-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_8521017-8682409

-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 GlimmerHMM_glimmerT_20187-T1
Valid prediction for GlimmerHMM_glimmerT_20171-T1
Valid prediction for Augustus_model.g13427.t1
Valid prediction for snap_scaffold_8-snap.1647-T1
Valid prediction for HiQ_model.g13420.t1
Valid prediction for GlimmerHMM_glimmerT_20176-T1
Valid prediction for snap_scaffold_8-snap.1653-T1
Valid prediction for snap_scaffold_8-snap.1670-T1
Valid prediction for CodingQuarry_transcript_59703-T1
Valid prediction for GlimmerHMM_glimmerT_20178-T1
Valid prediction for Augustus_model.g13422.t1
Valid prediction for GlimmerHMM_glimmerT_20186-T1
Valid prediction for Augustus_model.g13407.t1
Valid prediction for snap_scaffold_8-snap.1661-T1
Couldn't classify 129536, 129697
Couldn't classify 129850, 129893
Sorry, prediction pasa_asmbl_53024.p1 fails validation.
(ATG)	 CC	128727-128876	GT	TAG
(GCT)	 AG	129338-129447	GT	AAG
(GGG)	 AG	129536-129697	AT	CCA
(TCT)	 AC	129850-129893	GT	AGG
(GGA)	 AG	130030-130094	GT	CTG
(GTA)	 AG	130265-130535	GT	AGG
(CAG)	 AG	130654-130773	GT	CTG
(TGC)	 AG	131174-131221	GT	AGG
(AAA)	 AG	131719-131763	GT	AGG
(TCT)	 AG	131995-132110	CC	GAC
-recovered pasa_asmbl_53024.p1, initial, 128727, 128876
-recovered pasa_asmbl_53024.p1, terminal, 131995, 132110
-recovered pasa_asmbl_53024.p1, internal, 129338, 129447
-recovered pasa_asmbl_53024.p1, internal, 130030, 130094
-recovered pasa_asmbl_53024.p1, internal, 130265, 130535
-recovered pasa_asmbl_53024.p1, internal, 130654, 130773
-recovered pasa_asmbl_53024.p1, internal, 131174, 131221
-recovered pasa_asmbl_53024.p1, internal, 131719, 131763
Valid prediction for Augustus_model.g13418.t1
Valid prediction for snap_scaffold_8-snap.1679-T1
Valid prediction for snap_scaffold_8-snap.1675-T1
Valid prediction for snap_scaffold_8-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_20189-T1
Valid prediction for HiQ_model.g13412.t1
Valid prediction for snap_scaffold_8-snap.1656-T1
Valid prediction for Augustus_model.g13405.t1
Valid prediction for HiQ_model.g13414.t1
Valid prediction for GlimmerHMM_glimmerT_20184-T1
Valid prediction for snap_scaffold_8-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_20192-T1
Valid prediction for snap_scaffold_8-snap.1651-T1
Couldn't classify 117481, 117615
Couldn't classify 119193, 119289
Sorry, prediction pasa_asmbl_53020.p1 fails validation.
(GAC)	 GG	117481-117615	GT	TGG
(TTT)	 AG	117943-117996	GT	AGG
(GTC)	 AG	118164-118308	GT	ATG
(TGA)	 AG	118924-119062	GT	AGG
(TGC)	 AG	119193-119289	AG	CCA
add_exon() Sorry, pasa_asmbl_53020.p1 118924-119062-terminal-3 is invalid.
-recovered pasa_asmbl_53020.p1, terminal, 118924, 119062
-recovered pasa_asmbl_53020.p1, internal, 117943, 117996
-recovered pasa_asmbl_53020.p1, internal, 118164, 118308
-recovered pasa_asmbl_53020.p1, internal, 118924, 119062
Couldn't classify 129536, 129697
Couldn't classify 129850, 129893
Sorry, prediction CodingQuarry_transcript_59709-T1 fails validation.
(ATG)	 CC	128727-128876	GT	TAG
(GCT)	 AG	129338-129447	GT	AAG
(GGG)	 AG	129536-129697	AT	CCA
(TCT)	 AC	129850-129893	GT	AGG
(GGA)	 AG	130030-130094	GT	CTG
(GTA)	 AG	130265-130535	GT	AGG
(CAG)	 AG	130654-130773	GT	CTG
(TGC)	 AG	131174-131221	GT	AGG
(AAA)	 AG	131719-131763	GT	AGG
(TCT)	 AG	131995-132110	CC	GAC
-recovered CodingQuarry_transcript_59709-T1, initial, 128727, 128876
-recovered CodingQuarry_transcript_59709-T1, terminal, 131995, 132110
-recovered CodingQuarry_transcript_59709-T1, internal, 129338, 129447
-recovered CodingQuarry_transcript_59709-T1, internal, 130030, 130094
-recovered CodingQuarry_transcript_59709-T1, internal, 130265, 130535
-recovered CodingQuarry_transcript_59709-T1, internal, 130654, 130773
-recovered CodingQuarry_transcript_59709-T1, internal, 131174, 131221
-recovered CodingQuarry_transcript_59709-T1, internal, 131719, 131763
Couldn't classify 129536, 129697
Couldn't classify 129850, 129893
Sorry, prediction CodingQuarry_transcript_59708-T1 fails validation.
(ATG)	 CC	128727-128876	GT	TAG
(GCT)	 AG	129338-129447	GT	AAG
(GGG)	 AG	129536-129697	AT	CCA
(TCT)	 AC	129850-129893	GT	AGG
(GGA)	 AG	130030-130094	GT	CTG
(GTA)	 AG	130265-130535	GT	AGG
(AGA)	 AG	130657-130773	GT	CTG
(TGC)	 AG	131174-131221	GT	AGG
(AAA)	 AG	131719-131763	GT	AGG
(TCT)	 AG	131995-132110	CC	GAC
-recovered CodingQuarry_transcript_59708-T1, initial, 128727, 128876
-recovered CodingQuarry_transcript_59708-T1, terminal, 131995, 132110
-recovered CodingQuarry_transcript_59708-T1, internal, 129338, 129447
-recovered CodingQuarry_transcript_59708-T1, internal, 130030, 130094
-recovered CodingQuarry_transcript_59708-T1, internal, 130265, 130535
-recovered CodingQuarry_transcript_59708-T1, internal, 130657, 130773
-recovered CodingQuarry_transcript_59708-T1, internal, 131174, 131221
-recovered CodingQuarry_transcript_59708-T1, internal, 131719, 131763
Valid prediction for snap_scaffold_8-snap.1672-T1
Valid prediction for snap_scaffold_8-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_20181-T1
Valid prediction for GlimmerHMM_glimmerT_20185-T1
Valid prediction for Augustus_model.g13424.t1
Valid prediction for snap_scaffold_8-snap.1646-T1
Valid prediction for pasa_asmbl_53018.p1
Valid prediction for snap_scaffold_8-snap.1674-T1
Couldn't classify 119427, 119483
Sorry, prediction pasa_asmbl_53021.p1 fails validation.
(CCC)	 GC	119427-119483	GT	AGG
(TGC)	 AG	119684-119798	GT	AGG
(GCG)	 AG	119919-120066	GT	AGG
(GGC)	 AG	120177-120376	GT	AGG
(GTC)	 AG	120469-120520	GT	AGG
(CTG)	 AG	120629-120740	GG	AGG
-recovered pasa_asmbl_53021.p1, terminal, 120629, 120740
-recovered pasa_asmbl_53021.p1, internal, 119684, 119798
-recovered pasa_asmbl_53021.p1, internal, 119919, 120066
-recovered pasa_asmbl_53021.p1, internal, 120177, 120376
-recovered pasa_asmbl_53021.p1, internal, 120469, 120520
Valid prediction for GlimmerHMM_glimmerT_20168-T1
Valid prediction for GlimmerHMM_glimmerT_20182-T1
Valid prediction for snap_scaffold_8-snap.1671-T1
Valid prediction for CodingQuarry_transcript_59706-T1
Valid prediction for GlimmerHMM_glimmerT_20166-T1
Valid prediction for snap_scaffold_8-snap.1676-T1
Valid prediction for pasa_asmbl_53015.p1
Valid prediction for Augustus_model.g13419.t1
Couldn't classify 77584, 77646
Sorry, prediction pasa_asmbl_53016.p1 fails validation.
(ACT)	 CT	77584-77646	GT	AGG
(GAA)	 AG	77839-77971	GT	CGG
(TCA)	 AG	78056-78189	GC	AGG
(GTT)	 AG	78282-78353	GT	AGG
(AGG)	 AG	78513-78644	GT	TGG
(CAT)	 AG	78752-79048	GT	AGG
(AAT)	 AG	79139-79236	GT	AAG
(GAC)	 AG	79312-79456	GT	AGG
(TAC)	 AG	79609-79878	TG	AAT
-recovered pasa_asmbl_53016.p1, terminal, 79609, 79878
-recovered pasa_asmbl_53016.p1, internal, 77839, 77971
-recovered pasa_asmbl_53016.p1, internal, 78056, 78189
-recovered pasa_asmbl_53016.p1, internal, 78282, 78353
-recovered pasa_asmbl_53016.p1, internal, 78513, 78644
-recovered pasa_asmbl_53016.p1, internal, 78752, 79048
-recovered pasa_asmbl_53016.p1, internal, 79139, 79236
-recovered pasa_asmbl_53016.p1, internal, 79312, 79456
Valid prediction for snap_scaffold_8-snap.1649-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_8-snap.1667-T1
Valid prediction for snap_scaffold_8-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_20167-T1
Valid prediction for snap_scaffold_8-snap.1668-T1
Valid prediction for pasa_asmbl_51961.p1
Valid prediction for snap_scaffold_8-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_20173-T1
Valid prediction for Augustus_model.g13417.t1
Valid prediction for HiQ_model.g13406.t1
Valid prediction for pasa_asmbl_51964.p1
Valid prediction for GlimmerHMM_glimmerT_20170-T1
Valid prediction for snap_scaffold_8-snap.1660-T1
Valid prediction for snap_scaffold_8-snap.1648-T1
Valid prediction for GlimmerHMM_glimmerT_20177-T1
Valid prediction for Augustus_model.g13425.t1
Valid prediction for pasa_asmbl_51958.p1
Valid prediction for GlimmerHMM_glimmerT_20174-T1
Valid prediction for pasa_asmbl_51955.p1
Valid prediction for snap_scaffold_8-snap.1677-T1
Valid prediction for pasa_asmbl_51969.p1
Couldn't classify 101434, 101754
Sorry, prediction pasa_asmbl_52593.p1 fails validation.
(AAG)	 CG	101434-101754	GT	AGG
Valid prediction for GlimmerHMM_glimmerT_20191-T1
Valid prediction for pasa_asmbl_51970.p1
Valid prediction for GlimmerHMM_glimmerT_20190-T1
Valid prediction for Augustus_model.g13409.t1
Valid prediction for CodingQuarry_transcript_59705-T1
Valid prediction for Augustus_model.g13411.t1
Valid prediction for CodingQuarry_transcript_59704-T1
Valid prediction for HiQ_model.g13410.t1
Couldn't classify 72771, 72875
Sorry, prediction pasa_asmbl_51968.p1 fails validation.
(ATG)	 AC	70849-70996	GT	AAG
(ATC)	 AG	71182-71277	GT	AGG
(ACT)	 AG	71492-71619	GT	TGG
(CTG)	 AG	71872-71958	GT	AGG
(AAA)	 AG	72501-72641	GT	GGG
(GTT)	 AG	72771-72875	GA	CTG
-recovered pasa_asmbl_51968.p1, initial, 70849, 70996
add_exon() Sorry, pasa_asmbl_51968.p1 71182-71277-terminal-1 is invalid.
-recovered pasa_asmbl_51968.p1, terminal, 71182, 71277
-recovered pasa_asmbl_51968.p1, internal, 71182, 71277
-recovered pasa_asmbl_51968.p1, internal, 71492, 71619
-recovered pasa_asmbl_51968.p1, internal, 71872, 71958
-recovered pasa_asmbl_51968.p1, internal, 72501, 72641
Valid prediction for snap_scaffold_8-snap.1663-T1
Valid prediction for Augustus_model.g13426.t1
Valid prediction for GlimmerHMM_glimmerT_20164-T1
Couldn't classify 73906, 74384
Sorry, prediction pasa_asmbl_51965.p1 fails validation.
(GAT)	 CA	73906-74384	GT	GAG
(GGT)	 AG	74522-74650	GT	TGG
(GAA)	 AG	74965-75047	GT	CGG
(GGT)	 AG	75152-75198	GT	GAG
(ATG)	 AG	75474-75632	AA	GAA
-recovered pasa_asmbl_51965.p1, terminal, 75474, 75632
-recovered pasa_asmbl_51965.p1, internal, 74522, 74650
-recovered pasa_asmbl_51965.p1, internal, 74965, 75047
-recovered pasa_asmbl_51965.p1, internal, 75152, 75198
Valid prediction for HiQ_model.g13421.t1
Valid prediction for snap_scaffold_8-snap.1665-T1
Valid prediction for HiQ_model.g13413.t1
Valid prediction for Augustus_model.g13423.t1
Couldn't classify 88684, 88765
Sorry, prediction pasa_asmbl_51963.p1 fails validation.
(ATG)	 CT	84621-84661	GT	GGG
(GCG)	 AG	84929-85064	GT	CTG
(AGT)	 AG	85219-85304	GT	AGG
(TGA)	 AG	85475-85555	GT	AGG
(AGA)	 AG	85650-85687	GT	CGG
(CGG)	 AG	85822-85910	GT	GGG
(AAA)	 AG	86187-86303	GT	GGG
(TTC)	 AG	86402-86479	GT	CTG
(CCC)	 AG	86574-86730	GT	GGG
(GGT)	 AG	86961-87040	GT	AGG
(CTG)	 AG	87135-87258	GT	GGG
(ACC)	 AG	87504-87622	GT	AGG
(ATG)	 AG	87731-87895	GT	AGG
(ATT)	 AG	88158-88253	GT	TGG
(ACC)	 AG	88355-88581	GT	AGG
(GTC)	 AG	88684-88765	CT	GGC
-recovered pasa_asmbl_51963.p1, initial, 84621, 84661
-recovered pasa_asmbl_51963.p1, initial, 87731, 87895
-recovered pasa_asmbl_51963.p1, internal, 84929, 85064
-recovered pasa_asmbl_51963.p1, internal, 85219, 85304
-recovered pasa_asmbl_51963.p1, internal, 85475, 85555
-recovered pasa_asmbl_51963.p1, internal, 85650, 85687
-recovered pasa_asmbl_51963.p1, internal, 85822, 85910
-recovered pasa_asmbl_51963.p1, internal, 86187, 86303
-recovered pasa_asmbl_51963.p1, internal, 86402, 86479
-recovered pasa_asmbl_51963.p1, internal, 86574, 86730
-recovered pasa_asmbl_51963.p1, internal, 86961, 87040
-recovered pasa_asmbl_51963.p1, internal, 87135, 87258
-recovered pasa_asmbl_51963.p1, internal, 87504, 87622
-recovered pasa_asmbl_51963.p1, internal, 87731, 87895
-recovered pasa_asmbl_51963.p1, internal, 88158, 88253
-recovered pasa_asmbl_51963.p1, internal, 88355, 88581
Valid prediction for snap_scaffold_8-snap.1678-T1
Valid prediction for HiQ_model.g13408.t1
Valid prediction for Augustus_model.g13415.t1
Valid prediction for GlimmerHMM_glimmerT_20183-T1
Valid prediction for snap_scaffold_8-snap.1650-T1
Valid prediction for snap_scaffold_8-snap.1655-T1
Valid prediction for snap_scaffold_8-snap.1652-T1
Valid prediction for CodingQuarry_transcript_59707-T1
Valid prediction for snap_scaffold_8-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_20165-T1
Valid prediction for GlimmerHMM_glimmerT_20169-T1
Valid prediction for GlimmerHMM_glimmerT_20188-T1
Valid prediction for GlimmerHMM_glimmerT_20172-T1
Valid prediction for GlimmerHMM_glimmerT_20175-T1
Valid prediction for GlimmerHMM_glimmerT_20180-T1
Valid prediction for Augustus_model.g13416.t1
Valid prediction for GlimmerHMM_glimmerT_20179-T1
Valid prediction for snap_scaffold_8-snap.1673-T1
Valid prediction for snap_scaffold_8-snap.1658-T1
Valid prediction for snap_scaffold_8-snap.1657-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30399, rend_intergenic: 23696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51034, rend_intergenic: 38118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95119, rend_intergenic: 92750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98097, rend_intergenic: 95225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161393
-exon list size: 408


building trellis

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90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 30399, rend_intergenic: 23696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51034, rend_intergenic: 38118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95119, rend_intergenic: 92750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98097, rend_intergenic: 95225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11730
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support