-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_12972052-13156039

-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_12-snap.2389-T1
Valid prediction for Augustus_model.g20042.t1
Valid prediction for GlimmerHMM_glimmerT_30262-T1
Valid prediction for GlimmerHMM_glimmerT_30287-T1
Valid prediction for snap_scaffold_12-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_30264-T1
Valid prediction for snap_scaffold_12-snap.2413-T1
Valid prediction for snap_scaffold_12-snap.2397-T1
Valid prediction for snap_scaffold_12-snap.2394-T1
Valid prediction for snap_scaffold_12-snap.2384-T1
Valid prediction for snap_scaffold_12-snap.2401-T1
Valid prediction for HiQ_model.g20039.t1
Valid prediction for GlimmerHMM_glimmerT_30278-T1
Valid prediction for GlimmerHMM_glimmerT_30284-T1
Valid prediction for pasa_asmbl_8036.p1
Valid prediction for Augustus_model.g20052.t1
Valid prediction for snap_scaffold_12-snap.2419-T1
Valid prediction for snap_scaffold_12-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_30274-T1
Valid prediction for GlimmerHMM_glimmerT_30257-T1
Valid prediction for snap_scaffold_12-snap.2387-T1
Valid prediction for snap_scaffold_12-snap.2385-T1
Valid prediction for snap_scaffold_12-snap.2405-T1
Valid prediction for snap_scaffold_12-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_30286-T1
Valid prediction for GlimmerHMM_glimmerT_30270-T1
Valid prediction for CodingQuarry_transcript_10440-T1
Valid prediction for GlimmerHMM_glimmerT_30277-T1
Valid prediction for snap_scaffold_12-snap.2404-T1
Valid prediction for Augustus_model.g20050.t1
Valid prediction for GlimmerHMM_glimmerT_30275-T1
Valid prediction for GlimmerHMM_glimmerT_30260-T1
Valid prediction for snap_scaffold_12-snap.2416-T1
Valid prediction for snap_scaffold_12-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_30273-T1
Valid prediction for Augustus_model.g20035.t1
Valid prediction for Augustus_model.g20043.t1
Valid prediction for GlimmerHMM_glimmerT_30268-T1
Valid prediction for GlimmerHMM_glimmerT_30261-T1
Valid prediction for Augustus_model.g20047.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 pasa_asmbl_8913.p1
Valid prediction for GlimmerHMM_glimmerT_30269-T1
Couldn't classify 99268, 99421
Sorry, prediction pasa_asmbl_8912.p1 fails validation.
(GGG)	 GT	99268-99421	GT	GGG
(ACC)	 AG	99569-99683	GT	AGG
(TGA)	 AG	99770-99927	GT	CAG
(TCA)	 AG	100298-100455	GG	GAG
-recovered pasa_asmbl_8912.p1, terminal, 100298, 100455
-recovered pasa_asmbl_8912.p1, internal, 99569, 99683
-recovered pasa_asmbl_8912.p1, internal, 99770, 99927
Valid prediction for GlimmerHMM_glimmerT_30283-T1
Valid prediction for snap_scaffold_12-snap.2402-T1
Valid prediction for Augustus_model.g20036.t1
Valid prediction for pasa_asmbl_8911.p1
Valid prediction for snap_scaffold_12-snap.2414-T1
Valid prediction for snap_scaffold_12-snap.2398-T1
Valid prediction for snap_scaffold_12-snap.2388-T1
Valid prediction for snap_scaffold_12-snap.2391-T1
Couldn't classify 42996, 43724
Sorry, prediction pasa_asmbl_8919.p1 fails validation.
(ATG)	 AA	42996-43724	CA	CCC
Valid prediction for snap_scaffold_12-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_30271-T1
Valid prediction for Augustus_model.g20045.t1
Valid prediction for snap_scaffold_12-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_30258-T1
Valid prediction for HiQ_model.g20038.t1
Valid prediction for GlimmerHMM_glimmerT_30280-T1
Valid prediction for pasa_asmbl_8908.p1
Valid prediction for GlimmerHMM_glimmerT_30266-T1
Valid prediction for GlimmerHMM_glimmerT_30263-T1
Valid prediction for snap_scaffold_12-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_30288-T1
Valid prediction for pasa_asmbl_8916.p1
Valid prediction for snap_scaffold_12-snap.2412-T1
Valid prediction for snap_scaffold_12-snap.2408-T1
Valid prediction for HiQ_model.g20037.t1
Couldn't classify 123292, 123396
Couldn't classify 128568, 128814
Sorry, prediction pasa_asmbl_8902.p1 fails validation.
(GCG)	 CA	123292-123396	GT	GGG
(GTA)	 AG	123645-123737	GT	AGG
(TAT)	 AG	123904-123993	GT	AGG
(CAC)	 AG	124132-124335	GT	AGG
(GGA)	 AG	124459-124529	GT	AAG
(CGC)	 AG	125999-126086	GT	AGG
(ATA)	 AG	126194-126277	GT	AGG
(GAT)	 AG	126408-126500	GT	AGG
(GCG)	 AG	126635-126809	GT	CGG
(ACG)	 AG	126987-127126	GT	GGG
(TAC)	 AG	127850-127951	GT	AGG
(CTG)	 AG	128068-128216	GT	AAG
(GGA)	 AG	128347-128475	GT	GTG
(TCA)	 AG	128568-128814	GG	AAG
-recovered pasa_asmbl_8902.p1, internal, 123645, 123737
-recovered pasa_asmbl_8902.p1, internal, 123904, 123993
-recovered pasa_asmbl_8902.p1, internal, 124132, 124335
-recovered pasa_asmbl_8902.p1, internal, 124459, 124529
-recovered pasa_asmbl_8902.p1, internal, 125999, 126086
-recovered pasa_asmbl_8902.p1, internal, 126194, 126277
-recovered pasa_asmbl_8902.p1, internal, 126408, 126500
-recovered pasa_asmbl_8902.p1, internal, 126635, 126809
-recovered pasa_asmbl_8902.p1, internal, 126987, 127126
-recovered pasa_asmbl_8902.p1, internal, 127850, 127951
-recovered pasa_asmbl_8902.p1, internal, 128068, 128216
-recovered pasa_asmbl_8902.p1, internal, 128347, 128475
Valid prediction for GlimmerHMM_glimmerT_30285-T1
Valid prediction for GlimmerHMM_glimmerT_30282-T1
Valid prediction for snap_scaffold_12-snap.2390-T1
Valid prediction for HiQ_model.g20041.t1
Valid prediction for snap_scaffold_12-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_30281-T1
Valid prediction for GlimmerHMM_glimmerT_30259-T1
Valid prediction for snap_scaffold_12-snap.2395-T1
Valid prediction for Augustus_model.g20051.t1
Valid prediction for Augustus_model.g20044.t1
Valid prediction for snap_scaffold_12-snap.2411-T1
Valid prediction for snap_scaffold_12-snap.2386-T1
Valid prediction for Augustus_model.g20049.t1
Valid prediction for snap_scaffold_12-snap.2420-T1
Valid prediction for CodingQuarry_transcript_10439-T1
Valid prediction for GlimmerHMM_glimmerT_30265-T1
Valid prediction for Augustus_model.g20033.t1
Valid prediction for GlimmerHMM_glimmerT_30267-T1
Valid prediction for CodingQuarry_transcript_10441-T1
Valid prediction for CodingQuarry_transcript_10437-T1
Valid prediction for snap_scaffold_12-snap.2418-T1
Valid prediction for snap_scaffold_12-snap.2415-T1
Valid prediction for HiQ_model.g20048.t1
Valid prediction for GlimmerHMM_glimmerT_30272-T1
Valid prediction for Augustus_model.g20046.t1
Couldn't classify 33884, 34051
Sorry, prediction pasa_asmbl_8922.p1 fails validation.
(ATG)	 TA	30418-30556	GT	AGG
(CTG)	 AG	32911-33053	GT	AGG
(GGG)	 AG	33884-34051	GT	ACG
-recovered pasa_asmbl_8922.p1, initial, 30418, 30556
-recovered pasa_asmbl_8922.p1, internal, 32911, 33053
-recovered pasa_asmbl_8922.p1, internal, 33884, 34051
Valid prediction for snap_scaffold_12-snap.2403-T1
Valid prediction for snap_scaffold_12-snap.2406-T1
Valid prediction for Augustus_model.g20034.t1
Valid prediction for Augustus_model.g20040.t1
Valid prediction for snap_scaffold_12-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_30279-T1
Valid prediction for GlimmerHMM_glimmerT_30276-T1
Couldn't classify 118495, 118638
Couldn't classify 121467, 121508
Sorry, prediction pasa_asmbl_8905.p1 fails validation.
(GGG)	 AG	118495-118638	GT	AGG
(TCA)	 AG	118796-118892	GT	AGG
(GTG)	 AG	119031-119107	GT	AGG
(GAT)	 AG	119630-119834	GT	AGG
(CCA)	 AG	119945-120096	GT	AGG
(CTC)	 AG	120506-120579	GT	CGG
(CGA)	 AG	120947-121070	GT	AGG
(CAA)	 AG	121467-121508	CT	GGC
-recovered pasa_asmbl_8905.p1, internal, 118495, 118638
-recovered pasa_asmbl_8905.p1, internal, 118796, 118892
-recovered pasa_asmbl_8905.p1, internal, 119031, 119107
-recovered pasa_asmbl_8905.p1, internal, 119630, 119834
-recovered pasa_asmbl_8905.p1, internal, 119945, 120096
-recovered pasa_asmbl_8905.p1, internal, 120506, 120579
-recovered pasa_asmbl_8905.p1, internal, 120947, 121070

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26467, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30830, rend_intergenic: 28164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32482, rend_intergenic: 31260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35409, rend_intergenic: 32861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38835, rend_intergenic: 35584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52532, rend_intergenic: 46714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52876, rend_intergenic: 52715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61315, rend_intergenic: 53390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64386, rend_intergenic: 61598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108675, rend_intergenic: 105473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115534, rend_intergenic: 109508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170492, rend_intergenic: 162843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174634, rend_intergenic: 170594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178550, rend_intergenic: 176418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183988
-exon list size: 366


building trellis

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32.6    
32.9    
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34.8    
35.1    
35.3    
35.6    
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36.1    
36.4    
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37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
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41.6    
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44.0    
44.3    
44.6    
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47.6    
47.8    
48.1    
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48.9    
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49.5    
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50.3    
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51.4    
51.6    
51.9    
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55.4    
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86.1    
86.4    
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87.2    
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88.0    
88.3    
88.6    
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89.1    
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91.3    
91.6    
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92.4    
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97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 26467, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30830, rend_intergenic: 28164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32482, rend_intergenic: 31260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35409, rend_intergenic: 32861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38835, rend_intergenic: 35584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52532, rend_intergenic: 46714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52876, rend_intergenic: 52715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61315, rend_intergenic: 53390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64386, rend_intergenic: 61598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108675, rend_intergenic: 105473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115534, rend_intergenic: 109508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170492, rend_intergenic: 162843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174634, rend_intergenic: 170594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178550, rend_intergenic: 176418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support