-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_5031210-5328408

-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.29914_t
Valid prediction for pasa_asmbl_50682.p1
Valid prediction for CodingQuarry_transcript_57349-T1
Valid prediction for GeneMark_model.29921_t
Valid prediction for snap_scaffold_7-snap.1135-T1
Valid prediction for CodingQuarry_transcript_57353-T1
Valid prediction for snap_scaffold_7-snap.1134-T1
Valid prediction for GeneMark_model.29923_t
Valid prediction for GeneMark_model.29926_t
Valid prediction for GlimmerHMM_glimmerT_17801-T1
Valid prediction for Augustus_model.g11950.t1
Couldn't classify 54396, 54481
Sorry, prediction pasa_asmbl_50664.p1 fails validation.
(CTG)	 CT	54396-54481	GT	CTG
(AGA)	 AG	54598-54685	GT	AGG
(TAT)	 AG	54953-55129	GT	TGG
(CTA)	 AG	55307-55401	GT	ACG
(GCA)	 AG	55555-55642	GT	AGG
(TTG)	 AG	55746-55877	GT	AGG
(GCC)	 AG	56002-56079	GT	AGG
(AAC)	 AG	56178-56264	GT	AGG
(GTG)	 AG	56372-56440	GT	AGG
(GGT)	 AG	56529-57011	TT	AGT
-recovered pasa_asmbl_50664.p1, terminal, 56529, 57011
-recovered pasa_asmbl_50664.p1, internal, 54598, 54685
-recovered pasa_asmbl_50664.p1, internal, 54953, 55129
-recovered pasa_asmbl_50664.p1, internal, 55307, 55401
-recovered pasa_asmbl_50664.p1, internal, 55555, 55642
-recovered pasa_asmbl_50664.p1, internal, 55746, 55877
-recovered pasa_asmbl_50664.p1, internal, 56002, 56079
-recovered pasa_asmbl_50664.p1, internal, 56178, 56264
-recovered pasa_asmbl_50664.p1, internal, 56372, 56440
Valid prediction for snap_scaffold_7-snap.1136-T1
Valid prediction for GeneMark_model.29916_t
Valid prediction for GeneMark_model.29899_t
Valid prediction for GeneMark_model.29915_t
Valid prediction for Augustus_model.g11955.t1
Valid prediction for GeneMark_model.29902_t
Valid prediction for snap_scaffold_7-snap.1118-T1
Valid prediction for CodingQuarry_transcript_57352-T1
Valid prediction for GeneMark_model.29928_t
Valid prediction for GlimmerHMM_glimmerT_17793-T1
Valid prediction for snap_scaffold_7-snap.1107-T1
Valid prediction for GeneMark_model.29897_t
Valid prediction for snap_scaffold_7-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_17796-T1
Valid prediction for GeneMark_model.29906_t
Couldn't classify 230572, 230882
Sorry, prediction pasa_asmbl_50688.p1 fails validation.
(TCA)	 GC	230572-230882	GT	CGG
(GAC)	 AG	231469-231622	GG	GAG
-recovered pasa_asmbl_50688.p1, terminal, 231469, 231622
Couldn't classify 52441, 53085
Couldn't classify 53687, 53855
Sorry, prediction pasa_asmbl_51452.p1 fails validation.
(GCT)	 CA	52441-53085	GT	TTG
(CTA)	 AG	53284-53366	GT	AGG
(GTT)	 AG	53485-53598	GT	AAG
(AGA)	 AG	53687-53855	TA	GGT
-recovered pasa_asmbl_51452.p1, internal, 53284, 53366
-recovered pasa_asmbl_51452.p1, internal, 53485, 53598
Valid prediction for pasa_asmbl_50665.p1
Valid prediction for GeneMark_model.29913_t
Valid prediction for GlimmerHMM_glimmerT_17805-T1
Valid prediction for HiQ_model.g11936.t1
Valid prediction for GlimmerHMM_glimmerT_17807-T1
Valid prediction for snap_scaffold_7-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_17800-T1
Valid prediction for Augustus_model.g11951.t1
Valid prediction for Augustus_model.g11940.t1
Couldn't classify 261477, 261657
Sorry, prediction pasa_asmbl_50692.p1 fails validation.
(CAG)	 TG	261477-261657	GT	CAG
(GTG)	 AG	262177-262421	TC	AGT
-recovered pasa_asmbl_50692.p1, terminal, 262177, 262421
Valid prediction for GlimmerHMM_glimmerT_17791-T1
Valid prediction for HiQ_model.g11948.t1
Valid prediction for GlimmerHMM_glimmerT_17804-T1
Valid prediction for GeneMark_model.29904_t
Valid prediction for snap_scaffold_7-snap.1117-T1
Valid prediction for Augustus_model.g11934.t1
Couldn't classify 192765, 192832
Sorry, prediction pasa_asmbl_50678.p1 fails validation.
(ACG)	 CT	192765-192832	GT	AGG
(GTG)	 AG	193473-193579	GT	AGG
(TTC)	 AG	193682-193817	GT	AAG
(GGA)	 AG	194079-194145	GT	AGG
(GCA)	 AG	194242-194353	GT	TAG
(GTC)	 AG	194475-194538	GT	AGG
(ACC)	 AG	194683-194857	GT	AGG
(GTG)	 AG	194963-195034	AG	AAA
add_exon() Sorry, pasa_asmbl_50678.p1 193473-193579-terminal-2 is invalid.
-recovered pasa_asmbl_50678.p1, terminal, 193473, 193579
-recovered pasa_asmbl_50678.p1, terminal, 194963, 195034
-recovered pasa_asmbl_50678.p1, internal, 193473, 193579
-recovered pasa_asmbl_50678.p1, internal, 193682, 193817
-recovered pasa_asmbl_50678.p1, internal, 194079, 194145
-recovered pasa_asmbl_50678.p1, internal, 194242, 194353
-recovered pasa_asmbl_50678.p1, internal, 194475, 194538
-recovered pasa_asmbl_50678.p1, internal, 194683, 194857
Valid prediction for GeneMark_model.29924_t
Valid prediction for GlimmerHMM_glimmerT_17787-T1
Valid prediction for Augustus_model.g11954.t1
Valid prediction for snap_scaffold_7-snap.1120-T1
Valid prediction for snap_scaffold_7-snap.1114-T1
Valid prediction for snap_scaffold_7-snap.1132-T1
Valid prediction for GeneMark_model.29890_t
Valid prediction for GeneMark_model.29920_t
Valid prediction for snap_scaffold_7-snap.1112-T1
Valid prediction for GlimmerHMM_glimmerT_17811-T1
Valid prediction for GeneMark_model.29929_t
Valid prediction for snap_scaffold_7-snap.1126-T1
Valid prediction for Augustus_model.g11943.t1
Valid prediction for GeneMark_model.29917_t
Valid prediction for snap_scaffold_7-snap.1109-T1
Valid prediction for Augustus_model.g11942.t1
Couldn't classify 73581, 73591
Sorry, prediction pasa_asmbl_50669.p1 fails validation.
(GAA)	 CT	73581-73591	GT	GGG
(CGG)	 AG	73724-73871	GT	AGG
(CCC)	 AG	73959-75215	GT	TGG
(TCC)	 AG	75304-75358	GT	AGG
(GCA)	 AG	76525-76642	GT	AGG
(GTG)	 AG	77509-77644	CC	AAC
add_exon() Sorry, pasa_asmbl_50669.p1 75304-75358-terminal-3 is invalid.
-recovered pasa_asmbl_50669.p1, terminal, 75304, 75358
-recovered pasa_asmbl_50669.p1, terminal, 77509, 77644
-recovered pasa_asmbl_50669.p1, internal, 73724, 73871
-recovered pasa_asmbl_50669.p1, internal, 73959, 75215
-recovered pasa_asmbl_50669.p1, internal, 75304, 75358
-recovered pasa_asmbl_50669.p1, internal, 76525, 76642
Valid prediction for snap_scaffold_7-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_17809-T1
Valid prediction for GeneMark_model.29901_t
Valid prediction for GlimmerHMM_glimmerT_17814-T1
Valid prediction for GeneMark_model.29893_t
Valid prediction for pasa_asmbl_50686.p1
Valid prediction for snap_scaffold_7-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_17812-T1
Valid prediction for GlimmerHMM_glimmerT_17808-T1
Valid prediction for HiQ_model.g11939.t1
Valid prediction for GeneMark_model.29895_t
Valid prediction for GeneMark_model.29903_t
Valid prediction for pasa_asmbl_50675.p1
Valid prediction for GlimmerHMM_glimmerT_17785-T1
Valid prediction for snap_scaffold_7-snap.1130-T1
Valid prediction for snap_scaffold_7-snap.1139-T1
Valid prediction for snap_scaffold_7-snap.1115-T1
Valid prediction for Augustus_model.g11938.t1
Valid prediction for Augustus_model.g11952.t1
Couldn't classify 198234, 198278
Couldn't classify 201365, 201444
Sorry, prediction pasa_asmbl_50680.p1 fails validation.
(CTA)	 CC	198234-198278	GT	GGG
(CTC)	 AG	198408-198440	GT	AGG
(AAC)	 AG	198702-198728	GT	CGG
(CCC)	 AG	199167-199363	GT	AGG
(CGC)	 AG	199522-199648	GT	CGG
(CAC)	 AG	199891-200010	GT	ATG
(AAC)	 AG	201031-201220	GT	AGG
(ATG)	 AG	201365-201444	CC	CCC
-recovered pasa_asmbl_50680.p1, internal, 198408, 198440
-recovered pasa_asmbl_50680.p1, internal, 198702, 198728
-recovered pasa_asmbl_50680.p1, internal, 199167, 199363
-recovered pasa_asmbl_50680.p1, internal, 199522, 199648
-recovered pasa_asmbl_50680.p1, internal, 199891, 200010
-recovered pasa_asmbl_50680.p1, internal, 201031, 201220
Valid prediction for Augustus_model.g11947.t1
Valid prediction for GeneMark_model.29908_t
Valid prediction for GlimmerHMM_glimmerT_17802-T1
Valid prediction for GeneMark_model.29888_t
Valid prediction for GeneMark_model.29900_t
Valid prediction for GlimmerHMM_glimmerT_17792-T1
Valid prediction for CodingQuarry_transcript_57350-T1
Valid prediction for snap_scaffold_7-snap.1104-T1
Valid prediction for snap_scaffold_7-snap.1124-T1
Valid prediction for snap_scaffold_7-snap.1125-T1
Valid prediction for CodingQuarry_transcript_57348-T1
Valid prediction for GlimmerHMM_glimmerT_17783-T1
Valid prediction for snap_scaffold_7-snap.1129-T1
Valid prediction for snap_scaffold_7-snap.1119-T1
Valid prediction for GeneMark_model.29910_t
Valid prediction for Augustus_model.g11946.t1
Valid prediction for GlimmerHMM_glimmerT_17789-T1
Valid prediction for snap_scaffold_7-snap.1127-T1
Valid prediction for Augustus_model.g11958.t1
Valid prediction for GeneMark_model.29909_t
Valid prediction for GlimmerHMM_glimmerT_17795-T1
Valid prediction for HiQ_model.g11956.t1
Valid prediction for CodingQuarry_transcript_57346-T1
Valid prediction for GlimmerHMM_glimmerT_17806-T1
Valid prediction for CodingQuarry_transcript_57345-T1
Valid prediction for GeneMark_model.29919_t
Valid prediction for GlimmerHMM_glimmerT_17788-T1
Couldn't classify 73405, 73439
Sorry, prediction pasa_asmbl_50668.p1 fails validation.
(ATG)	 AT	70931-71114	GT	AGG
(GCA)	 AG	72703-72778	GT	AGG
(TAT)	 AG	73253-73320	GT	AGG
(TTG)	 AG	73405-73439	CT	ACC
-recovered pasa_asmbl_50668.p1, initial, 70931, 71114
-recovered pasa_asmbl_50668.p1, internal, 72703, 72778
-recovered pasa_asmbl_50668.p1, internal, 73253, 73320

-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.g11944.t1
Valid prediction for GeneMark_model.29907_t
Valid prediction for GlimmerHMM_glimmerT_17813-T1
Valid prediction for snap_scaffold_7-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_17815-T1
Valid prediction for pasa_asmbl_49684.p1
Valid prediction for Augustus_model.g11945.t1
Valid prediction for snap_scaffold_7-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_17799-T1
Valid prediction for Augustus_model.g11937.t1
Valid prediction for CodingQuarry_transcript_57344-T1
Valid prediction for GlimmerHMM_glimmerT_17810-T1
Valid prediction for Augustus_model.g11960.t1
Valid prediction for Augustus_model.g11933.t1
Couldn't classify 4949, 5129
Sorry, prediction pasa_asmbl_49695.p2 fails validation.
(ATG)	 GG	3568-3731	GT	AGG
(GGC)	 AG	4130-4300	GT	AGG
(GAC)	 AG	4949-5129	AC	GCA
-recovered pasa_asmbl_49695.p2, initial, 3568, 3731
-recovered pasa_asmbl_49695.p2, internal, 4130, 4300
Valid prediction for snap_scaffold_7-snap.1140-T1
Valid prediction for snap_scaffold_7-snap.1131-T1
Couldn't classify 146190, 146253
Sorry, prediction pasa_asmbl_49687.p1 fails validation.
(TGG)	 AG	146190-146253	GT	AGG
(GGA)	 AG	147120-147241	GT	AGG
(GAA)	 AG	147336-147402	GT	AGG
(GCT)	 AG	147509-147671	GT	TCG
(TTA)	 AG	147746-147814	GT	CGG
(CAC)	 AG	148130-148286	CC	AGC
-recovered pasa_asmbl_49687.p1, terminal, 148130, 148286
-recovered pasa_asmbl_49687.p1, internal, 146190, 146253
-recovered pasa_asmbl_49687.p1, internal, 147120, 147241
-recovered pasa_asmbl_49687.p1, internal, 147336, 147402
-recovered pasa_asmbl_49687.p1, internal, 147509, 147671
-recovered pasa_asmbl_49687.p1, internal, 147746, 147814
Valid prediction for snap_scaffold_7-snap.1123-T1
Valid prediction for snap_scaffold_7-snap.1121-T1
Valid prediction for GlimmerHMM_glimmerT_17784-T1
Valid prediction for GeneMark_model.29925_t
Valid prediction for GlimmerHMM_glimmerT_17786-T1
Valid prediction for Augustus_model.g11957.t1
Valid prediction for Augustus_model.g11953.t1
Valid prediction for snap_scaffold_7-snap.1110-T1
Valid prediction for CodingQuarry_transcript_57354-T1
Valid prediction for GeneMark_model.29891_t
Valid prediction for GeneMark_model.29889_t
Valid prediction for GlimmerHMM_glimmerT_17803-T1
Valid prediction for GeneMark_model.29930_t
Valid prediction for GeneMark_model.29898_t
Couldn't classify 5963, 6025
Sorry, prediction pasa_asmbl_49694.p2 fails validation.
(GCA)	 CA	5963-6025	GT	AGG
(CGT)	 AG	6321-6406	GT	AGG
(GGA)	 AG	6494-6621	GT	GGG
(CCA)	 AG	6784-6833	GT	AGG
(CGG)	 AG	6997-7046	GT	TGG
(CTT)	 AG	7165-7212	GT	AGG
(TTC)	 AG	7315-7411	GA	AGG
-recovered pasa_asmbl_49694.p2, terminal, 7315, 7411
-recovered pasa_asmbl_49694.p2, internal, 6321, 6406
-recovered pasa_asmbl_49694.p2, internal, 6494, 6621
-recovered pasa_asmbl_49694.p2, internal, 6784, 6833
-recovered pasa_asmbl_49694.p2, internal, 6997, 7046
-recovered pasa_asmbl_49694.p2, internal, 7165, 7212
Valid prediction for GeneMark_model.29912_t
Valid prediction for snap_scaffold_7-snap.1122-T1
Valid prediction for snap_scaffold_7-snap.1108-T1
Valid prediction for Augustus_model.g11959.t1
Valid prediction for Augustus_model.g11941.t1
Valid prediction for GeneMark_model.29927_t
Valid prediction for GeneMark_model.29905_t
Valid prediction for snap_scaffold_7-snap.1133-T1
Valid prediction for CodingQuarry_transcript_57355-T1
Valid prediction for snap_scaffold_7-snap.1106-T1
Valid prediction for GeneMark_model.29892_t
Valid prediction for snap_scaffold_7-snap.1141-T1
Valid prediction for GeneMark_model.29887_t
Valid prediction for snap_scaffold_7-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_17790-T1
Valid prediction for GlimmerHMM_glimmerT_17794-T1
Valid prediction for GeneMark_model.29911_t
Couldn't classify 159913, 160032
Sorry, prediction pasa_asmbl_49686.p1 fails validation.
(CCT)	 CC	159913-160032	GT	AGG
(GTA)	 AG	160164-160343	AA	GAA
-recovered pasa_asmbl_49686.p1, terminal, 160164, 160343
Valid prediction for Augustus_model.g11949.t1
Valid prediction for GlimmerHMM_glimmerT_17797-T1
Valid prediction for GeneMark_model.29894_t
Valid prediction for GlimmerHMM_glimmerT_17798-T1
Valid prediction for GeneMark_model.29918_t
Valid prediction for HiQ_model.g11935.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15733, rend_intergenic: 5179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20674, rend_intergenic: 16355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 297199
-exon list size: 571


building trellis

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64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 15733, rend_intergenic: 5179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20674, rend_intergenic: 16355  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