-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_12165094-12370984

-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 Augustus_model.g21724.t1
Valid prediction for Augustus_model.g21722.t1
Valid prediction for pasa_asmbl_11345.p1
Valid prediction for GlimmerHMM_glimmerT_32501-T1
Valid prediction for snap_scaffold_13-snap.2313-T1
Valid prediction for snap_scaffold_13-snap.2293-T1
Valid prediction for Augustus_model.g21728.t1
Valid prediction for GlimmerHMM_glimmerT_32505-T1
Valid prediction for snap_scaffold_13-snap.2310-T1
Valid prediction for GlimmerHMM_glimmerT_32502-T1
Valid prediction for GlimmerHMM_glimmerT_32500-T1
Valid prediction for pasa_asmbl_11348.p1
Valid prediction for CodingQuarry_transcript_13272-T1
Valid prediction for snap_scaffold_13-snap.2329-T1
Valid prediction for snap_scaffold_13-snap.2326-T1
Valid prediction for snap_scaffold_13-snap.2323-T1
Valid prediction for GlimmerHMM_glimmerT_32511-T1
Valid prediction for snap_scaffold_13-snap.2288-T1
Valid prediction for snap_scaffold_13-snap.2283-T1
Valid prediction for snap_scaffold_13-snap.2290-T1
Valid prediction for snap_scaffold_13-snap.2307-T1
Valid prediction for CodingQuarry_transcript_13273-T1
Valid prediction for GlimmerHMM_glimmerT_32496-T1
Valid prediction for Augustus_model.g21711.t1
Valid prediction for GlimmerHMM_glimmerT_32497-T1
Valid prediction for Augustus_model.g21729.t1
Valid prediction for snap_scaffold_13-snap.2322-T1
Valid prediction for snap_scaffold_13-snap.2292-T1
Valid prediction for pasa_asmbl_11341.p1
Valid prediction for GlimmerHMM_glimmerT_32499-T1
Valid prediction for snap_scaffold_13-snap.2300-T1
Valid prediction for Augustus_model.g21709.t1
Valid prediction for GlimmerHMM_glimmerT_32508-T1
Valid prediction for snap_scaffold_13-snap.2316-T1
Valid prediction for snap_scaffold_13-snap.2312-T1
Valid prediction for snap_scaffold_13-snap.2291-T1
Valid prediction for snap_scaffold_13-snap.2297-T1
Valid prediction for Augustus_model.g21710.t1
Valid prediction for GlimmerHMM_glimmerT_32503-T1
Valid prediction for Augustus_model.g21712.t1
Valid prediction for Augustus_model.g21718.t1
Valid prediction for GlimmerHMM_glimmerT_32504-T1
Valid prediction for GlimmerHMM_glimmerT_32507-T1
Valid prediction for Augustus_model.g21713.t1
Valid prediction for snap_scaffold_13-snap.2298-T1
Valid prediction for HiQ_model.g21715.t1
Valid prediction for HiQ_model.g21716.t1
Valid prediction for snap_scaffold_13-snap.2285-T1
Valid prediction for snap_scaffold_13-snap.2317-T1
Valid prediction for snap_scaffold_13-snap.2319-T1
Valid prediction for snap_scaffold_13-snap.2302-T1
Valid prediction for snap_scaffold_13-snap.2320-T1
Valid prediction for snap_scaffold_13-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_32498-T1
Valid prediction for snap_scaffold_13-snap.2294-T1
Valid prediction for GlimmerHMM_glimmerT_32516-T1
Valid prediction for snap_scaffold_13-snap.2304-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g21708.t1
Couldn't classify 22160, 22262
Couldn't classify 22491, 22599
Sorry, prediction CodingQuarry_transcript_13270-T1 fails validation.
(ATG)	 GT	17338-17481	GT	AGG
(GCT)	 AG	17813-18032	GT	AGG
(TCC)	 AG	18466-18638	GT	AGG
(GTG)	 AG	18821-19033	GT	AGG
(GTC)	 AG	20002-20297	GT	AGG
(TGG)	 AG	21379-21496	GT	CTG
(TCT)	 AG	21757-21882	GT	AGG
(ATG)	 AG	22160-22262	AC	GTA
(ACT)	 AC	22491-22599	GT	AAG
(AGA)	 AG	22937-23078	GT	ACG
(CAT)	 AG	23256-23378	GT	AGG
(GAG)	 AG	23757-23918	GT	CGG
(GGC)	 AG	25234-25355	GT	AGG
(GGA)	 AG	25595-25790	AA	AGA
-recovered CodingQuarry_transcript_13270-T1, initial, 17338, 17481
-recovered CodingQuarry_transcript_13270-T1, terminal, 25595, 25790
-recovered CodingQuarry_transcript_13270-T1, internal, 17813, 18032
-recovered CodingQuarry_transcript_13270-T1, internal, 18466, 18638
-recovered CodingQuarry_transcript_13270-T1, internal, 18821, 19033
-recovered CodingQuarry_transcript_13270-T1, internal, 20002, 20297
-recovered CodingQuarry_transcript_13270-T1, internal, 21379, 21496
-recovered CodingQuarry_transcript_13270-T1, internal, 21757, 21882
-recovered CodingQuarry_transcript_13270-T1, internal, 22937, 23078
-recovered CodingQuarry_transcript_13270-T1, internal, 23256, 23378
-recovered CodingQuarry_transcript_13270-T1, internal, 23757, 23918
-recovered CodingQuarry_transcript_13270-T1, internal, 25234, 25355
Couldn't classify 22160, 22262
Couldn't classify 22491, 22599
Sorry, prediction CodingQuarry_transcript_13269-T1 fails validation.
(ATG)	 GT	17338-17481	GT	AGG
(GCT)	 AG	17813-18032	GT	AGG
(TCC)	 AG	18466-18638	GT	AGG
(GTG)	 AG	18821-19033	GT	AGG
(GTC)	 AG	20002-20297	GT	AGG
(TGG)	 AG	21379-21496	GT	CTG
(TCT)	 AG	21757-21882	GT	AGG
(ATG)	 AG	22160-22262	AC	GTA
(ACT)	 AC	22491-22599	GT	AAG
(AGA)	 AG	22937-23078	GT	ACG
(CAT)	 AG	23256-23378	GT	AGG
(GAG)	 AG	23757-23918	GT	CGG
(GGC)	 AG	24424-24545	GT	AGG
(GGA)	 AG	25595-25790	AA	AGA
-recovered CodingQuarry_transcript_13269-T1, initial, 17338, 17481
-recovered CodingQuarry_transcript_13269-T1, terminal, 25595, 25790
-recovered CodingQuarry_transcript_13269-T1, internal, 17813, 18032
-recovered CodingQuarry_transcript_13269-T1, internal, 18466, 18638
-recovered CodingQuarry_transcript_13269-T1, internal, 18821, 19033
-recovered CodingQuarry_transcript_13269-T1, internal, 20002, 20297
-recovered CodingQuarry_transcript_13269-T1, internal, 21379, 21496
-recovered CodingQuarry_transcript_13269-T1, internal, 21757, 21882
-recovered CodingQuarry_transcript_13269-T1, internal, 22937, 23078
-recovered CodingQuarry_transcript_13269-T1, internal, 23256, 23378
-recovered CodingQuarry_transcript_13269-T1, internal, 23757, 23918
-recovered CodingQuarry_transcript_13269-T1, internal, 24424, 24545

-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_13-snap.2318-T1
Valid prediction for snap_scaffold_13-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_32512-T1
Valid prediction for snap_scaffold_13-snap.2282-T1
Valid prediction for snap_scaffold_13-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_32518-T1
Valid prediction for snap_scaffold_13-snap.2305-T1
Couldn't classify 45199, 45302
Couldn't classify 48761, 48823
Sorry, prediction pasa_asmbl_10343.p1 fails validation.
(GCA)	 GG	45199-45302	GT	AGG
(GCC)	 AG	45625-45793	GT	AGG
(AAC)	 AG	46906-47101	GT	AGG
(AGA)	 AG	47351-47520	GT	AGG
(GTG)	 AG	47764-47895	GT	TGG
(CAT)	 AG	48234-48341	GT	AGG
(ATT)	 AG	48761-48823	GT	ACG
add_exon() Sorry, pasa_asmbl_10343.p1 46906-47101-terminal-3 is invalid.
-recovered pasa_asmbl_10343.p1, terminal, 46906, 47101
-recovered pasa_asmbl_10343.p1, internal, 45625, 45793
-recovered pasa_asmbl_10343.p1, internal, 46906, 47101
-recovered pasa_asmbl_10343.p1, internal, 47351, 47520
-recovered pasa_asmbl_10343.p1, internal, 47764, 47895
-recovered pasa_asmbl_10343.p1, internal, 48234, 48341
-recovered pasa_asmbl_10343.p1, internal, 48761, 48823
Valid prediction for snap_scaffold_13-snap.2289-T1
Valid prediction for snap_scaffold_13-snap.2296-T1
Valid prediction for HiQ_model.g21714.t1
Valid prediction for snap_scaffold_13-snap.2306-T1
Valid prediction for snap_scaffold_13-snap.2315-T1
Valid prediction for pasa_asmbl_10124.p1
Valid prediction for snap_scaffold_13-snap.2314-T1
Valid prediction for GlimmerHMM_glimmerT_32495-T1
Valid prediction for GlimmerHMM_glimmerT_32514-T1
Valid prediction for GlimmerHMM_glimmerT_32510-T1
Couldn't classify 27516, 27584
Couldn't classify 27975, 28360
Sorry, prediction pasa_asmbl_10134.p1 fails validation.
(AAC)	 AC	27516-27584	GT	AGG
(TTT)	 AG	27787-27844	GT	CGG
(ATG)	 AG	27975-28360	CA	GTC
-recovered pasa_asmbl_10134.p1, internal, 27787, 27844
Valid prediction for snap_scaffold_13-snap.2321-T1
Valid prediction for snap_scaffold_13-snap.2311-T1
Valid prediction for snap_scaffold_13-snap.2295-T1
Valid prediction for snap_scaffold_13-snap.2309-T1
Valid prediction for snap_scaffold_13-snap.2303-T1
Valid prediction for Augustus_model.g21727.t1
Valid prediction for GlimmerHMM_glimmerT_32517-T1
Valid prediction for snap_scaffold_13-snap.2299-T1
Valid prediction for GlimmerHMM_glimmerT_32519-T1
Valid prediction for snap_scaffold_13-snap.2301-T1
Valid prediction for snap_scaffold_13-snap.2284-T1
Valid prediction for snap_scaffold_13-snap.2286-T1
Valid prediction for Augustus_model.g21721.t1
Valid prediction for GlimmerHMM_glimmerT_32513-T1
Valid prediction for GlimmerHMM_glimmerT_32515-T1
Valid prediction for Augustus_model.g21719.t1
Valid prediction for Augustus_model.g21726.t1
Valid prediction for Augustus_model.g21717.t1
Valid prediction for GlimmerHMM_glimmerT_32520-T1
Couldn't classify 44020, 44106
Couldn't classify 44609, 44708
Sorry, prediction pasa_asmbl_10412.p1 fails validation.
(TGC)	 CC	44020-44106	GT	AGG
(GTG)	 AG	44264-44382	GT	ATG
(GTT)	 AG	44609-44708	TT	GGT
-recovered pasa_asmbl_10412.p1, internal, 44264, 44382
Valid prediction for GlimmerHMM_glimmerT_32494-T1
Valid prediction for snap_scaffold_13-snap.2328-T1
Valid prediction for CodingQuarry_transcript_13271-T1
Valid prediction for Augustus_model.g21725.t1
Valid prediction for Augustus_model.g21723.t1
Valid prediction for snap_scaffold_13-snap.2325-T1
Valid prediction for snap_scaffold_13-snap.2287-T1
Valid prediction for GlimmerHMM_glimmerT_32506-T1
Valid prediction for Augustus_model.g21720.t1
Valid prediction for GlimmerHMM_glimmerT_32509-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5412, rend_intergenic: 3907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15466, rend_intergenic: 7373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22366, rend_intergenic: 18462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27357, rend_intergenic: 23506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35467, rend_intergenic: 34720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37066, rend_intergenic: 36583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66085, rend_intergenic: 57275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74245, rend_intergenic: 66490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83173, rend_intergenic: 79700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89237, rend_intergenic: 85750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99297, rend_intergenic: 94508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107309, rend_intergenic: 100907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115693, rend_intergenic: 110051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121257, rend_intergenic: 117476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122419, rend_intergenic: 121313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134343, rend_intergenic: 122442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138860, rend_intergenic: 134569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145670, rend_intergenic: 139235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151674, rend_intergenic: 147650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156698, rend_intergenic: 153883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170172, rend_intergenic: 158970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189386, rend_intergenic: 187923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205891
-exon list size: 525


building trellis

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93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 5412, rend_intergenic: 3907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15466, rend_intergenic: 7373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22366, rend_intergenic: 18462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27357, rend_intergenic: 23506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35467, rend_intergenic: 34720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37066, rend_intergenic: 36583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66085, rend_intergenic: 57275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74245, rend_intergenic: 66490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83173, rend_intergenic: 79700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89237, rend_intergenic: 85750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99297, rend_intergenic: 94508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107309, rend_intergenic: 100907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115693, rend_intergenic: 110051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121257, rend_intergenic: 117476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122419, rend_intergenic: 121313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134343, rend_intergenic: 122442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138860, rend_intergenic: 134569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145670, rend_intergenic: 139235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151674, rend_intergenic: 147650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156698, rend_intergenic: 153883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170172, rend_intergenic: 158970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189386, rend_intergenic: 187923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 190102 - 205891
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 190807 - 205891
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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
	-no exons in range 191265 - 205891