-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_3646091-3930754

-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 snap_scaffold_1-snap.591-T1
Valid prediction for pasa_asmbl_1622.p1
Valid prediction for Augustus_model.g366.t1
Valid prediction for snap_scaffold_1-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_443-T1
Valid prediction for GlimmerHMM_glimmerT_450-T1
Valid prediction for snap_scaffold_1-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_464-T1
Valid prediction for GlimmerHMM_glimmerT_457-T1
Valid prediction for Augustus_model.g362.t1
Valid prediction for GeneMark_model.514_t
Valid prediction for snap_scaffold_1-snap.590-T1
Valid prediction for snap_scaffold_1-snap.574-T1
Valid prediction for GeneMark_model.533_t
Valid prediction for GeneMark_model.523_t
Valid prediction for GeneMark_model.499_t
Valid prediction for GeneMark_model.525_t
Valid prediction for Augustus_model.g367.t1
Valid prediction for snap_scaffold_1-snap.558-T1
Valid prediction for GeneMark_model.511_t
Couldn't classify 50166, 50310
Sorry, prediction pasa_asmbl_2746.p1 fails validation.
(ATG)	 CC	49127-49635	GT	AGG
(GTT)	 AG	49907-50002	GT	AGG
(TGA)	 AG	50166-50310	TA	GGT
-recovered pasa_asmbl_2746.p1, initial, 49127, 49635
-recovered pasa_asmbl_2746.p1, internal, 49907, 50002
Valid prediction for GeneMark_model.513_t
Valid prediction for GeneMark_model.512_t
Valid prediction for GeneMark_model.520_t
Valid prediction for GeneMark_model.501_t
Valid prediction for CodingQuarry_transcript_2574-T1
Valid prediction for pasa_asmbl_1624.p1
Valid prediction for Augustus_model.g355.t1
Valid prediction for Augustus_model.g361.t1
Valid prediction for snap_scaffold_1-snap.567-T1
Valid prediction for GeneMark_model.504_t
Valid prediction for snap_scaffold_1-snap.580-T1
Valid prediction for snap_scaffold_1-snap.576-T1
Valid prediction for snap_scaffold_1-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_461-T1
Valid prediction for GeneMark_model.505_t
Valid prediction for GeneMark_model.509_t
Valid prediction for GeneMark_model.534_t
Valid prediction for GeneMark_model.531_t
Valid prediction for GeneMark_model.522_t
Valid prediction for snap_scaffold_1-snap.564-T1
Valid prediction for CodingQuarry_transcript_2575-T1
Valid prediction for Augustus_model.g363.t1
Valid prediction for GeneMark_model.518_t
Valid prediction for snap_scaffold_1-snap.568-T1
Valid prediction for snap_scaffold_1-snap.582-T1
Valid prediction for Augustus_model.g368.t1
Valid prediction for GlimmerHMM_glimmerT_453-T1
Valid prediction for CodingQuarry_transcript_2572-T1
Valid prediction for GeneMark_model.517_t
Valid prediction for Augustus_model.g359.t1
Valid prediction for GeneMark_model.535_t
Valid prediction for snap_scaffold_1-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_460-T1
Valid prediction for GeneMark_model.515_t
Valid prediction for GlimmerHMM_glimmerT_456-T1
Valid prediction for snap_scaffold_1-snap.561-T1
Valid prediction for GeneMark_model.507_t
Valid prediction for GlimmerHMM_glimmerT_447-T1
Valid prediction for snap_scaffold_1-snap.566-T1
Valid prediction for GeneMark_model.503_t
Valid prediction for GlimmerHMM_glimmerT_445-T1
Valid prediction for Augustus_model.g356.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.516_t
Valid prediction for snap_scaffold_1-snap.587-T1
Valid prediction for snap_scaffold_1-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_451-T1
Valid prediction for GeneMark_model.532_t
Valid prediction for snap_scaffold_1-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_463-T1
Valid prediction for CodingQuarry_transcript_2573-T1
Valid prediction for HiQ_model.g357.t1
Valid prediction for snap_scaffold_1-snap.562-T1
Valid prediction for snap_scaffold_1-snap.585-T1
Valid prediction for snap_scaffold_1-snap.565-T1
Valid prediction for Augustus_model.g370.t1
Valid prediction for GlimmerHMM_glimmerT_455-T1
Valid prediction for Augustus_model.g365.t1
Valid prediction for snap_scaffold_1-snap.569-T1
Couldn't classify 246794, 246918
Sorry, prediction pasa_asmbl_175.p1 fails validation.
(ATG)	 AA	245571-245646	GT	TGG
(AGA)	 AG	245821-245900	GT	AGG
(AAC)	 AG	246512-246599	GT	CAG
(ATG)	 AG	246794-246918	GA	AGG
-recovered pasa_asmbl_175.p1, initial, 245571, 245646
-recovered pasa_asmbl_175.p1, internal, 245821, 245900
-recovered pasa_asmbl_175.p1, internal, 246512, 246599
Valid prediction for GeneMark_model.530_t
Valid prediction for GlimmerHMM_glimmerT_458-T1
Valid prediction for GlimmerHMM_glimmerT_442-T1
Valid prediction for GlimmerHMM_glimmerT_448-T1
Valid prediction for snap_scaffold_1-snap.570-T1
Valid prediction for GeneMark_model.526_t
Valid prediction for HiQ_model.g354.t1
Valid prediction for snap_scaffold_1-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_446-T1
Valid prediction for snap_scaffold_1-snap.584-T1
Valid prediction for snap_scaffold_1-snap.559-T1
Valid prediction for GeneMark_model.529_t
Valid prediction for GeneMark_model.498_t
Valid prediction for GeneMark_model.510_t
Valid prediction for snap_scaffold_1-snap.573-T1
Valid prediction for HiQ_model.g358.t1
Valid prediction for GlimmerHMM_glimmerT_459-T1
Valid prediction for CodingQuarry_transcript_2571-T1
Valid prediction for snap_scaffold_1-snap.575-T1
Valid prediction for snap_scaffold_1-snap.581-T1
Valid prediction for GlimmerHMM_glimmerT_452-T1
Valid prediction for GeneMark_model.528_t
Valid prediction for GlimmerHMM_glimmerT_449-T1
Valid prediction for snap_scaffold_1-snap.563-T1
Valid prediction for GeneMark_model.502_t
Valid prediction for Augustus_model.g360.t1
Valid prediction for Augustus_model.g364.t1
Valid prediction for snap_scaffold_1-snap.588-T1
Valid prediction for GeneMark_model.524_t
Valid prediction for GeneMark_model.527_t
Valid prediction for GeneMark_model.506_t
Valid prediction for Augustus_model.g369.t1
Valid prediction for GlimmerHMM_glimmerT_444-T1
Valid prediction for GlimmerHMM_glimmerT_454-T1
Valid prediction for pasa_asmbl_171.p1
Valid prediction for GlimmerHMM_glimmerT_462-T1
Couldn't classify 259261, 259448
Sorry, prediction pasa_asmbl_1327.p1 fails validation.
(ATG)	 CT	254758-254920	GT	TGG
(GTA)	 AG	255909-256148	GT	AGG
(GCT)	 AG	257386-257475	GT	AGG
(ACC)	 AG	259261-259448	GG	GTG
-recovered pasa_asmbl_1327.p1, initial, 254758, 254920
-recovered pasa_asmbl_1327.p1, terminal, 257386, 257475
-recovered pasa_asmbl_1327.p1, internal, 255909, 256148
-recovered pasa_asmbl_1327.p1, internal, 257386, 257475
Valid prediction for GeneMark_model.519_t
Valid prediction for GeneMark_model.508_t
Valid prediction for GeneMark_model.500_t
Valid prediction for snap_scaffold_1-snap.586-T1
Valid prediction for snap_scaffold_1-snap.578-T1
Valid prediction for snap_scaffold_1-snap.572-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 85594, rend_intergenic: 83486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100630, rend_intergenic: 97432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105641, rend_intergenic: 100637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 284664
-exon list size: 427


building trellis

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99.1    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 85594, rend_intergenic: 83486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100630, rend_intergenic: 97432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105641, rend_intergenic: 100637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support