-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_11379896-11658420

-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 GeneMark_model.40063_t
Valid prediction for GlimmerHMM_glimmerT_23427-T1
Valid prediction for GlimmerHMM_glimmerT_23414-T1
Valid prediction for Augustus_model.g15695.t1
Valid prediction for GlimmerHMM_glimmerT_23419-T1
Valid prediction for Augustus_model.g15698.t1
Valid prediction for snap_scaffold_9-snap.2265-T1
Valid prediction for CodingQuarry_transcript_62161-T1
Couldn't classify 151122, 151252
Sorry, prediction pasa_asmbl_54338.p1 fails validation.
(ACA)	 CC	151122-151252	GT	AGG
(GGG)	 AG	152134-152273	GT	GTG
(TCC)	 AG	152379-152424	GT	TGG
(TGA)	 AG	152936-153030	GT	TGG
(TCC)	 AG	153153-153223	GT	AGG
(GAA)	 AG	153688-153828	GT	GAG
(CCT)	 AG	153973-154004	GT	TGG
(GGC)	 AG	154722-154816	GT	GGG
(CCT)	 AG	155005-155088	GT	AGG
(TTC)	 AG	155265-155329	AA	AAA
-recovered pasa_asmbl_54338.p1, terminal, 155265, 155329
-recovered pasa_asmbl_54338.p1, internal, 152134, 152273
-recovered pasa_asmbl_54338.p1, internal, 152379, 152424
-recovered pasa_asmbl_54338.p1, internal, 152936, 153030
-recovered pasa_asmbl_54338.p1, internal, 153153, 153223
-recovered pasa_asmbl_54338.p1, internal, 153688, 153828
-recovered pasa_asmbl_54338.p1, internal, 153973, 154004
-recovered pasa_asmbl_54338.p1, internal, 154722, 154816
-recovered pasa_asmbl_54338.p1, internal, 155005, 155088
Valid prediction for GlimmerHMM_glimmerT_23396-T1
Valid prediction for GlimmerHMM_glimmerT_23425-T1
Valid prediction for Augustus_model.g15677.t1
Valid prediction for Augustus_model.g15687.t1
Valid prediction for HiQ_model.g15694.t1
Valid prediction for GlimmerHMM_glimmerT_23422-T1
Valid prediction for snap_scaffold_9-snap.2271-T1
Valid prediction for snap_scaffold_9-snap.2287-T1
Valid prediction for GlimmerHMM_glimmerT_23397-T1
Valid prediction for snap_scaffold_9-snap.2253-T1
Valid prediction for GeneMark_model.40054_t
Valid prediction for snap_scaffold_9-snap.2266-T1
Valid prediction for snap_scaffold_9-snap.2268-T1
Couldn't classify 163054, 163189
Couldn't classify 163411, 163492
Sorry, prediction CodingQuarry_transcript_62162-T1 fails validation.
(ATG)	 CA	160052-160059	GT	ATG
(GCT)	 AG	160588-160651	GT	TGG
(CAA)	 AG	160941-161075	GT	AGG
(GGT)	 AG	161214-161387	GT	AAG
(GCT)	 AG	161513-161616	GT	GTG
(ACT)	 AG	161750-161860	GT	ACG
(AGA)	 AG	161950-162109	GT	AGG
(GGC)	 AG	162269-162351	GT	AGG
(ACT)	 AG	162516-162612	GT	TGG
(GGC)	 AG	162828-162975	GT	CGG
(GCT)	 AG	163054-163189	AC	GTA
(CTG)	 TC	163411-163492	GA	AGG
-recovered CodingQuarry_transcript_62162-T1, initial, 160052, 160059
-recovered CodingQuarry_transcript_62162-T1, internal, 160588, 160651
-recovered CodingQuarry_transcript_62162-T1, internal, 160941, 161075
-recovered CodingQuarry_transcript_62162-T1, internal, 161214, 161387
-recovered CodingQuarry_transcript_62162-T1, internal, 161513, 161616
-recovered CodingQuarry_transcript_62162-T1, internal, 161750, 161860
-recovered CodingQuarry_transcript_62162-T1, internal, 161950, 162109
-recovered CodingQuarry_transcript_62162-T1, internal, 162269, 162351
-recovered CodingQuarry_transcript_62162-T1, internal, 162516, 162612
-recovered CodingQuarry_transcript_62162-T1, internal, 162828, 162975
Valid prediction for GlimmerHMM_glimmerT_23398-T1
Valid prediction for snap_scaffold_9-snap.2284-T1
Valid prediction for snap_scaffold_9-snap.2251-T1
Valid prediction for HiQ_model.g15684.t1
Valid prediction for snap_scaffold_9-snap.2276-T1
Valid prediction for Augustus_model.g15697.t1
Valid prediction for GeneMark_model.40031_t
Valid prediction for Augustus_model.g15690.t1
Valid prediction for GlimmerHMM_glimmerT_23417-T1
Valid prediction for pasa_asmbl_54340.p1
Valid prediction for snap_scaffold_9-snap.2280-T1
Valid prediction for GeneMark_model.40043_t
Valid prediction for GeneMark_model.40044_t
Valid prediction for HiQ_model.g15682.t1
Valid prediction for GlimmerHMM_glimmerT_23402-T1
Valid prediction for GlimmerHMM_glimmerT_23394-T1
Valid prediction for snap_scaffold_9-snap.2278-T1
Valid prediction for snap_scaffold_9-snap.2277-T1
Valid prediction for snap_scaffold_9-snap.2290-T1
Valid prediction for snap_scaffold_9-snap.2285-T1
Valid prediction for GlimmerHMM_glimmerT_23401-T1
Valid prediction for Augustus_model.g15691.t1
Valid prediction for snap_scaffold_9-snap.2279-T1
Valid prediction for GeneMark_model.40064_t
Valid prediction for GeneMark_model.40067_t
Valid prediction for pasa_asmbl_54345.p1
Valid prediction for GlimmerHMM_glimmerT_23423-T1
Valid prediction for snap_scaffold_9-snap.2293-T1
Valid prediction for GeneMark_model.40033_t
Valid prediction for Augustus_model.g15692.t1
Couldn't classify 180404, 180478
Sorry, prediction pasa_asmbl_54342.p1 fails validation.
(CTG)	 TG	180404-180478	GT	AGG
(GTT)	 AG	180682-180828	GT	AGG
(CTG)	 AG	181439-181621	GT	AGG
(TTG)	 AG	182954-183118	GT	AGG
(GAG)	 AG	183781-183858	GT	AGG
(AAT)	 AG	184420-184529	GT	AAG
(GAA)	 AG	184989-185109	GT	AGG
(GAT)	 AG	185587-185820	TC	AAT
-recovered pasa_asmbl_54342.p1, terminal, 185587, 185820
-recovered pasa_asmbl_54342.p1, internal, 180682, 180828
-recovered pasa_asmbl_54342.p1, internal, 181439, 181621
-recovered pasa_asmbl_54342.p1, internal, 182954, 183118
-recovered pasa_asmbl_54342.p1, internal, 183781, 183858
-recovered pasa_asmbl_54342.p1, internal, 184420, 184529
-recovered pasa_asmbl_54342.p1, internal, 184989, 185109
Valid prediction for GeneMark_model.40036_t
Valid prediction for GeneMark_model.40048_t
Valid prediction for GeneMark_model.40032_t
Valid prediction for CodingQuarry_transcript_62159-T1
Valid prediction for Augustus_model.g15696.t1
Valid prediction for GlimmerHMM_glimmerT_23412-T1
Valid prediction for snap_scaffold_9-snap.2283-T1
Valid prediction for snap_scaffold_9-snap.2289-T1
Valid prediction for GlimmerHMM_glimmerT_23411-T1
Valid prediction for GeneMark_model.40065_t
Valid prediction for GlimmerHMM_glimmerT_23424-T1
Valid prediction for snap_scaffold_9-snap.2281-T1
Valid prediction for snap_scaffold_9-snap.2272-T1
Valid prediction for CodingQuarry_transcript_62165-T1
Valid prediction for GeneMark_model.40058_t
Valid prediction for GeneMark_model.40045_t
Valid prediction for snap_scaffold_9-snap.2256-T1
Valid prediction for snap_scaffold_9-snap.2291-T1
Valid prediction for GlimmerHMM_glimmerT_23395-T1
Valid prediction for Augustus_model.g15676.t1
Valid prediction for GlimmerHMM_glimmerT_23410-T1
Valid prediction for GeneMark_model.40030_t

-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 GlimmerHMM_glimmerT_23403-T1
Valid prediction for snap_scaffold_9-snap.2270-T1
Valid prediction for GeneMark_model.40046_t
Valid prediction for GlimmerHMM_glimmerT_23400-T1
Valid prediction for GlimmerHMM_glimmerT_23418-T1
Valid prediction for snap_scaffold_9-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_23416-T1
Valid prediction for GeneMark_model.40035_t
Valid prediction for GeneMark_model.40061_t
Couldn't classify 227611, 227720
Sorry, prediction pasa_asmbl_55248.p1 fails validation.
(GTC)	 AG	227611-227720	GT	TGG
(CGG)	 AG	228331-228528	GT	CAG
(GGT)	 AG	228861-228966	GT	AGG
(ATC)	 AG	229125-229312	GT	ACG
(GAG)	 AG	229819-230005	GT	AGG
(GTG)	 AG	230275-230361	GT	AGG
(GTT)	 AG	231736-231867	GT	TGG
(GAC)	 AG	232044-232103	GT	TGG
(GCA)	 AG	232526-232591	GT	AGG
(AAC)	 AG	233210-233378	GT	TGG
(GAA)	 AG	233677-233732	GT	AGG
(ATC)	 AG	234475-234632	GT	CGG
(CCC)	 AG	234816-234990	CA	AGC
-recovered pasa_asmbl_55248.p1, terminal, 234816, 234990
-recovered pasa_asmbl_55248.p1, internal, 227611, 227720
-recovered pasa_asmbl_55248.p1, internal, 228331, 228528
-recovered pasa_asmbl_55248.p1, internal, 228861, 228966
-recovered pasa_asmbl_55248.p1, internal, 229125, 229312
-recovered pasa_asmbl_55248.p1, internal, 229819, 230005
-recovered pasa_asmbl_55248.p1, internal, 230275, 230361
-recovered pasa_asmbl_55248.p1, internal, 231736, 231867
-recovered pasa_asmbl_55248.p1, internal, 232044, 232103
-recovered pasa_asmbl_55248.p1, internal, 232526, 232591
-recovered pasa_asmbl_55248.p1, internal, 233210, 233378
-recovered pasa_asmbl_55248.p1, internal, 233677, 233732
-recovered pasa_asmbl_55248.p1, internal, 234475, 234632
Valid prediction for GeneMark_model.40029_t
Valid prediction for CodingQuarry_transcript_62156-T1
Valid prediction for HiQ_model.g15685.t1
Valid prediction for GlimmerHMM_glimmerT_23393-T1
Valid prediction for snap_scaffold_9-snap.2260-T1
Valid prediction for GeneMark_model.40042_t
Valid prediction for snap_scaffold_9-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_23421-T1
Valid prediction for GlimmerHMM_glimmerT_23405-T1
Valid prediction for GlimmerHMM_glimmerT_23409-T1
Valid prediction for GeneMark_model.40041_t
Valid prediction for GlimmerHMM_glimmerT_23399-T1
Couldn't classify 120265, 120266
Sorry, prediction CodingQuarry_transcript_62160-T1 fails validation.
(ATG)	 AA	120265-120266	GT	ATG
(GAC)	 AG	120410-120544	GT	AAG
(GGA)	 AG	120691-120836	GT	TGG
(GTG)	 AG	121177-121325	GT	CTG
(AGT)	 AG	121475-121585	CC	AAC
-recovered CodingQuarry_transcript_62160-T1, terminal, 121475, 121585
-recovered CodingQuarry_transcript_62160-T1, internal, 120410, 120544
-recovered CodingQuarry_transcript_62160-T1, internal, 120691, 120836
-recovered CodingQuarry_transcript_62160-T1, internal, 121177, 121325
Valid prediction for snap_scaffold_9-snap.2274-T1
Valid prediction for snap_scaffold_9-snap.2264-T1
Valid prediction for CodingQuarry_transcript_62155-T1
Valid prediction for snap_scaffold_9-snap.2288-T1
Valid prediction for snap_scaffold_9-snap.2257-T1
Valid prediction for snap_scaffold_9-snap.2258-T1
Couldn't classify 59708, 59919
Sorry, prediction pasa_asmbl_55262.p1 fails validation.
(CTC)	 AA	59708-59919	GT	GCG
(AGA)	 AG	60277-60406	GT	AAG
(ATT)	 AG	60539-60739	GT	AGG
(GCT)	 AG	60934-61098	GT	TGG
(GTG)	 AG	61313-61441	CC	AGC
-recovered pasa_asmbl_55262.p1, terminal, 61313, 61441
-recovered pasa_asmbl_55262.p1, internal, 60277, 60406
-recovered pasa_asmbl_55262.p1, internal, 60539, 60739
-recovered pasa_asmbl_55262.p1, internal, 60934, 61098
Valid prediction for HiQ_model.g15678.t1
Valid prediction for Augustus_model.g15675.t1
Valid prediction for CodingQuarry_transcript_62157-T1
Valid prediction for GlimmerHMM_glimmerT_23407-T1
Valid prediction for snap_scaffold_9-snap.2267-T1
Valid prediction for GeneMark_model.40037_t
Valid prediction for snap_scaffold_9-snap.2286-T1
Valid prediction for snap_scaffold_9-snap.2275-T1
Valid prediction for snap_scaffold_9-snap.2273-T1
Valid prediction for GeneMark_model.40034_t
Valid prediction for Augustus_model.g15689.t1
Valid prediction for HiQ_model.g15683.t1
Valid prediction for HiQ_model.g15686.t1
Couldn't classify 180646, 180730
Couldn't classify 181149, 181199
Couldn't classify 181347, 181366
Sorry, prediction CodingQuarry_transcript_62158-T1 fails validation.
(ATG)	 CG	178329-178380	GT	AGG
(GAG)	 AG	179899-179940	GT	TGG
(GTT)	 AG	180646-180730	TA	GGT
(GGT)	 AG	180859-180908	GT	TGG
(GTG)	 AG	181149-181199	GA	TGG
(AGG)	 AC	181347-181366	AA	GAA
-recovered CodingQuarry_transcript_62158-T1, initial, 178329, 178380
-recovered CodingQuarry_transcript_62158-T1, internal, 179899, 179940
-recovered CodingQuarry_transcript_62158-T1, internal, 180859, 180908
Valid prediction for Augustus_model.g15680.t1
Valid prediction for snap_scaffold_9-snap.2255-T1
Valid prediction for snap_scaffold_9-snap.2261-T1
Valid prediction for snap_scaffold_9-snap.2282-T1
Valid prediction for pasa_asmbl_55256.p1
Valid prediction for Augustus_model.g15681.t1
Valid prediction for Augustus_model.g15688.t1
Valid prediction for HiQ_model.g15679.t1
Valid prediction for GeneMark_model.40038_t
Valid prediction for pasa_asmbl_55257.p1
Valid prediction for GlimmerHMM_glimmerT_23415-T1
Valid prediction for GeneMark_model.40039_t
Valid prediction for GeneMark_model.40047_t
Valid prediction for snap_scaffold_9-snap.2252-T1
Valid prediction for GeneMark_model.40059_t
Valid prediction for snap_scaffold_9-snap.2250-T1
Couldn't classify 271867, 271963
Sorry, prediction pasa_asmbl_55247.p1 fails validation.
(GAC)	 AG	271867-271963	GT	AGG
(GAG)	 AG	272056-272142	GT	AGG
(AAC)	 AG	272233-272356	GT	TGG
(CTG)	 AG	272659-272793	GT	GGG
(TCT)	 AG	273408-273525	GT	AGG
(ATC)	 AG	273696-273797	GT	AGG
(GAC)	 AG	274384-274480	GT	AGG
(TGG)	 AG	274654-274816	GT	AAG
(TAA)	 AG	275011-275110	GT	AGG
(TTG)	 AG	276463-276531	CC	AAC
-recovered pasa_asmbl_55247.p1, terminal, 276463, 276531
-recovered pasa_asmbl_55247.p1, internal, 271867, 271963
-recovered pasa_asmbl_55247.p1, internal, 272056, 272142
-recovered pasa_asmbl_55247.p1, internal, 272233, 272356
-recovered pasa_asmbl_55247.p1, internal, 272659, 272793
-recovered pasa_asmbl_55247.p1, internal, 273408, 273525
-recovered pasa_asmbl_55247.p1, internal, 273696, 273797
-recovered pasa_asmbl_55247.p1, internal, 274384, 274480
-recovered pasa_asmbl_55247.p1, internal, 274654, 274816
-recovered pasa_asmbl_55247.p1, internal, 275011, 275110
Valid prediction for CodingQuarry_transcript_62163-T1
Valid prediction for GlimmerHMM_glimmerT_23426-T1
Valid prediction for GeneMark_model.40057_t
Valid prediction for CodingQuarry_transcript_62164-T1
Valid prediction for GeneMark_model.40066_t
Valid prediction for HiQ_model.g15693.t1
Valid prediction for GlimmerHMM_glimmerT_23404-T1
Valid prediction for GlimmerHMM_glimmerT_23413-T1
Valid prediction for GeneMark_model.40060_t
Valid prediction for snap_scaffold_9-snap.2263-T1
Valid prediction for snap_scaffold_9-snap.2292-T1
Valid prediction for GeneMark_model.40062_t
Valid prediction for GlimmerHMM_glimmerT_23420-T1
Valid prediction for GlimmerHMM_glimmerT_23408-T1
Valid prediction for snap_scaffold_9-snap.2254-T1
Valid prediction for pasa_asmbl_55258.p1
Valid prediction for GlimmerHMM_glimmerT_23406-T1
Valid prediction for GeneMark_model.40040_t
Valid prediction for snap_scaffold_9-snap.2269-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46829, rend_intergenic: 43536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251784, rend_intergenic: 248817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273606, rend_intergenic: 270780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278525
-exon list size: 559


building trellis

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56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 46829, rend_intergenic: 43536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251784, rend_intergenic: 248817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273606, rend_intergenic: 270780  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