap.3581-T1
Valid prediction for CodingQuarry_transcript_52346-T1
Valid prediction for GlimmerHMM_glimmerT_14070-T1
Valid prediction for GlimmerHMM_glimmerT_14067-T1
Valid prediction for GeneMark_model.23593_t

-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 snap_scaffold_5-snap.3594-T1
Valid prediction for snap_scaffold_5-snap.3607-T1
Valid prediction for snap_scaffold_5-snap.3608-T1
Valid prediction for GeneMark_model.23591_t
Valid prediction for GlimmerHMM_glimmerT_14086-T1
Valid prediction for snap_scaffold_5-snap.3573-T1
Valid prediction for GeneMark_model.23600_t
Valid prediction for GlimmerHMM_glimmerT_14084-T1
Valid prediction for GlimmerHMM_glimmerT_14061-T1
Valid prediction for GeneMark_model.23584_t
Valid prediction for GeneMark_model.23568_t
Valid prediction for GlimmerHMM_glimmerT_14073-T1
Valid prediction for snap_scaffold_5-snap.3606-T1
Valid prediction for Augustus_model.g9408.t1
Valid prediction for snap_scaffold_5-snap.3591-T1
Valid prediction for GlimmerHMM_glimmerT_14090-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3580-T1
Valid prediction for CodingQuarry_transcript_52347-T1
Valid prediction for snap_scaffold_5-snap.3596-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 167019, 167115
Sorry, prediction pasa_asmbl_46268.p1 fails validation.
(GTC)	 CT	167019-167115	GT	TAG
(GTT)	 AG	167225-167361	GT	CGG
(TTC)	 AG	167554-167727	GT	GGG
(GCG)	 AG	168904-169044	GT	AGG
(ACG)	 AG	169194-169346	GT	AGG
(GTG)	 AG	169907-170020	CG	AAC
-recovered pasa_asmbl_46268.p1, terminal, 169907, 170020
-recovered pasa_asmbl_46268.p1, internal, 167225, 167361
-recovered pasa_asmbl_46268.p1, internal, 167554, 167727
-recovered pasa_asmbl_46268.p1, internal, 168904, 169044
-recovered pasa_asmbl_46268.p1, internal, 169194, 169346
Valid prediction for snap_scaffold_5-snap.3590-T1
Valid prediction for Augustus_model.g9412.t1
Valid prediction for Augustus_model.g9414.t1
Valid prediction for GlimmerHMM_glimmerT_14077-T1
Valid prediction for GlimmerHMM_glimmerT_14091-T1
Valid prediction for snap_scaffold_5-snap.3587-T1
Valid prediction for GlimmerHMM_glimmerT_14078-T1
Valid prediction for CodingQuarry_transcript_52344-T1
Valid prediction for Augustus_model.g9400.t1
Valid prediction for GeneMark_model.23578_t
Valid prediction for GlimmerHMM_glimmerT_14075-T1
Valid prediction for Augustus_model.g9393.t1
Valid prediction for Augustus_model.g9396.t1
Valid prediction for GeneMark_model.23596_t
Valid prediction for snap_scaffold_5-snap.3586-T1
Valid prediction for GlimmerHMM_glimmerT_14064-T1
Valid prediction for snap_scaffold_5-snap.3599-T1
Valid prediction for GlimmerHMM_glimmerT_14060-T1
Valid prediction for CodingQuarry_transcript_52353-T1
Valid prediction for GeneMark_model.23599_t
Valid prediction for CodingQuarry_transcript_52348-T1
Valid prediction for GlimmerHMM_glimmerT_14063-T1
Valid prediction for snap_scaffold_5-snap.3575-T1
Valid prediction for Augustus_model.g9411.t1
Valid prediction for GeneMark_model.23581_t
Couldn't classify 267181, 267492
Sorry, prediction pasa_asmbl_46254.p1 fails validation.
(CAG)	 GC	267181-267492	AA	GGA
Valid prediction for GeneMark_model.23604_t
Valid prediction for GeneMark_model.23594_t
Valid prediction for GeneMark_model.23592_t
Couldn't classify 190222, 190266
Sorry, prediction pasa_asmbl_46257.p1 fails validation.
(GTG)	 GG	190222-190266	GT	AGG
(AAC)	 AG	190342-190442	GT	AGG
(GTT)	 AG	191618-191828	CG	AGC
-recovered pasa_asmbl_46257.p1, terminal, 191618, 191828
-recovered pasa_asmbl_46257.p1, internal, 190342, 190442
Valid prediction for snap_scaffold_5-snap.3601-T1
Valid prediction for Augustus_model.g9402.t1
Valid prediction for snap_scaffold_5-snap.3593-T1
Valid prediction for GeneMark_model.23576_t
Valid prediction for Augustus_model.g9398.t1
Valid prediction for snap_scaffold_5-snap.3584-T1
Couldn't classify 48401, 48579
Sorry, prediction pasa_asmbl_46270.p1 fails validation.
(CTT)	 AC	48401-48579	GT	AGG
(GTT)	 AG	48831-48970	GT	GCG
(AGA)	 AG	49071-49140	GT	AGG
(GTA)	 AG	49252-49357	GT	AGG
(GGT)	 AG	50062-50160	GT	TAG
(TCA)	 AG	50246-50329	GT	CTG
(GGA)	 AG	50560-50682	AT	AGA
-recovered pasa_asmbl_46270.p1, terminal, 50560, 50682
-recovered pasa_asmbl_46270.p1, internal, 48831, 48970
-recovered pasa_asmbl_46270.p1, internal, 49071, 49140
-recovered pasa_asmbl_46270.p1, internal, 49252, 49357
-recovered pasa_asmbl_46270.p1, internal, 50062, 50160
-recovered pasa_asmbl_46270.p1, internal, 50246, 50329
Valid prediction for GlimmerHMM_glimmerT_14071-T1
Valid prediction for snap_scaffold_5-snap.3604-T1
Valid prediction for GeneMark_model.23572_t
Valid prediction for Augustus_model.g9413.t1
Valid prediction for HiQ_model.g9401.t1
Valid prediction for GeneMark_model.23575_t
Valid prediction for GeneMark_model.23601_t
Valid prediction for snap_scaffold_5-snap.3574-T1
Valid prediction for GeneMark_model.23583_t
Valid prediction for snap_scaffold_5-snap.3613-T1
Valid prediction for GeneMark_model.23585_t
Valid prediction for CodingQuarry_transcript_52351-T1
Valid prediction for GlimmerHMM_glimmerT_14069-T1
Valid prediction for CodingQuarry_transcript_52349-T1
Valid prediction for GlimmerHMM_glimmerT_14055-T1
Valid prediction for snap_scaffold_5-snap.3589-T1
Valid prediction for Augustus_model.g9403.t1
Valid prediction for Augustus_model.g9388.t1
Valid prediction for GeneMark_model.23571_t
Valid prediction for Augustus_model.g9392.t1
Valid prediction for snap_scaffold_5-snap.3576-T1
Valid prediction for GlimmerHMM_glimmerT_14095-T1
Valid prediction for GeneMark_model.23570_t
Valid prediction for GeneMark_model.23586_t
Valid prediction for Augustus_model.g9391.t1
Couldn't classify 188999, 189107
Couldn't classify 189849, 189946
Sorry, prediction pasa_asmbl_46399.p1 fails validation.
(CAC)	 GC	188999-189107	GT	AGG
(GTC)	 AG	189659-189769	GT	TGG
(TTA)	 AG	189849-189946	AC	CAA
-recovered pasa_asmbl_46399.p1, internal, 189659, 189769
Valid prediction for GlimmerHMM_glimmerT_14080-T1
Valid prediction for CodingQuarry_transcript_52350-T1
Valid prediction for pasa_asmbl_46267.p1
Valid prediction for snap_scaffold_5-snap.3588-T1
Valid prediction for Augustus_model.g9416.t1
Couldn't classify 266376, 266542
Sorry, prediction pasa_asmbl_46255.p1 fails validation.
(ATG)	 AA	265773-265964	GT	AGG
(GTG)	 AG	266084-266249	GC	TGG
(GTG)	 AG	266376-266542	CA	CCC
-recovered pasa_asmbl_46255.p1, initial, 265773, 265964
-recovered pasa_asmbl_46255.p1, internal, 266084, 266249
Valid prediction for GlimmerHMM_glimmerT_14057-T1
Valid prediction for GlimmerHMM_glimmerT_14089-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 149677, rend_intergenic: 142642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179316, rend_intergenic: 172680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223282, rend_intergenic: 219197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255228, rend_intergenic: 249745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282878, rend_intergenic: 278110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 288033
-exon list size: 625


building trellis

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85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 149677, rend_intergenic: 142642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179316, rend_intergenic: 172680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223282, rend_intergenic: 219197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255228, rend_intergenic: 249745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282878, rend_intergenic: 278110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support