-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_2722590-2901923

-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_14235-T1
Valid prediction for snap_scaffold_6-snap.649-T1
Valid prediction for Augustus_model.g9422.t1
Valid prediction for snap_scaffold_6-snap.652-T1
Valid prediction for GlimmerHMM_glimmerT_14233-T1
Valid prediction for snap_scaffold_6-snap.646-T1
Valid prediction for HiQ_model.g9416.t1
Valid prediction for snap_scaffold_6-snap.641-T1
Valid prediction for snap_scaffold_6-snap.648-T1
Valid prediction for Augustus_model.g9420.t1
Valid prediction for snap_scaffold_6-snap.678-T1
Valid prediction for snap_scaffold_6-snap.662-T1
Valid prediction for snap_scaffold_6-snap.644-T1
Valid prediction for GlimmerHMM_glimmerT_14218-T1
Valid prediction for pasa_asmbl_46771.p1
Valid prediction for HiQ_model.g9436.t1
Valid prediction for snap_scaffold_6-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_14226-T1
Valid prediction for snap_scaffold_6-snap.643-T1
Valid prediction for HiQ_model.g9417.t1
Valid prediction for snap_scaffold_6-snap.676-T1
Valid prediction for pasa_asmbl_46775.p3
Valid prediction for CodingQuarry_transcript_54945-T1
Valid prediction for GlimmerHMM_glimmerT_14215-T1
Valid prediction for snap_scaffold_6-snap.653-T1
Valid prediction for snap_scaffold_6-snap.659-T1
Valid prediction for Augustus_model.g9424.t1
Valid prediction for GlimmerHMM_glimmerT_14208-T1
Valid prediction for GlimmerHMM_glimmerT_14209-T1
Valid prediction for snap_scaffold_6-snap.674-T1
Valid prediction for CodingQuarry_transcript_54946-T1
Valid prediction for GlimmerHMM_glimmerT_14216-T1
Valid prediction for Augustus_model.g9427.t1
Valid prediction for GlimmerHMM_glimmerT_14224-T1
Valid prediction for GlimmerHMM_glimmerT_14223-T1
Valid prediction for GlimmerHMM_glimmerT_14214-T1
Valid prediction for snap_scaffold_6-snap.654-T1
Valid prediction for CodingQuarry_transcript_54956-T1
Valid prediction for HiQ_model.g9429.t1
Valid prediction for snap_scaffold_6-snap.650-T1
Valid prediction for pasa_asmbl_46778.p1
Valid prediction for snap_scaffold_6-snap.660-T1
Valid prediction for HiQ_model.g9431.t1
Valid prediction for snap_scaffold_6-snap.655-T1
Valid prediction for GlimmerHMM_glimmerT_14229-T1
Valid prediction for CodingQuarry_transcript_54952-T1
Valid prediction for pasa_asmbl_46779.p1
Valid prediction for snap_scaffold_6-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_14221-T1
Valid prediction for Augustus_model.g9418.t1
Valid prediction for snap_scaffold_6-snap.656-T1
Valid prediction for snap_scaffold_6-snap.669-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_6-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_14212-T1
Valid prediction for pasa_asmbl_48178.p1
Valid prediction for Augustus_model.g9415.t1
Valid prediction for GlimmerHMM_glimmerT_14227-T1
Valid prediction for GlimmerHMM_glimmerT_14225-T1
Valid prediction for CodingQuarry_transcript_54955-T1
Valid prediction for snap_scaffold_6-snap.681-T1
Valid prediction for snap_scaffold_6-snap.667-T1
Valid prediction for snap_scaffold_6-snap.675-T1
Valid prediction for snap_scaffold_6-snap.668-T1
Valid prediction for snap_scaffold_6-snap.645-T1
Valid prediction for CodingQuarry_transcript_54957-T1
Valid prediction for snap_scaffold_6-snap.647-T1
Valid prediction for snap_scaffold_6-snap.666-T1
Couldn't classify 174251, 174351
Couldn't classify 175413, 175481
Sorry, prediction pasa_asmbl_49337.p1 fails validation.
(AGC)	 AG	174251-174351	GT	AGG
(AGA)	 AG	174811-174970	GT	AGG
(GAG)	 AG	175413-175481	CC	CCC
-recovered pasa_asmbl_49337.p1, internal, 174251, 174351
-recovered pasa_asmbl_49337.p1, internal, 174811, 174970
Valid prediction for HiQ_model.g9432.t1
Valid prediction for snap_scaffold_6-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_14237-T1
Valid prediction for snap_scaffold_6-snap.679-T1
Valid prediction for pasa_asmbl_48165.p1
Valid prediction for CodingQuarry_transcript_54954-T1
Valid prediction for Augustus_model.g9421.t1
Valid prediction for HiQ_model.g9423.t1
Couldn't classify 15715, 15755
Sorry, prediction pasa_asmbl_48183.p1 fails validation.
(ACT)	 GC	15715-15755	GT	GGG
(GAA)	 AG	15853-15885	GT	AGG
(ACT)	 AG	15976-16081	GT	AGG
(TCC)	 AG	16431-16532	GC	AGG
(GAG)	 AG	16710-16780	GT	CTG
(GCT)	 AG	16954-17138	GT	TGG
(AGT)	 AG	17285-17342	GT	AGG
(CTA)	 AG	17597-17661	GT	TGG
(GCT)	 AG	17747-17899	GT	CGG
(ATT)	 AG	18039-18104	GT	AGG
(GCT)	 AG	18358-18443	AG	GAA
-recovered pasa_asmbl_48183.p1, terminal, 18358, 18443
-recovered pasa_asmbl_48183.p1, internal, 15853, 15885
-recovered pasa_asmbl_48183.p1, internal, 15976, 16081
-recovered pasa_asmbl_48183.p1, internal, 16431, 16532
-recovered pasa_asmbl_48183.p1, internal, 16710, 16780
-recovered pasa_asmbl_48183.p1, internal, 16954, 17138
-recovered pasa_asmbl_48183.p1, internal, 17285, 17342
-recovered pasa_asmbl_48183.p1, internal, 17597, 17661
-recovered pasa_asmbl_48183.p1, internal, 17747, 17899
-recovered pasa_asmbl_48183.p1, internal, 18039, 18104
Valid prediction for GlimmerHMM_glimmerT_14210-T1
Couldn't classify 7114, 7524
Sorry, prediction pasa_asmbl_48185.p1 fails validation.
(CTG)	 AG	7114-7524	GA	CAG
Valid prediction for snap_scaffold_6-snap.673-T1
Valid prediction for GlimmerHMM_glimmerT_14220-T1
Valid prediction for HiQ_model.g9425.t1
Valid prediction for Augustus_model.g9435.t1
Valid prediction for GlimmerHMM_glimmerT_14211-T1
Valid prediction for GlimmerHMM_glimmerT_14230-T1
Valid prediction for Augustus_model.g9426.t1
Valid prediction for HiQ_model.g9434.t1
Valid prediction for GlimmerHMM_glimmerT_14222-T1
Valid prediction for CodingQuarry_transcript_54951-T1
Valid prediction for Augustus_model.g9428.t1
Valid prediction for Augustus_model.g9437.t1
Couldn't classify 156278, 156328
Sorry, prediction pasa_asmbl_48157.p1 fails validation.
(TCC)	 TC	156278-156328	GT	AGG
(GCA)	 AG	156943-157029	GT	CTG
(ACG)	 AG	157991-158233	GT	AGG
(ATC)	 AG	159398-159529	TC	GAT
-recovered pasa_asmbl_48157.p1, terminal, 159398, 159529
-recovered pasa_asmbl_48157.p1, internal, 156943, 157029
-recovered pasa_asmbl_48157.p1, internal, 157991, 158233
Couldn't classify 54650, 54767
Sorry, prediction pasa_asmbl_48168.p1 fails validation.
(ACA)	 CG	54650-54767	GT	AGG
(GTG)	 AG	54879-54992	GT	AGG
(GCG)	 AG	55800-55838	GT	AGG
(GCT)	 AG	56104-56154	GT	AGG
(GAA)	 AG	56267-56323	GT	AGG
(GCC)	 AG	56625-56678	GT	CGG
(GGG)	 AG	56828-56974	GT	AGG
(GGG)	 AG	57149-57190	GT	TGG
(GTG)	 AG	57280-57339	GT	TGG
(GTG)	 AG	57641-57712	GT	TGG
(GAA)	 AG	58471-58506	GT	AGG
(GTT)	 AG	58680-58718	GT	TGG
(GAG)	 AG	59011-59070	GT	AGG
(GTT)	 AG	59211-59215	TC	AAT
-recovered pasa_asmbl_48168.p1, terminal, 56828, 56974
-recovered pasa_asmbl_48168.p1, terminal, 59211, 59215
-recovered pasa_asmbl_48168.p1, internal, 54879, 54992
-recovered pasa_asmbl_48168.p1, internal, 55800, 55838
-recovered pasa_asmbl_48168.p1, internal, 56104, 56154
-recovered pasa_asmbl_48168.p1, internal, 56267, 56323
-recovered pasa_asmbl_48168.p1, internal, 56625, 56678
-recovered pasa_asmbl_48168.p1, internal, 56828, 56974
-recovered pasa_asmbl_48168.p1, internal, 57149, 57190
-recovered pasa_asmbl_48168.p1, internal, 57280, 57339
-recovered pasa_asmbl_48168.p1, internal, 57641, 57712
-recovered pasa_asmbl_48168.p1, internal, 58471, 58506
-recovered pasa_asmbl_48168.p1, internal, 58680, 58718
-recovered pasa_asmbl_48168.p1, internal, 59011, 59070
Valid prediction for GlimmerHMM_glimmerT_14231-T1
Valid prediction for HiQ_model.g9433.t1
Valid prediction for Augustus_model.g9419.t1
Valid prediction for snap_scaffold_6-snap.658-T1
Valid prediction for GlimmerHMM_glimmerT_14207-T1
Valid prediction for GlimmerHMM_glimmerT_14232-T1
Valid prediction for CodingQuarry_transcript_54947-T1
Valid prediction for GlimmerHMM_glimmerT_14213-T1
Valid prediction for snap_scaffold_6-snap.642-T1
Valid prediction for snap_scaffold_6-snap.670-T1
Valid prediction for snap_scaffold_6-snap.680-T1
Valid prediction for pasa_asmbl_48186.p1
Valid prediction for snap_scaffold_6-snap.640-T1
Valid prediction for CodingQuarry_transcript_54949-T1
Couldn't classify 26922, 26960
Sorry, prediction pasa_asmbl_48177.p1 fails validation.
(GAA)	 CT	26922-26960	GT	AGG
(TGT)	 AG	27058-27298	GT	TGG
(TTT)	 AG	27443-28164	TG	GAT
-recovered pasa_asmbl_48177.p1, terminal, 27443, 28164
-recovered pasa_asmbl_48177.p1, internal, 27058, 27298
Couldn't classify 148522, 148597
Sorry, prediction pasa_asmbl_49351.p1 fails validation.
(ATG)	 AT	147310-147358	GT	AGG
(AGA)	 AG	147955-148201	GT	AGG
(TTA)	 AG	148522-148597	AC	TCA
-recovered pasa_asmbl_49351.p1, initial, 147310, 147358
-recovered pasa_asmbl_49351.p1, internal, 147955, 148201
Valid prediction for GlimmerHMM_glimmerT_14228-T1
Valid prediction for GlimmerHMM_glimmerT_14219-T1
Valid prediction for HiQ_model.g9438.t1
Valid prediction for GlimmerHMM_glimmerT_14236-T1
Valid prediction for snap_scaffold_6-snap.651-T1
Valid prediction for pasa_asmbl_48182.p1
Couldn't classify 47372, 47398
Couldn't classify 54428, 54460
Sorry, prediction pasa_asmbl_48173.p1 fails validation.
(CAT)	 AG	47372-47398	GT	AGG
(GTT)	 AG	47714-47755	GT	TGG
(GTG)	 AG	48084-48134	GT	GGG
(GCA)	 AG	48498-48554	GT	CGG
(GCT)	 AG	49044-49100	GT	TGG
(GAT)	 AG	51915-51962	GT	TGG
(GAT)	 AG	52133-52177	GT	AGG
(GAG)	 AG	52937-52972	GT	TGG
(GAT)	 AG	53065-53121	GT	CGG
(GCT)	 AG	54254-54313	GT	AGG
(GTG)	 AG	54428-54460	CA	AGC
-recovered pasa_asmbl_48173.p1, internal, 47372, 47398
-recovered pasa_asmbl_48173.p1, internal, 47714, 47755
-recovered pasa_asmbl_48173.p1, internal, 48084, 48134
-recovered pasa_asmbl_48173.p1, internal, 48498, 48554
-recovered pasa_asmbl_48173.p1, internal, 49044, 49100
-recovered pasa_asmbl_48173.p1, internal, 51915, 51962
-recovered pasa_asmbl_48173.p1, internal, 52133, 52177
-recovered pasa_asmbl_48173.p1, internal, 52937, 52972
-recovered pasa_asmbl_48173.p1, internal, 53065, 53121
-recovered pasa_asmbl_48173.p1, internal, 54254, 54313
Valid prediction for GlimmerHMM_glimmerT_14234-T1
Valid prediction for snap_scaffold_6-snap.677-T1
Valid prediction for CodingQuarry_transcript_54948-T1
Valid prediction for GlimmerHMM_glimmerT_14217-T1
Valid prediction for CodingQuarry_transcript_54944-T1
Valid prediction for snap_scaffold_6-snap.665-T1
Couldn't classify 34023, 35282
Sorry, prediction pasa_asmbl_48176.p1 fails validation.
(CAA)	 AC	34023-35282	GA	GAG
Valid prediction for snap_scaffold_6-snap.657-T1
Valid prediction for Augustus_model.g9413.t1
Valid prediction for CodingQuarry_transcript_54950-T1
Valid prediction for Augustus_model.g9414.t1
Valid prediction for snap_scaffold_6-snap.661-T1
Couldn't classify 172921, 173430
Sorry, prediction pasa_asmbl_48154.p1 fails validation.
(GCG)	 TG	172921-173430	TC	CAT
Valid prediction for Augustus_model.g9430.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9018, rend_intergenic: 2906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9467, rend_intergenic: 9308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16518, rend_intergenic: 9570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24090, rend_intergenic: 19806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31480, rend_intergenic: 24775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36263, rend_intergenic: 32032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44547, rend_intergenic: 44373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51694, rend_intergenic: 44748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68911, rend_intergenic: 61975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80619, rend_intergenic: 70085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85532, rend_intergenic: 85313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88688, rend_intergenic: 86285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127417, rend_intergenic: 123463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167650, rend_intergenic: 166595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179334
-exon list size: 459


building trellis

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95.4    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
97.0    
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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 9018, rend_intergenic: 2906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9467, rend_intergenic: 9308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16518, rend_intergenic: 9570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24090, rend_intergenic: 19806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31480, rend_intergenic: 24775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36263, rend_intergenic: 32032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44547, rend_intergenic: 44373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51694, rend_intergenic: 44748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68911, rend_intergenic: 61975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80619, rend_intergenic: 70085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85532, rend_intergenic: 85313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88688, rend_intergenic: 86285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127417, rend_intergenic: 123463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167650, rend_intergenic: 166595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support