-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_5785636-6051264

-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.g7850.t1
Valid prediction for GlimmerHMM_glimmerT_12005-T1
Valid prediction for GlimmerHMM_glimmerT_11986-T1
Valid prediction for Augustus_model.g7881.t1
Valid prediction for CodingQuarry_transcript_52084-T1
Valid prediction for snap_scaffold_5-snap.1152-T1
Valid prediction for snap_scaffold_5-snap.1170-T1
Valid prediction for Augustus_model.g7869.t1
Valid prediction for GlimmerHMM_glimmerT_12001-T1
Valid prediction for snap_scaffold_5-snap.1136-T1
Valid prediction for snap_scaffold_5-snap.1169-T1
Valid prediction for Augustus_model.g7864.t1
Valid prediction for pasa_asmbl_45389.p1
Valid prediction for GlimmerHMM_glimmerT_11993-T1
Valid prediction for GlimmerHMM_glimmerT_11999-T1
Couldn't classify 105698, 105778
Couldn't classify 106424, 106562
Sorry, prediction pasa_asmbl_45379.p1 fails validation.
(AAA)	 AG	105698-105778	GT	ATG
(ATC)	 AG	106099-106316	GT	AGG
(ATC)	 AG	106424-106562	GA	AGG
-recovered pasa_asmbl_45379.p1, internal, 105698, 105778
-recovered pasa_asmbl_45379.p1, internal, 106099, 106316
Valid prediction for CodingQuarry_transcript_52078-T1
Valid prediction for GlimmerHMM_glimmerT_11985-T1
Valid prediction for GlimmerHMM_glimmerT_12016-T1
Valid prediction for snap_scaffold_5-snap.1175-T1
Valid prediction for pasa_asmbl_45386.p1
Valid prediction for snap_scaffold_5-snap.1133-T1
Valid prediction for snap_scaffold_5-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_12021-T1
Valid prediction for snap_scaffold_5-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_12000-T1
Valid prediction for snap_scaffold_5-snap.1154-T1
Valid prediction for HiQ_model.g7857.t1
Valid prediction for snap_scaffold_5-snap.1155-T1
Valid prediction for snap_scaffold_5-snap.1135-T1
Valid prediction for Augustus_model.g7874.t1
Valid prediction for HiQ_model.g7859.t1
Valid prediction for GlimmerHMM_glimmerT_12013-T1
Couldn't classify 205619, 205626
Couldn't classify 207521, 207616
Sorry, prediction pasa_asmbl_45387.p1 fails validation.
(CAG)	 TA	205619-205626	GT	GAG
(GTC)	 AG	205741-205768	GT	AGG
(GAA)	 AG	205884-205913	GT	AGG
(GAG)	 AG	206055-206150	GT	CAG
(ATC)	 AG	206681-206752	GT	AGG
(AAG)	 AG	207040-207180	GT	AGG
(GAG)	 AG	207291-207428	GT	AGG
(ATG)	 AG	207521-207616	GA	AGG
-recovered pasa_asmbl_45387.p1, internal, 205741, 205768
-recovered pasa_asmbl_45387.p1, internal, 205884, 205913
-recovered pasa_asmbl_45387.p1, internal, 206055, 206150
-recovered pasa_asmbl_45387.p1, internal, 206681, 206752
-recovered pasa_asmbl_45387.p1, internal, 207040, 207180
-recovered pasa_asmbl_45387.p1, internal, 207291, 207428
Valid prediction for Augustus_model.g7863.t1
Couldn't classify 186764, 186765
Sorry, prediction CodingQuarry_transcript_52077-T1 fails validation.
(ATG)	 TG	186764-186765	GT	ATG
(GCA)	 AG	186914-187034	GT	AGG
(GCC)	 AG	187386-187559	GT	AGG
(GAG)	 AG	187824-187934	GT	AGG
(GTA)	 AG	188108-188323	GG	GAG
-recovered CodingQuarry_transcript_52077-T1, terminal, 188108, 188323
-recovered CodingQuarry_transcript_52077-T1, internal, 186914, 187034
-recovered CodingQuarry_transcript_52077-T1, internal, 187386, 187559
-recovered CodingQuarry_transcript_52077-T1, internal, 187824, 187934
Valid prediction for snap_scaffold_5-snap.1163-T1
Valid prediction for Augustus_model.g7873.t1
Valid prediction for GlimmerHMM_glimmerT_12010-T1
Valid prediction for HiQ_model.g7870.t1
Couldn't classify 107556, 107849
Sorry, prediction pasa_asmbl_45380.p2 fails validation.
(AAG)	 GG	107556-107849	GT	GAG
(CCA)	 AG	108044-108085	AA	GAA
-recovered pasa_asmbl_45380.p2, terminal, 108044, 108085
Valid prediction for GlimmerHMM_glimmerT_12009-T1
Valid prediction for snap_scaffold_5-snap.1153-T1
Valid prediction for pasa_asmbl_45375.p1
Valid prediction for snap_scaffold_5-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_12008-T1
Valid prediction for Augustus_model.g7862.t1
Valid prediction for GlimmerHMM_glimmerT_12014-T1
Valid prediction for snap_scaffold_5-snap.1150-T1
Couldn't classify 183307, 183374
Couldn't classify 185054, 185158
Sorry, prediction pasa_asmbl_45382.p1 fails validation.
(TTT)	 GG	183307-183374	GT	GAG
(ATT)	 AG	183469-183580	GT	GGG
(GTG)	 AG	183739-183925	GT	TGG
(ACG)	 AG	184328-184469	GT	AAG
(AAG)	 AG	184629-184718	GT	GTG
(AAA)	 AG	184820-184949	GT	AGG
(GTG)	 AG	185054-185158	AG	AGA
-recovered pasa_asmbl_45382.p1, internal, 183469, 183580
-recovered pasa_asmbl_45382.p1, internal, 183739, 183925
-recovered pasa_asmbl_45382.p1, internal, 184328, 184469
-recovered pasa_asmbl_45382.p1, internal, 184629, 184718
-recovered pasa_asmbl_45382.p1, internal, 184820, 184949
Valid prediction for pasa_asmbl_45393.p1
Valid prediction for Augustus_model.g7868.t1
Valid prediction for GlimmerHMM_glimmerT_11996-T1
Valid prediction for snap_scaffold_5-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_11995-T1
Valid prediction for snap_scaffold_5-snap.1159-T1
Valid prediction for HiQ_model.g7875.t1
Valid prediction for pasa_asmbl_45378.p1
Valid prediction for CodingQuarry_transcript_52075-T1
Valid prediction for Augustus_model.g7866.t1
Valid prediction for snap_scaffold_5-snap.1168-T1
Valid prediction for pasa_asmbl_45390.p1
Valid prediction for HiQ_model.g7877.t1
Valid prediction for snap_scaffold_5-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_11997-T1
Valid prediction for Augustus_model.g7860.t1
Couldn't classify 208088, 208204
Sorry, prediction pasa_asmbl_45388.p1 fails validation.
(TGT)	 AG	208088-208204	GT	AGG
(TCG)	 AG	208529-208726	AA	GAA
-recovered pasa_asmbl_45388.p1, terminal, 208529, 208726
-recovered pasa_asmbl_45388.p1, internal, 208088, 208204
Valid prediction for CodingQuarry_transcript_52076-T1
Valid prediction for snap_scaffold_5-snap.1149-T1
Valid prediction for snap_scaffold_5-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_11984-T1
Valid prediction for CodingQuarry_transcript_52080-T1
Valid prediction for pasa_asmbl_45383.p2

-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_12012-T1
Valid prediction for CodingQuarry_transcript_52072-T1
Valid prediction for CodingQuarry_transcript_52071-T1
Valid prediction for snap_scaffold_5-snap.1165-T1
Valid prediction for snap_scaffold_5-snap.1174-T1
Valid prediction for snap_scaffold_5-snap.1158-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_12006-T1
Valid prediction for snap_scaffold_5-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_12020-T1
Valid prediction for snap_scaffold_5-snap.1166-T1
Valid prediction for snap_scaffold_5-snap.1173-T1
Valid prediction for CodingQuarry_transcript_52083-T1
Valid prediction for GlimmerHMM_glimmerT_12007-T1
Valid prediction for snap_scaffold_5-snap.1148-T1
Valid prediction for CodingQuarry_transcript_52068-T1
Valid prediction for Augustus_model.g7854.t1
Valid prediction for GlimmerHMM_glimmerT_12011-T1
Valid prediction for HiQ_model.g7856.t1
Valid prediction for pasa_asmbl_44068.p1
Valid prediction for pasa_asmbl_44077.p1
Valid prediction for Augustus_model.g7871.t1
Couldn't classify 170582, 170601
Sorry, prediction pasa_asmbl_44066.p1 fails validation.
(CAG)	 GC	170582-170601	GT	AGG
(CGG)	 AG	170714-170816	GT	AGG
(GTC)	 AG	171119-171280	GT	CTG
(AAT)	 AG	171547-171620	GT	TGG
(GGG)	 AG	173204-173253	GT	CAG
(ATG)	 AG	173375-173502	GT	AGG
(GAC)	 AG	173782-173926	GT	GGG
(ACA)	 AG	174096-174251	GT	GGG
(ATC)	 AG	175154-175260	GT	AGG
(TGC)	 AG	175708-175810	GT	CGG
(GAA)	 AG	176060-176231	GT	AAG
(GTT)	 AG	176450-176640	GT	CTG
(GCG)	 AG	176900-177089	GT	TGG
(TGA)	 AG	177316-177432	GT	GGG
(TTA)	 AG	177734-177842	GT	TGG
(ACT)	 AG	178097-178209	GT	CGG
(GTT)	 AG	178416-178545	GT	AGG
(GAC)	 AG	178663-178677	CT	AGC
add_exon() Sorry, pasa_asmbl_44066.p1 173375-173502-initial-1 is invalid.
-recovered pasa_asmbl_44066.p1, initial, 173375, 173502
-recovered pasa_asmbl_44066.p1, terminal, 178663, 178677
-recovered pasa_asmbl_44066.p1, internal, 170714, 170816
-recovered pasa_asmbl_44066.p1, internal, 171119, 171280
-recovered pasa_asmbl_44066.p1, internal, 171547, 171620
-recovered pasa_asmbl_44066.p1, internal, 173204, 173253
-recovered pasa_asmbl_44066.p1, internal, 173375, 173502
-recovered pasa_asmbl_44066.p1, internal, 173782, 173926
-recovered pasa_asmbl_44066.p1, internal, 174096, 174251
-recovered pasa_asmbl_44066.p1, internal, 175154, 175260
-recovered pasa_asmbl_44066.p1, internal, 175708, 175810
-recovered pasa_asmbl_44066.p1, internal, 176060, 176231
-recovered pasa_asmbl_44066.p1, internal, 176450, 176640
-recovered pasa_asmbl_44066.p1, internal, 176900, 177089
-recovered pasa_asmbl_44066.p1, internal, 177316, 177432
-recovered pasa_asmbl_44066.p1, internal, 177734, 177842
-recovered pasa_asmbl_44066.p1, internal, 178097, 178209
-recovered pasa_asmbl_44066.p1, internal, 178416, 178545
Valid prediction for snap_scaffold_5-snap.1144-T1
Valid prediction for snap_scaffold_5-snap.1134-T1
Valid prediction for snap_scaffold_5-snap.1137-T1
Valid prediction for HiQ_model.g7876.t1
Valid prediction for GlimmerHMM_glimmerT_11994-T1
Valid prediction for GlimmerHMM_glimmerT_11990-T1
Couldn't classify 202555, 203711
Couldn't classify 204699, 204777
Sorry, prediction CodingQuarry_transcript_52070-T1 fails validation.
(ATG)	 AG	202555-203711	CT	ACC
(CTC)	 AC	204699-204777	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_11992-T1
Valid prediction for GlimmerHMM_glimmerT_12015-T1
Valid prediction for snap_scaffold_5-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_11988-T1
Valid prediction for Augustus_model.g7861.t1
Valid prediction for CodingQuarry_transcript_52069-T1
Valid prediction for pasa_asmbl_44083.p1
Valid prediction for pasa_asmbl_44070.p1
Valid prediction for GlimmerHMM_glimmerT_11998-T1
Couldn't classify 186363, 186461
Couldn't classify 187339, 187427
Couldn't classify 187624, 187798
Sorry, prediction CodingQuarry_transcript_52073-T1 fails validation.
(ATG)	 TC	183782-183862	GT	AGG
(GTC)	 AG	184727-184873	GT	AGG
(ATC)	 AG	184968-185099	GT	AGG
(GGC)	 AG	185509-185611	GT	GGG
(GAA)	 AG	185696-185847	GT	TGG
(ATG)	 AG	186363-186461	TA	AGT
(CAA)	 AG	187339-187427	CT	ACC
(CAC)	 AC	187624-187798	CC	AGC
-recovered CodingQuarry_transcript_52073-T1, initial, 183782, 183862
-recovered CodingQuarry_transcript_52073-T1, internal, 184727, 184873
-recovered CodingQuarry_transcript_52073-T1, internal, 184968, 185099
-recovered CodingQuarry_transcript_52073-T1, internal, 185509, 185611
-recovered CodingQuarry_transcript_52073-T1, internal, 185696, 185847
Valid prediction for CodingQuarry_transcript_52079-T1
Valid prediction for GlimmerHMM_glimmerT_11989-T1
Valid prediction for snap_scaffold_5-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_12019-T1
Valid prediction for snap_scaffold_5-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_11991-T1
Valid prediction for HiQ_model.g7878.t1
Valid prediction for CodingQuarry_transcript_52074-T1
Valid prediction for Augustus_model.g7852.t1
Valid prediction for snap_scaffold_5-snap.1142-T1
Valid prediction for Augustus_model.g7867.t1
Valid prediction for GlimmerHMM_glimmerT_11987-T1
Valid prediction for Augustus_model.g7855.t1
Valid prediction for CodingQuarry_transcript_52081-T1
Valid prediction for snap_scaffold_5-snap.1164-T1
Valid prediction for pasa_asmbl_44073.p1
Valid prediction for pasa_asmbl_44062.p1
Valid prediction for HiQ_model.g7872.t1
Valid prediction for GlimmerHMM_glimmerT_12003-T1
Valid prediction for GlimmerHMM_glimmerT_12002-T1
Valid prediction for snap_scaffold_5-snap.1151-T1
Valid prediction for pasa_asmbl_44064.p1
Valid prediction for GlimmerHMM_glimmerT_12004-T1
Valid prediction for snap_scaffold_5-snap.1141-T1
Valid prediction for Augustus_model.g7853.t1
Valid prediction for snap_scaffold_5-snap.1171-T1
Valid prediction for snap_scaffold_5-snap.1160-T1
Couldn't classify 98360, 98450
Couldn't classify 99831, 99919
Sorry, prediction pasa_asmbl_44963.p1 fails validation.
(GTT)	 GC	98360-98450	GT	AGG
(TTC)	 AG	98627-98775	GT	AGG
(CTC)	 AG	99017-99112	GT	AGG
(GAT)	 AG	99661-99727	GT	AGG
(GGC)	 AG	99831-99919	AC	CCA
-recovered pasa_asmbl_44963.p1, internal, 98627, 98775
-recovered pasa_asmbl_44963.p1, internal, 99017, 99112
-recovered pasa_asmbl_44963.p1, internal, 99661, 99727
Valid prediction for Augustus_model.g7880.t1
Valid prediction for snap_scaffold_5-snap.1145-T1
Valid prediction for snap_scaffold_5-snap.1138-T1
Valid prediction for HiQ_model.g7879.t1
Valid prediction for GlimmerHMM_glimmerT_12018-T1
Valid prediction for snap_scaffold_5-snap.1162-T1
Couldn't classify 208066, 208848
Sorry, prediction pasa_asmbl_44989.p1 fails validation.
(ATG)	 AG	208066-208848	TT	CGT
Valid prediction for CodingQuarry_transcript_52082-T1
Valid prediction for GlimmerHMM_glimmerT_12017-T1
Valid prediction for Augustus_model.g7865.t1
Valid prediction for HiQ_model.g7858.t1
Valid prediction for snap_scaffold_5-snap.1147-T1
Valid prediction for Augustus_model.g7851.t1
Valid prediction for snap_scaffold_5-snap.1157-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15593, rend_intergenic: 12856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188323, rend_intergenic: 181219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265629
-exon list size: 476


building trellis

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78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 15593, rend_intergenic: 12856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188323, rend_intergenic: 181219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support