-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_1141789-1296612

-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.69940_t
Valid prediction for snap_scaffold_17-snap.221-T1
Valid prediction for snap_scaffold_17-snap.253-T1
Couldn't classify 133788, 133917
Sorry, prediction pasa_asmbl_17723.p1 fails validation.
(ATG)	 CC	132623-132722	GT	AGG
(AGC)	 AG	132937-133025	GT	AGG
(GTG)	 AG	133301-133650	GT	AGG
(GCC)	 AG	133788-133917	CC	AAC
-recovered pasa_asmbl_17723.p1, initial, 132623, 132722
-recovered pasa_asmbl_17723.p1, internal, 132937, 133025
-recovered pasa_asmbl_17723.p1, internal, 133301, 133650
Valid prediction for Augustus_model.g27199.t1
Valid prediction for GlimmerHMM_glimmerT_40596-T1
Valid prediction for snap_scaffold_17-snap.235-T1
Valid prediction for snap_scaffold_17-snap.226-T1
Valid prediction for GeneMark_model.69908_t
Valid prediction for GeneMark_model.69917_t
Valid prediction for GeneMark_model.69919_t
Valid prediction for snap_scaffold_17-snap.246-T1
Valid prediction for GeneMark_model.69901_t
Valid prediction for GeneMark_model.69939_t
Valid prediction for snap_scaffold_17-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_40606-T1
Valid prediction for snap_scaffold_17-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_40603-T1
Valid prediction for Augustus_model.g27197.t1
Valid prediction for snap_scaffold_17-snap.254-T1
Valid prediction for GeneMark_model.69906_t
Valid prediction for GeneMark_model.69881_t
Valid prediction for GeneMark_model.69914_t
Valid prediction for GlimmerHMM_glimmerT_40605-T1
Valid prediction for GeneMark_model.69886_t
Couldn't classify 136311, 136459
Couldn't classify 139365, 139381
Sorry, prediction pasa_asmbl_17725.p1 fails validation.
(GAC)	 TG	136311-136459	GT	AAG
(GTG)	 AG	136609-136749	GT	AGG
(GAG)	 AG	138090-138167	GT	AAG
(GGC)	 AG	139050-139108	GT	TGG
(CGG)	 AG	139365-139381	AC	CCA
-recovered pasa_asmbl_17725.p1, internal, 136609, 136749
-recovered pasa_asmbl_17725.p1, internal, 138090, 138167
-recovered pasa_asmbl_17725.p1, internal, 139050, 139108
Valid prediction for GeneMark_model.69930_t
Valid prediction for GlimmerHMM_glimmerT_40601-T1
Valid prediction for snap_scaffold_17-snap.256-T1
Valid prediction for GeneMark_model.69903_t
Valid prediction for GeneMark_model.69936_t
Valid prediction for snap_scaffold_17-snap.227-T1
Valid prediction for snap_scaffold_17-snap.237-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_40615-T1
Valid prediction for snap_scaffold_17-snap.224-T1
Valid prediction for GeneMark_model.69879_t
Valid prediction for GeneMark_model.69888_t
Valid prediction for snap_scaffold_17-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_40609-T1
Valid prediction for snap_scaffold_17-snap.243-T1
Valid prediction for snap_scaffold_17-snap.260-T1
Valid prediction for GeneMark_model.69926_t
Valid prediction for snap_scaffold_17-snap.238-T1
Valid prediction for GeneMark_model.69938_t
Valid prediction for GlimmerHMM_glimmerT_40614-T1
Valid prediction for GeneMark_model.69922_t
Valid prediction for GlimmerHMM_glimmerT_40613-T1
Valid prediction for snap_scaffold_17-snap.255-T1
Valid prediction for GeneMark_model.69893_t
Valid prediction for GlimmerHMM_glimmerT_40604-T1
Valid prediction for snap_scaffold_17-snap.261-T1
Valid prediction for snap_scaffold_17-snap.230-T1
Valid prediction for Augustus_model.g27203.t1
Valid prediction for snap_scaffold_17-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_40610-T1
Valid prediction for GeneMark_model.69928_t
Valid prediction for GeneMark_model.69924_t
Valid prediction for GeneMark_model.69884_t
Valid prediction for GeneMark_model.69898_t
Valid prediction for GeneMark_model.69934_t
Valid prediction for GeneMark_model.69894_t
Valid prediction for GeneMark_model.69895_t
Valid prediction for snap_scaffold_17-snap.223-T1
Valid prediction for GeneMark_model.69890_t
Valid prediction for snap_scaffold_17-snap.258-T1
Valid prediction for Augustus_model.g27200.t1
Valid prediction for snap_scaffold_17-snap.228-T1
Valid prediction for GeneMark_model.69897_t
Valid prediction for Augustus_model.g27202.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 snap_scaffold_17-snap.249-T1
Valid prediction for snap_scaffold_17-snap.262-T1
Valid prediction for GeneMark_model.69935_t
Valid prediction for CodingQuarry_transcript_21802-T1
Valid prediction for snap_scaffold_17-snap.240-T1
Valid prediction for GeneMark_model.69889_t
Valid prediction for GeneMark_model.69933_t
Valid prediction for GlimmerHMM_glimmerT_40612-T1
Valid prediction for Augustus_model.g27201.t1
Valid prediction for snap_scaffold_17-snap.257-T1
Valid prediction for GeneMark_model.69911_t
Valid prediction for snap_scaffold_17-snap.263-T1
Valid prediction for GeneMark_model.69880_t
Valid prediction for GlimmerHMM_glimmerT_40608-T1
Valid prediction for snap_scaffold_17-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_40598-T1
Valid prediction for GeneMark_model.69892_t
Valid prediction for GlimmerHMM_glimmerT_40611-T1
Valid prediction for GeneMark_model.69937_t
Valid prediction for GlimmerHMM_glimmerT_40597-T1
Valid prediction for Augustus_model.g27198.t1
Valid prediction for snap_scaffold_17-snap.233-T1
Valid prediction for GeneMark_model.69905_t
Valid prediction for GeneMark_model.69927_t
Valid prediction for snap_scaffold_17-snap.229-T1
Valid prediction for snap_scaffold_17-snap.250-T1
Valid prediction for pasa_asmbl_18731.p1
Valid prediction for GeneMark_model.69932_t
Valid prediction for GeneMark_model.69899_t
Valid prediction for snap_scaffold_17-snap.225-T1
Valid prediction for GlimmerHMM_glimmerT_40602-T1
Valid prediction for GeneMark_model.69904_t
Valid prediction for GeneMark_model.69896_t
Valid prediction for GeneMark_model.69916_t
Couldn't classify 151595, 151705
Sorry, prediction pasa_asmbl_18722.p1 fails validation.
(GTG)	 AG	151595-151705	GT	AGG
(GTG)	 AG	152284-152526	AG	GAA
-recovered pasa_asmbl_18722.p1, terminal, 152284, 152526
-recovered pasa_asmbl_18722.p1, internal, 151595, 151705
Valid prediction for Augustus_model.g27196.t1
Valid prediction for snap_scaffold_17-snap.232-T1
Valid prediction for snap_scaffold_17-snap.239-T1
Valid prediction for GeneMark_model.69923_t
Valid prediction for GeneMark_model.69887_t
Valid prediction for Augustus_model.g27204.t1
Valid prediction for CodingQuarry_transcript_21803-T1
Valid prediction for GlimmerHMM_glimmerT_40616-T1
Valid prediction for GeneMark_model.69883_t
Valid prediction for GlimmerHMM_glimmerT_40600-T1
Valid prediction for CodingQuarry_transcript_21801-T1
Valid prediction for GeneMark_model.69909_t
Valid prediction for snap_scaffold_17-snap.245-T1
Valid prediction for GeneMark_model.69891_t
Valid prediction for snap_scaffold_17-snap.247-T1
Valid prediction for GeneMark_model.69910_t
Valid prediction for GeneMark_model.69942_t
Valid prediction for snap_scaffold_17-snap.251-T1
Valid prediction for GeneMark_model.69912_t
Valid prediction for snap_scaffold_17-snap.248-T1
Valid prediction for GeneMark_model.69913_t
Valid prediction for GeneMark_model.69921_t
Valid prediction for GeneMark_model.69941_t
Valid prediction for GlimmerHMM_glimmerT_40595-T1
Valid prediction for GeneMark_model.69907_t
Valid prediction for GeneMark_model.69915_t
Valid prediction for GeneMark_model.69931_t
Valid prediction for snap_scaffold_17-snap.222-T1
Valid prediction for GlimmerHMM_glimmerT_40607-T1
Valid prediction for snap_scaffold_17-snap.252-T1
Valid prediction for GeneMark_model.69882_t
Valid prediction for GeneMark_model.69878_t
Valid prediction for GeneMark_model.69929_t
Valid prediction for GlimmerHMM_glimmerT_40599-T1
Valid prediction for GeneMark_model.69900_t
Valid prediction for snap_scaffold_17-snap.234-T1
Valid prediction for GeneMark_model.69925_t
Valid prediction for GeneMark_model.69920_t
Valid prediction for snap_scaffold_17-snap.241-T1
Valid prediction for GeneMark_model.69885_t
Valid prediction for GeneMark_model.69902_t
Valid prediction for GeneMark_model.69918_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4053, rend_intergenic: 2299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7801, rend_intergenic: 4060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11025, rend_intergenic: 8815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18928, rend_intergenic: 11963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27753, rend_intergenic: 26197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33841, rend_intergenic: 27823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38019, rend_intergenic: 37133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52947, rend_intergenic: 49250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95137, rend_intergenic: 82211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117762, rend_intergenic: 96093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127051, rend_intergenic: 120256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140106, rend_intergenic: 135470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142641, rend_intergenic: 140205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152073, rend_intergenic: 147306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154824
-exon list size: 734


building trellis

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96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 4053, rend_intergenic: 2299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7801, rend_intergenic: 4060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11025, rend_intergenic: 8815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18928, rend_intergenic: 11963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27753, rend_intergenic: 26197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33841, rend_intergenic: 27823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38019, rend_intergenic: 37133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52947, rend_intergenic: 49250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95137, rend_intergenic: 82211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117762, rend_intergenic: 96093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127051, rend_intergenic: 120256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140106, rend_intergenic: 135470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142641, rend_intergenic: 140205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152073, rend_intergenic: 147306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support