-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_11287538-11571404

-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_22890-T1
Valid prediction for snap_scaffold_9-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_22908-T1
Valid prediction for Augustus_model.g15239.t1
Valid prediction for snap_scaffold_9-snap.2218-T1
Valid prediction for snap_scaffold_9-snap.2249-T1
Valid prediction for snap_scaffold_9-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_22882-T1
Valid prediction for CodingQuarry_transcript_62321-T1
Valid prediction for HiQ_model.g15243.t1
Valid prediction for snap_scaffold_9-snap.2248-T1
Valid prediction for GlimmerHMM_glimmerT_22895-T1
Valid prediction for GlimmerHMM_glimmerT_22906-T1
Valid prediction for pasa_asmbl_54349.p1
Valid prediction for GlimmerHMM_glimmerT_22907-T1
Valid prediction for GlimmerHMM_glimmerT_22881-T1
Valid prediction for GlimmerHMM_glimmerT_22889-T1
Valid prediction for Augustus_model.g15248.t1
Valid prediction for CodingQuarry_transcript_62312-T1
Valid prediction for CodingQuarry_transcript_62313-T1
Couldn't classify 13364, 13742
Couldn't classify 14369, 14454
Sorry, prediction pasa_asmbl_54342.p1 fails validation.
(CTC)	 CC	13364-13742	GT	TGG
(ACC)	 AG	14369-14454	GA	CAG
Valid prediction for HiQ_model.g15257.t1
Valid prediction for snap_scaffold_9-snap.2251-T1
Valid prediction for GlimmerHMM_glimmerT_22897-T1
Valid prediction for Augustus_model.g15249.t1
Valid prediction for snap_scaffold_9-snap.2224-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22912-T1
Valid prediction for Augustus_model.g15242.t1
Couldn't classify 61550, 61648
Couldn't classify 65845, 65958
Sorry, prediction pasa_asmbl_54346.p1 fails validation.
(AAG)	 AG	61550-61648	GT	AGG
(GGG)	 AG	62141-62283	GT	CGG
(GTG)	 AG	64519-64588	GT	GCG
(GTG)	 AG	65845-65958	GA	TGG
-recovered pasa_asmbl_54346.p1, internal, 61550, 61648
-recovered pasa_asmbl_54346.p1, internal, 62141, 62283
-recovered pasa_asmbl_54346.p1, internal, 64519, 64588
Valid prediction for GlimmerHMM_glimmerT_22914-T1
Valid prediction for GlimmerHMM_glimmerT_22896-T1
Couldn't classify 14836, 14982
Sorry, prediction pasa_asmbl_54343.p1 fails validation.
(GAC)	 AG	14836-14982	GT	ATG
(AGA)	 AG	15107-15169	GT	AGG
(GGT)	 AG	15289-15533	GT	TGG
(TGA)	 AG	15773-15857	GT	AGG
(ATC)	 AG	15957-16110	GT	AGG
(GTT)	 AG	16223-16362	GT	AGG
(GCT)	 AG	16536-16616	GT	ATG
(ATG)	 AG	16715-16840	GT	ATG
(AGT)	 AG	17043-17164	GT	AGG
(TCA)	 AG	17281-17374	GT	AGG
(GTG)	 AG	17481-17615	GT	AGG
(TTC)	 AG	17797-17870	GT	AGG
(CCA)	 AG	18115-18244	TG	AAT
-recovered pasa_asmbl_54343.p1, initial, 16715, 16840
-recovered pasa_asmbl_54343.p1, terminal, 18115, 18244
-recovered pasa_asmbl_54343.p1, internal, 14836, 14982
-recovered pasa_asmbl_54343.p1, internal, 15107, 15169
-recovered pasa_asmbl_54343.p1, internal, 15289, 15533
-recovered pasa_asmbl_54343.p1, internal, 15773, 15857
-recovered pasa_asmbl_54343.p1, internal, 15957, 16110
-recovered pasa_asmbl_54343.p1, internal, 16223, 16362
-recovered pasa_asmbl_54343.p1, internal, 16536, 16616
-recovered pasa_asmbl_54343.p1, internal, 16715, 16840
-recovered pasa_asmbl_54343.p1, internal, 17043, 17164
-recovered pasa_asmbl_54343.p1, internal, 17281, 17374
-recovered pasa_asmbl_54343.p1, internal, 17481, 17615
-recovered pasa_asmbl_54343.p1, internal, 17797, 17870
Valid prediction for GlimmerHMM_glimmerT_22883-T1
Valid prediction for snap_scaffold_9-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_22885-T1
Valid prediction for snap_scaffold_9-snap.2239-T1
Valid prediction for GlimmerHMM_glimmerT_22888-T1
Couldn't classify 272762, 272836
Sorry, prediction pasa_asmbl_54360.p1 fails validation.
(CTG)	 TG	272762-272836	GT	AGG
(GTT)	 AG	273040-273186	GT	AGG
(CTG)	 AG	273797-273979	GT	AGG
(TTG)	 AG	275312-275476	GT	AGG
(GAG)	 AG	276139-276216	GT	AGG
(AAT)	 AG	276778-276887	GT	AAG
(GAA)	 AG	277347-277467	GT	AGG
(GAT)	 AG	277945-278178	TC	AAT
-recovered pasa_asmbl_54360.p1, terminal, 277945, 278178
-recovered pasa_asmbl_54360.p1, internal, 273040, 273186
-recovered pasa_asmbl_54360.p1, internal, 273797, 273979
-recovered pasa_asmbl_54360.p1, internal, 275312, 275476
-recovered pasa_asmbl_54360.p1, internal, 276139, 276216
-recovered pasa_asmbl_54360.p1, internal, 276778, 276887
-recovered pasa_asmbl_54360.p1, internal, 277347, 277467
Valid prediction for GlimmerHMM_glimmerT_22901-T1
Valid prediction for pasa_asmbl_54355.p1
Valid prediction for snap_scaffold_9-snap.2219-T1
Valid prediction for snap_scaffold_9-snap.2231-T1
Valid prediction for Augustus_model.g15260.t1
Valid prediction for snap_scaffold_9-snap.2255-T1
Valid prediction for pasa_asmbl_54352.p1
Valid prediction for GlimmerHMM_glimmerT_22910-T1
Valid prediction for snap_scaffold_9-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_22902-T1
Couldn't classify 9274, 9369
Couldn't classify 12902, 12970
Sorry, prediction pasa_asmbl_54341.p1 fails validation.
(GGG)	 GT	9274-9369	GT	AGG
(GTG)	 AG	9463-9634	GT	AGG
(AGC)	 AG	10010-10153	GT	AGG
(ATA)	 AG	10534-10661	GT	AGG
(CCC)	 AG	11041-11195	GT	CAG
(GTC)	 AG	11519-11644	GT	AGG
(GGT)	 AG	11782-11929	GT	AGG
(ACA)	 AG	12031-12123	GT	AGG
(GTA)	 AG	12305-12739	GT	AGG
(GTC)	 AG	12902-12970	GG	AGG
-recovered pasa_asmbl_54341.p1, internal, 9463, 9634
-recovered pasa_asmbl_54341.p1, internal, 10010, 10153
-recovered pasa_asmbl_54341.p1, internal, 10534, 10661
-recovered pasa_asmbl_54341.p1, internal, 11041, 11195
-recovered pasa_asmbl_54341.p1, internal, 11519, 11644
-recovered pasa_asmbl_54341.p1, internal, 11782, 11929
-recovered pasa_asmbl_54341.p1, internal, 12031, 12123
-recovered pasa_asmbl_54341.p1, internal, 12305, 12739
Valid prediction for Augustus_model.g15245.t1
Couldn't classify 76449, 77044
Couldn't classify 77861, 78047
Sorry, prediction pasa_asmbl_54351.p1 fails validation.
(GAG)	 CA	76449-77044	GT	GGG
(GGC)	 AG	77413-77454	GT	AGG
(ACG)	 AG	77861-78047	AC	CCA
-recovered pasa_asmbl_54351.p1, internal, 77413, 77454
Valid prediction for CodingQuarry_transcript_62319-T1
Valid prediction for CodingQuarry_transcript_62311-T1
Valid prediction for pasa_asmbl_54353.p1
Valid prediction for HiQ_model.g15255.t1
Valid prediction for snap_scaffold_9-snap.2217-T1
Couldn't classify 60176, 60389
Couldn't classify 61273, 61394
Sorry, prediction pasa_asmbl_54785.p1 fails validation.
(CCT)	 AG	60176-60389	GT	AGG
(GTA)	 AG	61273-61394	CT	AGC
add_exon() Sorry, pasa_asmbl_54785.p1 60176-60389-terminal-3 is invalid.
-recovered pasa_asmbl_54785.p1, terminal, 60176, 60389
-recovered pasa_asmbl_54785.p1, internal, 60176, 60389
Valid prediction for GlimmerHMM_glimmerT_22894-T1
Valid prediction for CodingQuarry_transcript_62322-T1
Valid prediction for snap_scaffold_9-snap.2229-T1
Valid prediction for pasa_asmbl_54344.p1
Valid prediction for snap_scaffold_9-snap.2235-T1
Valid prediction for Augustus_model.g15240.t1
Valid prediction for snap_scaffold_9-snap.2254-T1
Valid prediction for snap_scaffold_9-snap.2216-T1
Valid prediction for Augustus_model.g15244.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 CodingQuarry_transcript_62317-T1
Valid prediction for GlimmerHMM_glimmerT_22911-T1
Valid prediction for Augustus_model.g15246.t1
Valid prediction for snap_scaffold_9-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_22898-T1
Couldn't classify 32280, 32371
Sorry, prediction pasa_asmbl_55293.p1 fails validation.
(CTG)	 AG	32280-32371	GT	AAG
(CAT)	 AG	33107-33250	GT	ATG
(GAC)	 AG	33394-33528	GT	AAG
(GGA)	 AG	33675-33820	GT	TGG
(GTG)	 AG	34161-34309	GT	CTG
(AGT)	 AG	34459-34569	CC	AAC
-recovered pasa_asmbl_55293.p1, terminal, 34459, 34569
-recovered pasa_asmbl_55293.p1, internal, 32280, 32371
-recovered pasa_asmbl_55293.p1, internal, 33107, 33250
-recovered pasa_asmbl_55293.p1, internal, 33394, 33528
-recovered pasa_asmbl_55293.p1, internal, 33675, 33820
-recovered pasa_asmbl_55293.p1, internal, 34161, 34309
Valid prediction for snap_scaffold_9-snap.2244-T1
Valid prediction for GlimmerHMM_glimmerT_22913-T1
Couldn't classify 33249, 33250
Sorry, prediction CodingQuarry_transcript_62320-T1 fails validation.
(ATG)	 AA	33249-33250	GT	ATG
(GAC)	 AG	33394-33528	GT	AAG
(GGA)	 AG	33675-33820	GT	TGG
(GTG)	 AG	34161-34309	GT	CTG
(AGT)	 AG	34459-34569	CC	AAC
-recovered CodingQuarry_transcript_62320-T1, terminal, 34459, 34569
-recovered CodingQuarry_transcript_62320-T1, internal, 33394, 33528
-recovered CodingQuarry_transcript_62320-T1, internal, 33675, 33820
-recovered CodingQuarry_transcript_62320-T1, internal, 34161, 34309
Valid prediction for GlimmerHMM_glimmerT_22905-T1
Valid prediction for Augustus_model.g15253.t1
Valid prediction for GlimmerHMM_glimmerT_22892-T1
Valid prediction for HiQ_model.g15250.t1
Valid prediction for Augustus_model.g15252.t1
Valid prediction for snap_scaffold_9-snap.2250-T1
Valid prediction for Augustus_model.g15254.t1
Valid prediction for GlimmerHMM_glimmerT_22899-T1
Valid prediction for GlimmerHMM_glimmerT_22886-T1
Valid prediction for CodingQuarry_transcript_62316-T1
Valid prediction for GlimmerHMM_glimmerT_22904-T1
Valid prediction for Augustus_model.g15247.t1
Valid prediction for CodingQuarry_transcript_62324-T1
Valid prediction for snap_scaffold_9-snap.2232-T1
Valid prediction for snap_scaffold_9-snap.2238-T1
Valid prediction for HiQ_model.g15259.t1
Valid prediction for snap_scaffold_9-snap.2241-T1
Valid prediction for pasa_asmbl_55294.p1
Valid prediction for snap_scaffold_9-snap.2252-T1
Couldn't classify 93630, 93714
Couldn't classify 94133, 94183
Couldn't classify 94331, 94350
Sorry, prediction CodingQuarry_transcript_62318-T1 fails validation.
(ATG)	 CG	91313-91364	GT	AGG
(GAG)	 AG	92883-92924	GT	TGG
(GTT)	 AG	93630-93714	TA	GGT
(GGT)	 AG	93843-93892	GT	TGG
(GTG)	 AG	94133-94183	GA	TGG
(AGG)	 AC	94331-94350	AA	GAA
-recovered CodingQuarry_transcript_62318-T1, initial, 91313, 91364
-recovered CodingQuarry_transcript_62318-T1, internal, 92883, 92924
-recovered CodingQuarry_transcript_62318-T1, internal, 93843, 93892
Valid prediction for GlimmerHMM_glimmerT_22891-T1
Valid prediction for snap_scaffold_9-snap.2225-T1
Valid prediction for snap_scaffold_9-snap.2223-T1
Valid prediction for snap_scaffold_9-snap.2227-T1
Valid prediction for CodingQuarry_transcript_62323-T1
Valid prediction for snap_scaffold_9-snap.2230-T1
Couldn't classify 140595, 140704
Sorry, prediction pasa_asmbl_55283.p1 fails validation.
(GTC)	 AG	140595-140704	GT	TGG
(CGG)	 AG	141315-141512	GT	CAG
(GGT)	 AG	141845-141950	GT	AGG
(ATC)	 AG	142109-142296	GT	ACG
(GAG)	 AG	142803-142989	GT	AGG
(GTG)	 AG	143259-143345	GT	AGG
(GTT)	 AG	144720-144851	GT	TGG
(GAC)	 AG	145028-145087	GT	TGG
(GCA)	 AG	145510-145575	GT	AGG
(AAC)	 AG	146194-146362	GT	TGG
(GAA)	 AG	146661-146716	GT	AGG
(ATC)	 AG	147459-147616	GT	CGG
(CCC)	 AG	147800-147974	CA	AGC
-recovered pasa_asmbl_55283.p1, terminal, 147800, 147974
-recovered pasa_asmbl_55283.p1, internal, 140595, 140704
-recovered pasa_asmbl_55283.p1, internal, 141315, 141512
-recovered pasa_asmbl_55283.p1, internal, 141845, 141950
-recovered pasa_asmbl_55283.p1, internal, 142109, 142296
-recovered pasa_asmbl_55283.p1, internal, 142803, 142989
-recovered pasa_asmbl_55283.p1, internal, 143259, 143345
-recovered pasa_asmbl_55283.p1, internal, 144720, 144851
-recovered pasa_asmbl_55283.p1, internal, 145028, 145087
-recovered pasa_asmbl_55283.p1, internal, 145510, 145575
-recovered pasa_asmbl_55283.p1, internal, 146194, 146362
-recovered pasa_asmbl_55283.p1, internal, 146661, 146716
-recovered pasa_asmbl_55283.p1, internal, 147459, 147616
Valid prediction for Augustus_model.g15241.t1
Valid prediction for snap_scaffold_9-snap.2240-T1
Valid prediction for snap_scaffold_9-snap.2222-T1
Valid prediction for CodingQuarry_transcript_62315-T1
Valid prediction for snap_scaffold_9-snap.2237-T1
Valid prediction for pasa_asmbl_55282.p1
Valid prediction for HiQ_model.g15251.t1
Valid prediction for snap_scaffold_9-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_22909-T1
Valid prediction for GlimmerHMM_glimmerT_22893-T1
Valid prediction for snap_scaffold_9-snap.2247-T1
Valid prediction for snap_scaffold_9-snap.2243-T1
Valid prediction for snap_scaffold_9-snap.2236-T1
Valid prediction for snap_scaffold_9-snap.2245-T1
Valid prediction for GlimmerHMM_glimmerT_22903-T1
Valid prediction for GlimmerHMM_glimmerT_22900-T1
Valid prediction for snap_scaffold_9-snap.2246-T1
Valid prediction for GlimmerHMM_glimmerT_22887-T1
Valid prediction for HiQ_model.g15256.t1
Valid prediction for HiQ_model.g15258.t1
Valid prediction for CodingQuarry_transcript_62314-T1
Valid prediction for pasa_asmbl_55297.p1
Valid prediction for snap_scaffold_9-snap.2242-T1
Valid prediction for GlimmerHMM_glimmerT_22884-T1
Valid prediction for snap_scaffold_9-snap.2234-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48884, rend_intergenic: 34799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67005, rend_intergenic: 65154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69339, rend_intergenic: 67239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139187, rend_intergenic: 135894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161356, rend_intergenic: 154487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 283867
-exon list size: 489


building trellis

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71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 48884, rend_intergenic: 34799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67005, rend_intergenic: 65154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69339, rend_intergenic: 67239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139187, rend_intergenic: 135894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161356, rend_intergenic: 154487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support