-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_6781627-7335314

-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 51635, 51714
Couldn't classify 52307, 52380
Sorry, prediction pasa_asmbl_21895.p1 fails validation.
(CAG)	 TT	51635-51714	GT	AAG
(ACA)	 AG	51880-51970	GT	TGG
(CTC)	 AG	52148-52223	GT	TGG
(GCC)	 AG	52307-52380	GA	GGG
-recovered pasa_asmbl_21895.p1, internal, 51880, 51970
-recovered pasa_asmbl_21895.p1, internal, 52148, 52223
Valid prediction for snap_scaffold_19-snap.1418-T1
Couldn't classify 329384, 329683
Sorry, prediction pasa_asmbl_21447.p1 fails validation.
(GCA)	 TT	329384-329683	GA	CAG
Valid prediction for snap_scaffold_19-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_44326-T1
Valid prediction for snap_scaffold_19-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_44319-T1
Valid prediction for GlimmerHMM_glimmerT_44296-T1
Valid prediction for snap_scaffold_19-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_44304-T1
Valid prediction for snap_scaffold_19-snap.1413-T1
Valid prediction for CodingQuarry_transcript_25694-T1
Valid prediction for snap_scaffold_19-snap.1388-T1
Valid prediction for snap_scaffold_19-snap.1396-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44294-T1
Valid prediction for pasa_asmbl_21448.p1
Valid prediction for snap_scaffold_19-snap.1397-T1
Valid prediction for snap_scaffold_19-snap.1419-T1
Valid prediction for CodingQuarry_transcript_25695-T1
Valid prediction for GlimmerHMM_glimmerT_44328-T1
Valid prediction for GlimmerHMM_glimmerT_44320-T1
Valid prediction for GlimmerHMM_glimmerT_44317-T1
Valid prediction for snap_scaffold_19-snap.1402-T1
Valid prediction for Augustus_model.g29386.t1
Valid prediction for snap_scaffold_19-snap.1427-T1
Valid prediction for snap_scaffold_19-snap.1395-T1
Valid prediction for HiQ_model.g29373.t1
Couldn't classify 53071, 53244
Sorry, prediction pasa_asmbl_21446.p1 fails validation.
(GAC)	 AG	53071-53244	GT	AGG
(ACA)	 AG	53356-53442	GT	TGG
(ATG)	 AG	53538-53646	GT	TGG
(GTC)	 AG	53801-53896	GT	CGG
(AGT)	 AG	53984-54051	GT	AGG
(GCG)	 AG	54181-54363	TG	AAT
-recovered pasa_asmbl_21446.p1, initial, 53538, 53646
-recovered pasa_asmbl_21446.p1, terminal, 54181, 54363
-recovered pasa_asmbl_21446.p1, internal, 53071, 53244
-recovered pasa_asmbl_21446.p1, internal, 53356, 53442
-recovered pasa_asmbl_21446.p1, internal, 53538, 53646
-recovered pasa_asmbl_21446.p1, internal, 53801, 53896
-recovered pasa_asmbl_21446.p1, internal, 53984, 54051
Valid prediction for snap_scaffold_19-snap.1424-T1
Valid prediction for Augustus_model.g29380.t1
Valid prediction for snap_scaffold_19-snap.1408-T1
Valid prediction for snap_scaffold_19-snap.1417-T1
Valid prediction for Augustus_model.g29382.t1
Valid prediction for GlimmerHMM_glimmerT_44311-T1
Valid prediction for snap_scaffold_19-snap.1412-T1
Valid prediction for Augustus_model.g29383.t1
Valid prediction for Augustus_model.g29377.t1
Valid prediction for GlimmerHMM_glimmerT_44300-T1
Valid prediction for GlimmerHMM_glimmerT_44299-T1
Valid prediction for snap_scaffold_19-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_44313-T1
Valid prediction for GlimmerHMM_glimmerT_44318-T1
Valid prediction for snap_scaffold_19-snap.1411-T1
Valid prediction for snap_scaffold_19-snap.1393-T1
Valid prediction for snap_scaffold_19-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_44315-T1
Valid prediction for snap_scaffold_19-snap.1422-T1
Valid prediction for Augustus_model.g29385.t1
Valid prediction for snap_scaffold_19-snap.1410-T1
Valid prediction for GlimmerHMM_glimmerT_44308-T1
Valid prediction for snap_scaffold_19-snap.1425-T1
Valid prediction for GlimmerHMM_glimmerT_44325-T1
Valid prediction for pasa_asmbl_21445.p1
Valid prediction for GlimmerHMM_glimmerT_44327-T1
Valid prediction for snap_scaffold_19-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_44303-T1
Valid prediction for GlimmerHMM_glimmerT_44312-T1
Valid prediction for snap_scaffold_19-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_44301-T1
Valid prediction for GlimmerHMM_glimmerT_44305-T1
Valid prediction for snap_scaffold_19-snap.1409-T1
Valid prediction for snap_scaffold_19-snap.1407-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 Augustus_model.g29381.t1
Valid prediction for GlimmerHMM_glimmerT_44307-T1
Valid prediction for snap_scaffold_19-snap.1398-T1
Valid prediction for GlimmerHMM_glimmerT_44316-T1
Valid prediction for GlimmerHMM_glimmerT_44323-T1
Valid prediction for Augustus_model.g29378.t1
Valid prediction for Augustus_model.g29379.t1
Valid prediction for snap_scaffold_19-snap.1414-T1
Valid prediction for snap_scaffold_19-snap.1416-T1
Couldn't classify 508363, 508635
Sorry, prediction pasa_asmbl_22228.p1 fails validation.
(ATG)	 AC	508363-508635	AG	ACA
Valid prediction for snap_scaffold_19-snap.1403-T1
Couldn't classify 485823, 486031
Couldn't classify 487482, 487525
Sorry, prediction pasa_asmbl_22235.p3 fails validation.
(GGT)	 CA	485823-486031	GT	AGG
(CAG)	 AG	486878-486987	GT	GAG
(CAA)	 AG	487482-487525	CT	CCC
-recovered pasa_asmbl_22235.p3, internal, 486878, 486987
Valid prediction for snap_scaffold_19-snap.1385-T1
Valid prediction for GlimmerHMM_glimmerT_44302-T1
Couldn't classify 508687, 508717
Couldn't classify 510532, 510582
Sorry, prediction pasa_asmbl_22227.p1 fails validation.
(AGG)	 AT	508687-508717	GT	AGG
(GTG)	 AG	510100-510368	GT	AGG
(GTC)	 AG	510532-510582	TC	AGT
-recovered pasa_asmbl_22227.p1, internal, 510100, 510368
Valid prediction for Augustus_model.g29374.t1
Valid prediction for snap_scaffold_19-snap.1389-T1
Couldn't classify 510964, 511716
Sorry, prediction pasa_asmbl_22226.p1 fails validation.
(AGG)	 CC	510964-511716	GT	AGG
(GTG)	 AG	511908-511981	GT	AAG
(AGC)	 AG	512544-512619	GT	CGG
(GTT)	 AG	513300-513371	CA	AAC
-recovered pasa_asmbl_22226.p1, terminal, 513300, 513371
-recovered pasa_asmbl_22226.p1, internal, 511908, 511981
-recovered pasa_asmbl_22226.p1, internal, 512544, 512619
Valid prediction for GlimmerHMM_glimmerT_44314-T1
Valid prediction for snap_scaffold_19-snap.1386-T1
Valid prediction for snap_scaffold_19-snap.1394-T1
Valid prediction for snap_scaffold_19-snap.1401-T1
Valid prediction for Augustus_model.g29376.t1
Valid prediction for GlimmerHMM_glimmerT_44297-T1
Valid prediction for GlimmerHMM_glimmerT_44310-T1
Valid prediction for GlimmerHMM_glimmerT_44309-T1
Valid prediction for GlimmerHMM_glimmerT_44321-T1
Valid prediction for snap_scaffold_19-snap.1415-T1
Couldn't classify 492796, 492933
Sorry, prediction pasa_asmbl_22233.p1 fails validation.
(GGG)	 CC	492796-492933	GT	AGG
(GAC)	 AG	493163-493306	GT	AGG
(GGC)	 AG	494146-494291	GT	AGG
(AGA)	 AG	494745-494859	GT	AGG
(GTG)	 AG	495082-495220	GT	CGG
(GCC)	 AG	495604-495734	GT	CGG
(GGT)	 AG	495910-496104	TT	GAT
-recovered pasa_asmbl_22233.p1, terminal, 495910, 496104
-recovered pasa_asmbl_22233.p1, internal, 493163, 493306
-recovered pasa_asmbl_22233.p1, internal, 494146, 494291
-recovered pasa_asmbl_22233.p1, internal, 494745, 494859
-recovered pasa_asmbl_22233.p1, internal, 495082, 495220
-recovered pasa_asmbl_22233.p1, internal, 495604, 495734
Valid prediction for snap_scaffold_19-snap.1400-T1
Valid prediction for Augustus_model.g29372.t1
Valid prediction for Augustus_model.g29375.t1
Couldn't classify 77925, 78035
Couldn't classify 81396, 81422
Sorry, prediction pasa_asmbl_22237.p1 fails validation.
(AGG)	 AC	77925-78035	GT	AGG
(GGC)	 AG	80019-80117	GC	AGG
(TAT)	 AG	80237-80310	GT	GCG
(GCT)	 AG	80443-80495	GT	TGG
(AAA)	 AG	80709-80794	GT	AGG
(ATT)	 AG	80982-81212	GT	CTG
(TGT)	 AG	81396-81422	CG	TGC
-recovered pasa_asmbl_22237.p1, internal, 80019, 80117
-recovered pasa_asmbl_22237.p1, internal, 80237, 80310
-recovered pasa_asmbl_22237.p1, internal, 80443, 80495
-recovered pasa_asmbl_22237.p1, internal, 80709, 80794
-recovered pasa_asmbl_22237.p1, internal, 80982, 81212
Valid prediction for snap_scaffold_19-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_44306-T1
Valid prediction for snap_scaffold_19-snap.1391-T1
Valid prediction for snap_scaffold_19-snap.1390-T1
Valid prediction for GlimmerHMM_glimmerT_44324-T1
Valid prediction for snap_scaffold_19-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_44298-T1
Valid prediction for Augustus_model.g29384.t1
Valid prediction for snap_scaffold_19-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_44322-T1
Valid prediction for snap_scaffold_19-snap.1384-T1
Valid prediction for snap_scaffold_19-snap.1399-T1
Valid prediction for GlimmerHMM_glimmerT_44295-T1
Couldn't classify 539278, 539347
Couldn't classify 540030, 540197
Sorry, prediction pasa_asmbl_22225.p1 fails validation.
(TTC)	 GC	539278-539347	GT	AGG
(AAA)	 AG	539683-539813	GT	AGG
(GTC)	 AG	540030-540197	CA	GCC
-recovered pasa_asmbl_22225.p1, internal, 539683, 539813

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 553688
-exon list size: 473


building trellis

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31.8    
32.0    
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32.6    
32.8    
33.1    
33.3    
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33.9    
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34.9    
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38.9    
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51.8    
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80.0    
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81.9    
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85.9    
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88.0    
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88.8    
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89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
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91.4    
91.6    
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92.0    
92.2    
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92.6    
92.8    
93.1    
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93.5    
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93.9    
94.1    
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96.8    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support