-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_385

-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: +)Couldn't classify 7294, 7383
Sorry, prediction snap_scaffold_385-snap.2-T1 fails validation.
(ATG)	 AC	900-1129	GT	GCG
(GGC)	 AG	1391-1483	GT	ACG
(TGA)	 AG	2225-2378	GT	CTG
(CAC)	 AG	7294-7383	GT	GAG
-recovered snap_scaffold_385-snap.2-T1, initial, 900, 1129
-recovered snap_scaffold_385-snap.2-T1, internal, 1391, 1483
-recovered snap_scaffold_385-snap.2-T1, internal, 2225, 2378
-recovered snap_scaffold_385-snap.2-T1, internal, 7294, 7383

-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: -)Couldn't classify 6440, 6535
Sorry, prediction CodingQuarry_transcript_46576-T1 fails validation.
(ATG)	 AA	6173-6175	GT	TGG
(CAG)	 TG	6440-6535	GC	GAG
-recovered CodingQuarry_transcript_46576-T1, initial, 6173, 6175
Couldn't classify 7341, 7451
Sorry, prediction snap_scaffold_385-snap.1-T1 fails validation.
(ATG)	 CC	3017-3062	GT	ACG
(CTG)	 AG	4722-4800	GT	GGG
(AAT)	 AG	5189-5271	GT	AGG
(GGG)	 AG	5645-5730	GT	ACG
(TCC)	 AG	5985-6175	GT	TGG
(GGA)	 AG	6443-6672	GT	CAG
(GTA)	 AG	6962-7131	GT	AGG
(AGT)	 AG	7341-7451	GT	AGG
-recovered snap_scaffold_385-snap.1-T1, initial, 3017, 3062
add_exon() Sorry, snap_scaffold_385-snap.1-T1 5189-5271-terminal-2 is invalid.
-recovered snap_scaffold_385-snap.1-T1, terminal, 5189, 5271
-recovered snap_scaffold_385-snap.1-T1, internal, 4722, 4800
-recovered snap_scaffold_385-snap.1-T1, internal, 5189, 5271
-recovered snap_scaffold_385-snap.1-T1, internal, 5645, 5730
-recovered snap_scaffold_385-snap.1-T1, internal, 5985, 6175
-recovered snap_scaffold_385-snap.1-T1, internal, 6443, 6672
-recovered snap_scaffold_385-snap.1-T1, internal, 6962, 7131
-recovered snap_scaffold_385-snap.1-T1, internal, 7341, 7451
Couldn't classify 196, 294
Couldn't classify 7341, 7451
Sorry, prediction Augustus_model.g39896.t1 fails validation.
(GTG)	 AG	196-294	GT	AGG
(TGT)	 AG	4367-4400	GT	TGG
(CTG)	 AG	4722-4768	GT	AGG
(TCC)	 AG	5985-6175	GT	TGG
(GGA)	 AG	6443-6672	GT	CAG
(GTA)	 AG	6962-7131	GT	AGG
(AGT)	 AG	7341-7451	GT	AGG
-recovered Augustus_model.g39896.t1, internal, 196, 294
-recovered Augustus_model.g39896.t1, internal, 4367, 4400
-recovered Augustus_model.g39896.t1, internal, 4722, 4768
-recovered Augustus_model.g39896.t1, internal, 5985, 6175
-recovered Augustus_model.g39896.t1, internal, 6443, 6672
-recovered Augustus_model.g39896.t1, internal, 6962, 7131
-recovered Augustus_model.g39896.t1, internal, 7341, 7451
Couldn't classify 5982, 6175
Couldn't classify 7341, 7469
Sorry, prediction pasa_asmbl_41061.p1 fails validation.
(CAG)	 CC	5982-6175	GT	TGG
(GGA)	 AG	6443-6672	GT	CAG
(GTA)	 AG	6962-7131	GT	AGG
(AGT)	 AG	7341-7469	CC	CCC
-recovered pasa_asmbl_41061.p1, internal, 6443, 6672
-recovered pasa_asmbl_41061.p1, internal, 6962, 7131
Couldn't classify 115, 147
Sorry, prediction snap_scaffold_385-snap.3-T1 fails validation.
(AGG)	 AG	115-147	GT	ACG
(GTG)	 AG	196-294	GT	AGG
(ACA)	 AG	2714-2959	AG	GAA
-recovered snap_scaffold_385-snap.3-T1, terminal, 2714, 2959
-recovered snap_scaffold_385-snap.3-T1, internal, 115, 147
-recovered snap_scaffold_385-snap.3-T1, internal, 196, 294
Couldn't classify 196, 294
Sorry, prediction GlimmerHMM_glimmerT_60273-T1 fails validation.
(GTG)	 AG	196-294	GT	AGG
(CTG)	 AG	4722-4784	GT	GGG
(TCC)	 AG	5985-6175	GT	TGG
(GGA)	 AG	6443-6731	TT	GAT
-recovered GlimmerHMM_glimmerT_60273-T1, terminal, 6443, 6731
-recovered GlimmerHMM_glimmerT_60273-T1, internal, 196, 294
-recovered GlimmerHMM_glimmerT_60273-T1, internal, 4722, 4784
-recovered GlimmerHMM_glimmerT_60273-T1, internal, 5985, 6175
Valid prediction for CodingQuarry_transcript_46575-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4475, rend_intergenic: 900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7383, rend_intergenic: 4533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7491
-exon list size: 31


building trellis

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39.4    
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48.5    
51.5    
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60.6    
63.6    
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69.7    
72.7    
75.8    
78.8    
81.8    
84.8    
87.9    
90.9    
93.9    
97.0    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 4475, rend_intergenic: 900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7383, rend_intergenic: 4533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support