-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_14980214-15321300

-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_5-snap.2752-T1
Valid prediction for snap_scaffold_5-snap.2765-T1
Valid prediction for snap_scaffold_5-snap.2753-T1
Valid prediction for GlimmerHMM_glimmerT_13183-T1
Valid prediction for GlimmerHMM_glimmerT_13182-T1
Couldn't classify 242256, 242329
Sorry, prediction pasa_asmbl_45979.p1 fails validation.
(ATG)	 CC	237199-237330	GT	AGG
(GTG)	 AG	237464-237566	GT	CGG
(CCT)	 AG	238512-238714	GT	AGG
(TCT)	 AG	239091-239303	GT	AGG
(GAG)	 AG	239716-239864	GT	AGG
(GAT)	 AG	240044-240113	GT	AGG
(GCC)	 AG	240323-240478	GT	AGG
(GCG)	 AG	240713-240967	GT	AGG
(AAG)	 AG	241337-241462	GT	GGG
(GTT)	 AG	241620-241715	GT	AGG
(GAG)	 AG	241864-241951	GT	TAG
(GTC)	 AG	242256-242329	TC	CCT
-recovered pasa_asmbl_45979.p1, initial, 237199, 237330
-recovered pasa_asmbl_45979.p1, internal, 237464, 237566
-recovered pasa_asmbl_45979.p1, internal, 238512, 238714
-recovered pasa_asmbl_45979.p1, internal, 239091, 239303
-recovered pasa_asmbl_45979.p1, internal, 239716, 239864
-recovered pasa_asmbl_45979.p1, internal, 240044, 240113
-recovered pasa_asmbl_45979.p1, internal, 240323, 240478
-recovered pasa_asmbl_45979.p1, internal, 240713, 240967
-recovered pasa_asmbl_45979.p1, internal, 241337, 241462
-recovered pasa_asmbl_45979.p1, internal, 241620, 241715
-recovered pasa_asmbl_45979.p1, internal, 241864, 241951
Valid prediction for GlimmerHMM_glimmerT_13194-T1
Valid prediction for snap_scaffold_5-snap.2789-T1
Valid prediction for Augustus_model.g8749.t1
Valid prediction for snap_scaffold_5-snap.2779-T1
Valid prediction for GlimmerHMM_glimmerT_13158-T1
Valid prediction for GlimmerHMM_glimmerT_13189-T1
Valid prediction for GlimmerHMM_glimmerT_13180-T1
Couldn't classify 60246, 60635
Sorry, prediction pasa_asmbl_45976.p1 fails validation.
(TTA)	 CC	60246-60635	AG	AGA
Valid prediction for HiQ_model.g8752.t1
Couldn't classify 322995, 323046
Sorry, prediction pasa_asmbl_45985.p1 fails validation.
(CCC)	 TC	322995-323046	GT	AGG
(CCC)	 AG	323183-323246	GT	AGG
(CGT)	 AG	323342-323380	GT	CTG
(GAC)	 AG	323518-323602	GT	AGG
(CGG)	 AG	323755-323898	GT	AGG
(GCG)	 AG	324161-324292	GT	AGG
(GTG)	 AG	324487-324690	GT	CGG
(GTG)	 AG	324926-325005	GT	CTG
(GCA)	 AG	325274-325358	GT	ATG
(GAG)	 AG	325442-325537	GT	AAG
(AAA)	 AG	325625-325687	AA	GAA
-recovered pasa_asmbl_45985.p1, terminal, 325625, 325687
-recovered pasa_asmbl_45985.p1, internal, 323183, 323246
-recovered pasa_asmbl_45985.p1, internal, 323342, 323380
-recovered pasa_asmbl_45985.p1, internal, 323518, 323602
-recovered pasa_asmbl_45985.p1, internal, 323755, 323898
-recovered pasa_asmbl_45985.p1, internal, 324161, 324292
-recovered pasa_asmbl_45985.p1, internal, 324487, 324690
-recovered pasa_asmbl_45985.p1, internal, 324926, 325005
-recovered pasa_asmbl_45985.p1, internal, 325274, 325358
-recovered pasa_asmbl_45985.p1, internal, 325442, 325537
Valid prediction for Augustus_model.g8745.t1
Valid prediction for snap_scaffold_5-snap.2758-T1
Valid prediction for Augustus_model.g8772.t1
Valid prediction for snap_scaffold_5-snap.2790-T1
Valid prediction for HiQ_model.g8764.t1
Valid prediction for snap_scaffold_5-snap.2784-T1
Valid prediction for snap_scaffold_5-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_13187-T1
Valid prediction for GlimmerHMM_glimmerT_13169-T1
Valid prediction for snap_scaffold_5-snap.2777-T1
Valid prediction for pasa_asmbl_45984.p1
Valid prediction for pasa_asmbl_45977.p1
Valid prediction for GlimmerHMM_glimmerT_13193-T1
Valid prediction for GlimmerHMM_glimmerT_13153-T1
Valid prediction for snap_scaffold_5-snap.2751-T1
Valid prediction for snap_scaffold_5-snap.2750-T1
Valid prediction for GlimmerHMM_glimmerT_13192-T1
Valid prediction for snap_scaffold_5-snap.2760-T1
Valid prediction for snap_scaffold_5-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_13172-T1
Valid prediction for HiQ_model.g8771.t1
Valid prediction for Augustus_model.g8770.t1
Valid prediction for snap_scaffold_5-snap.2762-T1
Valid prediction for Augustus_model.g8746.t1
Valid prediction for CodingQuarry_transcript_52368-T1
Valid prediction for snap_scaffold_5-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_13196-T1
Valid prediction for GlimmerHMM_glimmerT_13171-T1
Valid prediction for GlimmerHMM_glimmerT_13190-T1
Valid prediction for snap_scaffold_5-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_13185-T1
Valid prediction for snap_scaffold_5-snap.2787-T1
Valid prediction for CodingQuarry_transcript_52376-T1
Valid prediction for Augustus_model.g8766.t1
Valid prediction for GlimmerHMM_glimmerT_13159-T1
Valid prediction for snap_scaffold_5-snap.2781-T1
Valid prediction for GlimmerHMM_glimmerT_13167-T1
Valid prediction for GlimmerHMM_glimmerT_13174-T1
Valid prediction for snap_scaffold_5-snap.2748-T1
Valid prediction for snap_scaffold_5-snap.2764-T1
Valid prediction for Augustus_model.g8769.t1
Valid prediction for Augustus_model.g8747.t1
Valid prediction for GlimmerHMM_glimmerT_13191-T1
Valid prediction for snap_scaffold_5-snap.2785-T1
Valid prediction for snap_scaffold_5-snap.2792-T1
Couldn't classify 37776, 37910
Sorry, prediction pasa_asmbl_45973.p2 fails validation.
(ATG)	 CG	36947-36991	GT	GGG
(GCT)	 AG	37203-37454	GT	GGG
(CTA)	 AG	37776-37910	GT	AGG
-recovered pasa_asmbl_45973.p2, initial, 36947, 36991
-recovered pasa_asmbl_45973.p2, internal, 37203, 37454
-recovered pasa_asmbl_45973.p2, internal, 37776, 37910
Couldn't classify 34292, 34410
Sorry, prediction pasa_asmbl_45972.p1 fails validation.
(GGG)	 CG	34292-34410	GT	AGG
(ATA)	 AG	34587-34638	GT	AGG
(CCA)	 AG	34886-34975	GT	AGG
(GTG)	 AG	35077-35250	CA	AAC
-recovered pasa_asmbl_45972.p1, terminal, 35077, 35250
-recovered pasa_asmbl_45972.p1, internal, 34587, 34638
-recovered pasa_asmbl_45972.p1, internal, 34886, 34975
Valid prediction for GlimmerHMM_glimmerT_13157-T1
Valid prediction for GlimmerHMM_glimmerT_13161-T1
Valid prediction for GlimmerHMM_glimmerT_13163-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_5-snap.2775-T1
Valid prediction for pasa_asmbl_44647.p1
Valid prediction for pasa_asmbl_44662.p1
Valid prediction for GlimmerHMM_glimmerT_13179-T1
Couldn't classify 84551, 84691
Sorry, prediction pasa_asmbl_44655.p1 fails validation.
(ACC)	 AG	84551-84691	GT	AGG
(GGC)	 AG	85241-85382	GT	AGG
(CGG)	 AG	86751-86914	GT	CGG
(AAC)	 AG	87652-87828	GT	TGG
(ATG)	 AG	88127-88331	GT	AGG
(ACC)	 AG	89007-89165	GT	GGG
(GAG)	 AG	89393-89769	AT	GAA
-recovered pasa_asmbl_44655.p1, initial, 88127, 88331
-recovered pasa_asmbl_44655.p1, terminal, 89393, 89769
-recovered pasa_asmbl_44655.p1, internal, 84551, 84691
-recovered pasa_asmbl_44655.p1, internal, 85241, 85382
-recovered pasa_asmbl_44655.p1, internal, 86751, 86914
-recovered pasa_asmbl_44655.p1, internal, 87652, 87828
-recovered pasa_asmbl_44655.p1, internal, 88127, 88331
-recovered pasa_asmbl_44655.p1, internal, 89007, 89165
Valid prediction for CodingQuarry_transcript_52366-T1
Valid prediction for Augustus_model.g8754.t1
Valid prediction for snap_scaffold_5-snap.2756-T1
Valid prediction for CodingQuarry_transcript_52372-T1
Valid prediction for snap_scaffold_5-snap.2783-T1
Valid prediction for GlimmerHMM_glimmerT_13184-T1
Valid prediction for snap_scaffold_5-snap.2782-T1
Valid prediction for Augustus_model.g8768.t1
Valid prediction for GlimmerHMM_glimmerT_13170-T1
Valid prediction for GlimmerHMM_glimmerT_13156-T1
Valid prediction for HiQ_model.g8755.t1
Valid prediction for Augustus_model.g8760.t1
Valid prediction for GlimmerHMM_glimmerT_13178-T1
Valid prediction for HiQ_model.g8759.t1
Valid prediction for snap_scaffold_5-snap.2749-T1
Valid prediction for HiQ_model.g8756.t1
Valid prediction for Augustus_model.g8765.t1
Valid prediction for snap_scaffold_5-snap.2769-T1
Valid prediction for Augustus_model.g8774.t1
Valid prediction for Augustus_model.g8773.t1
Valid prediction for GlimmerHMM_glimmerT_13181-T1
Valid prediction for CodingQuarry_transcript_52371-T1
Couldn't classify 275497, 275580
Sorry, prediction pasa_asmbl_44633.p1 fails validation.
(TTT)	 CA	275497-275580	GT	AGG
(GCT)	 AG	276128-276244	GT	TGG
(GTT)	 AG	276362-276508	GT	AGG
(GAC)	 AG	276607-276817	GT	CAG
(TCC)	 AG	276912-277007	GT	AGG
(GTG)	 AG	277270-277359	GT	TGG
(GTG)	 AG	277438-277590	GT	TGG
(GAA)	 AG	277676-277819	GT	AGG
(GTG)	 AG	277921-277997	AT	AGA
-recovered pasa_asmbl_44633.p1, terminal, 277921, 277997
-recovered pasa_asmbl_44633.p1, internal, 276128, 276244
-recovered pasa_asmbl_44633.p1, internal, 276362, 276508
-recovered pasa_asmbl_44633.p1, internal, 276607, 276817
-recovered pasa_asmbl_44633.p1, internal, 276912, 277007
-recovered pasa_asmbl_44633.p1, internal, 277270, 277359
-recovered pasa_asmbl_44633.p1, internal, 277438, 277590
-recovered pasa_asmbl_44633.p1, internal, 277676, 277819
Valid prediction for Augustus_model.g8753.t1
Valid prediction for pasa_asmbl_44652.p1
Valid prediction for GlimmerHMM_glimmerT_13162-T1
Valid prediction for HiQ_model.g8757.t1
Valid prediction for GlimmerHMM_glimmerT_13154-T1
Valid prediction for snap_scaffold_5-snap.2754-T1
Valid prediction for GlimmerHMM_glimmerT_13165-T1
Valid prediction for GlimmerHMM_glimmerT_13186-T1
Valid prediction for Augustus_model.g8750.t1
Valid prediction for HiQ_model.g8762.t1
Valid prediction for GlimmerHMM_glimmerT_13177-T1
Valid prediction for CodingQuarry_transcript_52374-T1
Valid prediction for GlimmerHMM_glimmerT_13168-T1
Valid prediction for pasa_asmbl_44654.p1
Valid prediction for GlimmerHMM_glimmerT_13173-T1
Valid prediction for GlimmerHMM_glimmerT_13175-T1
Valid prediction for GlimmerHMM_glimmerT_13176-T1
Valid prediction for snap_scaffold_5-snap.2774-T1
Valid prediction for CodingQuarry_transcript_52369-T1
Valid prediction for snap_scaffold_5-snap.2786-T1
Valid prediction for HiQ_model.g8758.t1
Valid prediction for CodingQuarry_transcript_52370-T1
Valid prediction for HiQ_model.g8761.t1
Valid prediction for GlimmerHMM_glimmerT_13195-T1
Valid prediction for GlimmerHMM_glimmerT_13164-T1
Valid prediction for snap_scaffold_5-snap.2771-T1
Valid prediction for snap_scaffold_5-snap.2763-T1
Valid prediction for snap_scaffold_5-snap.2791-T1
Valid prediction for snap_scaffold_5-snap.2770-T1
Valid prediction for HiQ_model.g8748.t1
Valid prediction for snap_scaffold_5-snap.2767-T1
Valid prediction for snap_scaffold_5-snap.2773-T1
Valid prediction for Augustus_model.g8767.t1
Valid prediction for snap_scaffold_5-snap.2768-T1
Valid prediction for Augustus_model.g8763.t1
Valid prediction for snap_scaffold_5-snap.2772-T1
Valid prediction for pasa_asmbl_44630.p1
Valid prediction for GlimmerHMM_glimmerT_13188-T1
Valid prediction for Augustus_model.g8751.t1
Valid prediction for snap_scaffold_5-snap.2757-T1
Valid prediction for snap_scaffold_5-snap.2759-T1
Valid prediction for pasa_asmbl_44643.p1
Valid prediction for GlimmerHMM_glimmerT_13166-T1
Valid prediction for snap_scaffold_5-snap.2778-T1
Valid prediction for GlimmerHMM_glimmerT_13155-T1
Valid prediction for snap_scaffold_5-snap.2776-T1
Valid prediction for CodingQuarry_transcript_52373-T1
Valid prediction for snap_scaffold_5-snap.2780-T1
Valid prediction for GlimmerHMM_glimmerT_13160-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 84625, rend_intergenic: 75771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91941, rend_intergenic: 91512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98217, rend_intergenic: 93296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243790, rend_intergenic: 237979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252085, rend_intergenic: 251074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262349, rend_intergenic: 252735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280814, rend_intergenic: 262722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287068, rend_intergenic: 282953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 339609, rend_intergenic: 330976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 341087
-exon list size: 458


building trellis

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97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 84625, rend_intergenic: 75771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91941, rend_intergenic: 91512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98217, rend_intergenic: 93296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243790, rend_intergenic: 237979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252085, rend_intergenic: 251074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262349, rend_intergenic: 252735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280814, rend_intergenic: 262722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287068, rend_intergenic: 282953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 339609, rend_intergenic: 330976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support