-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_3336636-3518124

-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_25-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_55151-T1
Valid prediction for GeneMark_model.96371_t
Valid prediction for snap_scaffold_25-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_55149-T1
Valid prediction for GeneMark_model.96355_t
Valid prediction for Augustus_model.g36787.t1
Valid prediction for GeneMark_model.96376_t
Valid prediction for HiQ_model.g36794.t1
Valid prediction for snap_scaffold_25-snap.702-T1
Valid prediction for GlimmerHMM_glimmerT_55162-T1
Valid prediction for GlimmerHMM_glimmerT_55155-T1
Valid prediction for GeneMark_model.96373_t
Valid prediction for GeneMark_model.96362_t
Valid prediction for Augustus_model.g36786.t1
Valid prediction for GeneMark_model.96353_t
Valid prediction for GeneMark_model.96359_t
Valid prediction for GeneMark_model.96351_t
Valid prediction for snap_scaffold_25-snap.732-T1
Valid prediction for GeneMark_model.96343_t
Valid prediction for snap_scaffold_25-snap.706-T1
Valid prediction for pasa_asmbl_33419.p1
Valid prediction for GeneMark_model.96334_t
Valid prediction for GeneMark_model.96357_t
Valid prediction for snap_scaffold_25-snap.717-T1
Valid prediction for snap_scaffold_25-snap.726-T1
Valid prediction for GeneMark_model.96339_t
Valid prediction for GeneMark_model.96349_t
Valid prediction for GeneMark_model.96342_t
Valid prediction for pasa_asmbl_33416.p1
Valid prediction for GeneMark_model.96366_t
Valid prediction for GeneMark_model.96341_t
Valid prediction for GlimmerHMM_glimmerT_55150-T1
Valid prediction for snap_scaffold_25-snap.725-T1
Valid prediction for snap_scaffold_25-snap.737-T1
Valid prediction for GeneMark_model.96336_t
Valid prediction for GeneMark_model.96347_t
Valid prediction for GeneMark_model.96364_t
Couldn't classify 81568, 81680
Sorry, prediction pasa_asmbl_33415.p2 fails validation.
(TTG)	 GT	81568-81680	GT	GGG
(GTT)	 AG	81761-82127	GA	AAG
-recovered pasa_asmbl_33415.p2, terminal, 81761, 82127
Valid prediction for CodingQuarry_transcript_38583-T1
Valid prediction for snap_scaffold_25-snap.735-T1
Couldn't classify 74581, 74641
Couldn't classify 75322, 75561
Sorry, prediction pasa_asmbl_33413.p1 fails validation.
(AAT)	 CC	74581-74641	GT	AGG
(GTG)	 AG	74942-75063	GT	AGG
(GAT)	 AG	75322-75561	GA	GTG
-recovered pasa_asmbl_33413.p1, internal, 74942, 75063
Valid prediction for Augustus_model.g36791.t1
Valid prediction for snap_scaffold_25-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_55158-T1
Valid prediction for GeneMark_model.96361_t
Valid prediction for GlimmerHMM_glimmerT_55148-T1
Valid prediction for GeneMark_model.96368_t
Valid prediction for Augustus_model.g36792.t1
Valid prediction for GlimmerHMM_glimmerT_55156-T1
Valid prediction for snap_scaffold_25-snap.700-T1
Valid prediction for snap_scaffold_25-snap.719-T1
Valid prediction for Augustus_model.g36790.t1
Valid prediction for GeneMark_model.96337_t
Valid prediction for GlimmerHMM_glimmerT_55161-T1
Valid prediction for GeneMark_model.96369_t
Valid prediction for GeneMark_model.96345_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_25-snap.730-T1
Valid prediction for snap_scaffold_25-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_55164-T1
Couldn't classify 29684, 29792
Sorry, prediction pasa_asmbl_34114.p2 fails validation.
(GGG)	 CA	29684-29792	GT	AGG
(TGT)	 AG	30040-30168	GT	ATG
(CGA)	 AG	30795-30910	CA	GAC
-recovered pasa_asmbl_34114.p2, terminal, 30795, 30910
-recovered pasa_asmbl_34114.p2, internal, 30040, 30168
Valid prediction for snap_scaffold_25-snap.707-T1
Valid prediction for snap_scaffold_25-snap.728-T1
Valid prediction for GeneMark_model.96375_t
Valid prediction for GeneMark_model.96370_t
Valid prediction for CodingQuarry_transcript_38584-T1
Valid prediction for GeneMark_model.96356_t
Valid prediction for snap_scaffold_25-snap.718-T1
Valid prediction for snap_scaffold_25-snap.705-T1
Valid prediction for pasa_asmbl_34115.p1
Valid prediction for snap_scaffold_25-snap.710-T1
Valid prediction for GeneMark_model.96333_t
Valid prediction for GeneMark_model.96365_t
Valid prediction for Augustus_model.g36788.t1
Valid prediction for snap_scaffold_25-snap.711-T1
Valid prediction for GeneMark_model.96340_t
Valid prediction for snap_scaffold_25-snap.734-T1
Valid prediction for GeneMark_model.96363_t
Valid prediction for GeneMark_model.96348_t
Valid prediction for snap_scaffold_25-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_55154-T1
Valid prediction for snap_scaffold_25-snap.738-T1
Valid prediction for snap_scaffold_25-snap.736-T1
Valid prediction for snap_scaffold_25-snap.727-T1
Valid prediction for GeneMark_model.96358_t
Valid prediction for snap_scaffold_25-snap.716-T1
Valid prediction for GeneMark_model.96367_t
Valid prediction for Augustus_model.g36789.t1
Valid prediction for GeneMark_model.96360_t
Valid prediction for GlimmerHMM_glimmerT_55165-T1
Couldn't classify 93429, 93569
Couldn't classify 94459, 94530
Sorry, prediction CodingQuarry_transcript_38582-T1 fails validation.
(ATG)	 AA	93429-93569	TA	AAT
(GGG)	 CA	94459-94530	GT	AGG
(GAT)	 AG	95547-95723	GT	AGG
(GCT)	 AG	96724-96786	GA	AGG
-recovered CodingQuarry_transcript_38582-T1, terminal, 96724, 96786
-recovered CodingQuarry_transcript_38582-T1, internal, 95547, 95723
Valid prediction for snap_scaffold_25-snap.733-T1
Valid prediction for GeneMark_model.96335_t
Valid prediction for snap_scaffold_25-snap.721-T1
Valid prediction for snap_scaffold_25-snap.715-T1
Valid prediction for GeneMark_model.96350_t
Valid prediction for GeneMark_model.96352_t
Valid prediction for GeneMark_model.96377_t
Valid prediction for snap_scaffold_25-snap.724-T1
Valid prediction for Augustus_model.g36793.t1
Valid prediction for HiQ_model.g36797.t1
Valid prediction for Augustus_model.g36795.t1
Valid prediction for snap_scaffold_25-snap.704-T1
Valid prediction for snap_scaffold_25-snap.699-T1
Valid prediction for snap_scaffold_25-snap.731-T1
Valid prediction for Augustus_model.g36796.t1
Valid prediction for GlimmerHMM_glimmerT_55157-T1
Valid prediction for GlimmerHMM_glimmerT_55152-T1
Valid prediction for GeneMark_model.96346_t
Valid prediction for snap_scaffold_25-snap.701-T1
Valid prediction for snap_scaffold_25-snap.709-T1
Valid prediction for snap_scaffold_25-snap.722-T1
Valid prediction for GeneMark_model.96378_t
Valid prediction for snap_scaffold_25-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_55153-T1
Valid prediction for GlimmerHMM_glimmerT_55163-T1
Valid prediction for GeneMark_model.96374_t
Valid prediction for snap_scaffold_25-snap.713-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.96344_t
Valid prediction for GlimmerHMM_glimmerT_55159-T1
Valid prediction for GeneMark_model.96338_t
Valid prediction for snap_scaffold_25-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_55160-T1
Valid prediction for GeneMark_model.96332_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15552, rend_intergenic: 12423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26750, rend_intergenic: 15563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33229, rend_intergenic: 28154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37701, rend_intergenic: 33286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44404, rend_intergenic: 38028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82127, rend_intergenic: 45064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88061, rend_intergenic: 84462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121563, rend_intergenic: 117300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150185, rend_intergenic: 135787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172102, rend_intergenic: 170156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176113, rend_intergenic: 172364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181489
-exon list size: 803


building trellis

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98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 15552, rend_intergenic: 12423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26750, rend_intergenic: 15563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33229, rend_intergenic: 28154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37701, rend_intergenic: 33286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44404, rend_intergenic: 38028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82127, rend_intergenic: 45064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88061, rend_intergenic: 84462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121563, rend_intergenic: 117300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150185, rend_intergenic: 135787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172102, rend_intergenic: 170156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176113, rend_intergenic: 172364  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

-building DP trellis

-building trellis in range 1 - 12058
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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