-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_11867489-12275645

-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_8-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_20562-T1
Valid prediction for GlimmerHMM_glimmerT_20561-T1
Valid prediction for snap_scaffold_8-snap.2204-T1
Couldn't classify 165838, 165899
Sorry, prediction pasa_asmbl_53304.p1 fails validation.
(GGT)	 CA	165838-165899	GT	TGG
(GGA)	 AG	166370-166430	GT	TGG
(GGC)	 AG	167604-167681	GT	AGG
(CAT)	 AG	167950-168039	GT	AGG
(CTG)	 AG	168224-168289	GT	AGG
(GCC)	 AG	168404-168454	GT	TGG
(AAT)	 AG	168567-168659	TT	AGT
-recovered pasa_asmbl_53304.p1, terminal, 168567, 168659
-recovered pasa_asmbl_53304.p1, internal, 166370, 166430
-recovered pasa_asmbl_53304.p1, internal, 167604, 167681
-recovered pasa_asmbl_53304.p1, internal, 167950, 168039
-recovered pasa_asmbl_53304.p1, internal, 168224, 168289
-recovered pasa_asmbl_53304.p1, internal, 168404, 168454
Valid prediction for GlimmerHMM_glimmerT_20543-T1
Valid prediction for snap_scaffold_8-snap.2195-T1
Valid prediction for snap_scaffold_8-snap.2203-T1
Valid prediction for GlimmerHMM_glimmerT_20555-T1
Valid prediction for Augustus_model.g13706.t1
Valid prediction for CodingQuarry_transcript_59837-T1
Valid prediction for CodingQuarry_transcript_59838-T1
Couldn't classify 91806, 91919
Sorry, prediction pasa_asmbl_53300.p1 fails validation.
(ATG)	 CG	90598-90678	GT	AGG
(AAT)	 AG	91321-91363	GT	AGG
(CAC)	 AG	91456-91529	GT	AGG
(GTA)	 AG	91806-91919	TT	ACT
-recovered pasa_asmbl_53300.p1, initial, 90598, 90678
-recovered pasa_asmbl_53300.p1, internal, 91321, 91363
-recovered pasa_asmbl_53300.p1, internal, 91456, 91529
Valid prediction for CodingQuarry_transcript_59839-T1
Valid prediction for snap_scaffold_8-snap.2229-T1
Valid prediction for Augustus_model.g13701.t1
Valid prediction for snap_scaffold_8-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_20565-T1
Valid prediction for GlimmerHMM_glimmerT_20540-T1
Valid prediction for HiQ_model.g13704.t1
Couldn't classify 92165, 92180
Sorry, prediction pasa_asmbl_53301.p1 fails validation.
(AGA)	 CC	92165-92180	GT	TCG
(CAT)	 AG	92314-92424	GT	AGG
(AGT)	 AG	92628-92755	GT	AGG
(GTT)	 AG	92905-93017	GT	AGG
(GTA)	 AG	93125-93231	GT	GGG
(CTG)	 AG	93437-93568	GT	GGG
(GTC)	 AG	93837-93913	AG	GAA
-recovered pasa_asmbl_53301.p1, terminal, 93837, 93913
-recovered pasa_asmbl_53301.p1, internal, 92314, 92424
-recovered pasa_asmbl_53301.p1, internal, 92628, 92755
-recovered pasa_asmbl_53301.p1, internal, 92905, 93017
-recovered pasa_asmbl_53301.p1, internal, 93125, 93231
-recovered pasa_asmbl_53301.p1, internal, 93437, 93568
Valid prediction for pasa_asmbl_53302.p1
Valid prediction for GlimmerHMM_glimmerT_20559-T1
Couldn't classify 208915, 209220
Sorry, prediction pasa_asmbl_53306.p1 fails validation.
(TCA)	 TT	208915-209220	TG	AAT
Valid prediction for snap_scaffold_8-snap.2213-T1
Valid prediction for snap_scaffold_8-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_20566-T1
Valid prediction for snap_scaffold_8-snap.2200-T1
Valid prediction for CodingQuarry_transcript_59840-T1
Valid prediction for snap_scaffold_8-snap.2210-T1
Valid prediction for Augustus_model.g13705.t1
Valid prediction for snap_scaffold_8-snap.2225-T1
Valid prediction for snap_scaffold_8-snap.2220-T1
Valid prediction for snap_scaffold_8-snap.2208-T1
Valid prediction for snap_scaffold_8-snap.2202-T1
Valid prediction for HiQ_model.g13710.t1
Valid prediction for HiQ_model.g13709.t1
Couldn't classify 80719, 81159
Sorry, prediction pasa_asmbl_53298.p1 fails validation.
(TCT)	 CG	80719-81159	GT	AGG
(AAC)	 AG	82281-82348	GT	AGG
(GTA)	 AG	82632-82776	GT	CGG
(TAC)	 AG	83085-83177	GT	AGG
(ACA)	 AG	83473-83528	GT	ATG
(GCG)	 AG	83675-83741	GT	AGG
(TGC)	 AG	84237-84343	GT	TGG
(CTT)	 AG	84538-84580	GT	AGG
(TGG)	 AG	84711-84782	GT	AGG
(GAG)	 AG	85209-85339	GT	TGG
(GTA)	 AG	87083-87140	GT	AGG
(CGT)	 AG	87627-87887	GT	AGG
(AAC)	 AG	88013-88125	GT	AGG
(ATA)	 AG	88278-88362	GG	AAG
-recovered pasa_asmbl_53298.p1, terminal, 88278, 88362
-recovered pasa_asmbl_53298.p1, internal, 82281, 82348
-recovered pasa_asmbl_53298.p1, internal, 82632, 82776
-recovered pasa_asmbl_53298.p1, internal, 83085, 83177
-recovered pasa_asmbl_53298.p1, internal, 83473, 83528
-recovered pasa_asmbl_53298.p1, internal, 83675, 83741
-recovered pasa_asmbl_53298.p1, internal, 84237, 84343
-recovered pasa_asmbl_53298.p1, internal, 84538, 84580
-recovered pasa_asmbl_53298.p1, internal, 84711, 84782
-recovered pasa_asmbl_53298.p1, internal, 85209, 85339
-recovered pasa_asmbl_53298.p1, internal, 87083, 87140
-recovered pasa_asmbl_53298.p1, internal, 87627, 87887
-recovered pasa_asmbl_53298.p1, internal, 88013, 88125
Valid prediction for GlimmerHMM_glimmerT_20547-T1
Valid prediction for snap_scaffold_8-snap.2226-T1
Valid prediction for Augustus_model.g13712.t1
Valid prediction for snap_scaffold_8-snap.2219-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_20549-T1
Valid prediction for Augustus_model.g13718.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.g13717.t1
Valid prediction for GlimmerHMM_glimmerT_20558-T1
Valid prediction for snap_scaffold_8-snap.2205-T1
Couldn't classify 294823, 295374
Sorry, prediction pasa_asmbl_52178.p1 fails validation.
(AGG)	 GC	294823-295374	AT	AGA
Valid prediction for GlimmerHMM_glimmerT_20550-T1
Valid prediction for GlimmerHMM_glimmerT_20560-T1
Valid prediction for GlimmerHMM_glimmerT_20556-T1
Valid prediction for CodingQuarry_transcript_59836-T1
Valid prediction for snap_scaffold_8-snap.2192-T1
Valid prediction for snap_scaffold_8-snap.2187-T1
Valid prediction for snap_scaffold_8-snap.2222-T1
Couldn't classify 62541, 63051
Sorry, prediction pasa_asmbl_52607.p1 fails validation.
(CTA)	 AC	62541-63051	GT	AGG
(AGC)	 AG	63802-63923	GT	AGG
(TCT)	 AG	64052-64184	GT	AGG
(GTT)	 AG	64748-64855	GT	AGG
(GCT)	 AG	65353-65463	GT	AGG
(ATC)	 AG	65722-65834	GT	AGG
(TTA)	 AG	66139-66303	CC	AGC
add_exon() Sorry, pasa_asmbl_52607.p1 64748-64855-terminal-1 is invalid.
-recovered pasa_asmbl_52607.p1, terminal, 64748, 64855
-recovered pasa_asmbl_52607.p1, terminal, 66139, 66303
-recovered pasa_asmbl_52607.p1, internal, 63802, 63923
-recovered pasa_asmbl_52607.p1, internal, 64052, 64184
-recovered pasa_asmbl_52607.p1, internal, 64748, 64855
-recovered pasa_asmbl_52607.p1, internal, 65353, 65463
-recovered pasa_asmbl_52607.p1, internal, 65722, 65834
Valid prediction for GlimmerHMM_glimmerT_20538-T1
Valid prediction for Augustus_model.g13703.t1
Valid prediction for snap_scaffold_8-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_20548-T1
Valid prediction for GlimmerHMM_glimmerT_20553-T1
Valid prediction for pasa_asmbl_52186.p1
Valid prediction for HiQ_model.g13716.t1
Valid prediction for snap_scaffold_8-snap.2211-T1
Couldn't classify 295705, 295857
Sorry, prediction pasa_asmbl_52175.p1 fails validation.
(GTC)	 AG	295705-295857	GT	AGG
(GAT)	 AG	296222-296435	GT	AGG
(GCT)	 AG	297023-297132	GT	AGG
(CTG)	 AG	297397-297572	GT	AGG
(GTT)	 AG	297841-298008	GT	GGG
(GGT)	 AG	298731-298914	GT	CCG
(GAC)	 AG	299150-299404	GT	AGG
(GTC)	 AG	300083-300200	GT	CAG
(ACG)	 AG	300938-301100	GT	AGG
(GAG)	 AG	301236-301300	GT	TGG
(ACG)	 AG	301414-301550	CC	GAC
-recovered pasa_asmbl_52175.p1, terminal, 301414, 301550
-recovered pasa_asmbl_52175.p1, internal, 295705, 295857
-recovered pasa_asmbl_52175.p1, internal, 296222, 296435
-recovered pasa_asmbl_52175.p1, internal, 297023, 297132
-recovered pasa_asmbl_52175.p1, internal, 297397, 297572
-recovered pasa_asmbl_52175.p1, internal, 297841, 298008
-recovered pasa_asmbl_52175.p1, internal, 298731, 298914
-recovered pasa_asmbl_52175.p1, internal, 299150, 299404
-recovered pasa_asmbl_52175.p1, internal, 300083, 300200
-recovered pasa_asmbl_52175.p1, internal, 300938, 301100
-recovered pasa_asmbl_52175.p1, internal, 301236, 301300
Valid prediction for snap_scaffold_8-snap.2216-T1
Valid prediction for HiQ_model.g13715.t1
Valid prediction for GlimmerHMM_glimmerT_20554-T1
Valid prediction for pasa_asmbl_52173.p1
Valid prediction for Augustus_model.g13698.t1
Valid prediction for snap_scaffold_8-snap.2186-T1
Valid prediction for snap_scaffold_8-snap.2223-T1
Valid prediction for snap_scaffold_8-snap.2194-T1
Valid prediction for CodingQuarry_transcript_59841-T1
Valid prediction for GlimmerHMM_glimmerT_20545-T1
Valid prediction for snap_scaffold_8-snap.2188-T1
Valid prediction for snap_scaffold_8-snap.2199-T1
Couldn't classify 282715, 282931
Couldn't classify 294301, 294452
Sorry, prediction pasa_asmbl_52179.p1 fails validation.
(GGC)	 CA	282715-282931	GT	AGG
(GCT)	 AG	284595-284740	GT	AAG
(CTC)	 AG	285063-285101	GT	AGG
(GTG)	 AG	288064-288197	GT	AGG
(CTA)	 AG	288293-288425	GT	AGG
(GAG)	 AG	288534-288740	GT	AGG
(GTA)	 AG	288982-289110	GT	AGG
(GCG)	 AG	290490-290634	GT	AGG
(ATG)	 AG	291938-292066	GT	AGG
(GTG)	 AG	293912-294031	GT	CTG
(TGT)	 AG	294301-294452	TC	GCT
add_exon() Sorry, pasa_asmbl_52179.p1 291938-292066-initial-1 is invalid.
-recovered pasa_asmbl_52179.p1, initial, 291938, 292066
-recovered pasa_asmbl_52179.p1, internal, 284595, 284740
-recovered pasa_asmbl_52179.p1, internal, 285063, 285101
-recovered pasa_asmbl_52179.p1, internal, 288064, 288197
-recovered pasa_asmbl_52179.p1, internal, 288293, 288425
-recovered pasa_asmbl_52179.p1, internal, 288534, 288740
-recovered pasa_asmbl_52179.p1, internal, 288982, 289110
-recovered pasa_asmbl_52179.p1, internal, 290490, 290634
-recovered pasa_asmbl_52179.p1, internal, 291938, 292066
-recovered pasa_asmbl_52179.p1, internal, 293912, 294031
Valid prediction for CodingQuarry_transcript_59844-T1
Valid prediction for snap_scaffold_8-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_20535-T1
Valid prediction for snap_scaffold_8-snap.2191-T1
Valid prediction for snap_scaffold_8-snap.2198-T1
Valid prediction for Augustus_model.g13702.t1
Valid prediction for pasa_asmbl_52180.p1
Valid prediction for Augustus_model.g13711.t1
Valid prediction for GlimmerHMM_glimmerT_20541-T1
Valid prediction for GlimmerHMM_glimmerT_20552-T1
Valid prediction for snap_scaffold_8-snap.2217-T1
Valid prediction for Augustus_model.g13714.t1
Valid prediction for snap_scaffold_8-snap.2209-T1
Valid prediction for snap_scaffold_8-snap.2212-T1
Valid prediction for CodingQuarry_transcript_59843-T1
Valid prediction for GlimmerHMM_glimmerT_20537-T1
Valid prediction for snap_scaffold_8-snap.2207-T1
Valid prediction for GlimmerHMM_glimmerT_20536-T1
Valid prediction for GlimmerHMM_glimmerT_20544-T1
Valid prediction for GlimmerHMM_glimmerT_20539-T1
Valid prediction for HiQ_model.g13700.t1
Valid prediction for snap_scaffold_8-snap.2206-T1
Valid prediction for snap_scaffold_8-snap.2218-T1
Valid prediction for pasa_asmbl_52183.p2
Valid prediction for GlimmerHMM_glimmerT_20546-T1
Valid prediction for GlimmerHMM_glimmerT_20564-T1
Valid prediction for Augustus_model.g13697.t1
Valid prediction for snap_scaffold_8-snap.2193-T1
Valid prediction for Augustus_model.g13708.t1
Valid prediction for snap_scaffold_8-snap.2214-T1
Valid prediction for snap_scaffold_8-snap.2221-T1
Valid prediction for snap_scaffold_8-snap.2189-T1
Valid prediction for snap_scaffold_8-snap.2196-T1
Valid prediction for Augustus_model.g13713.t1
Valid prediction for snap_scaffold_8-snap.2185-T1
Valid prediction for snap_scaffold_8-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_20563-T1
Valid prediction for GlimmerHMM_glimmerT_20542-T1
Valid prediction for Augustus_model.g13699.t1
Valid prediction for GlimmerHMM_glimmerT_20551-T1
Valid prediction for GlimmerHMM_glimmerT_20557-T1
Valid prediction for Augustus_model.g13707.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 222788, rend_intergenic: 222645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235674, rend_intergenic: 224937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 408157
-exon list size: 489


building trellis

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90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 222788, rend_intergenic: 222645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235674, rend_intergenic: 224937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 388671 - 408157
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 388671 - 400854
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 388671 - 399430
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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