-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_5760773-5985712

-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_12263-T1
Valid prediction for GeneMark_model.20802_t
Couldn't classify 208170, 208237
Couldn't classify 209917, 210021
Sorry, prediction pasa_asmbl_44043.p1 fails validation.
(TTT)	 GG	208170-208237	GT	GAG
(ATT)	 AG	208332-208443	GT	GGG
(GTG)	 AG	208602-208788	GT	TGG
(ACG)	 AG	209191-209332	GT	AAG
(AAG)	 AG	209492-209581	GT	GTG
(AAA)	 AG	209683-209812	GT	AGG
(GTG)	 AG	209917-210021	AG	AGA
-recovered pasa_asmbl_44043.p1, internal, 208332, 208443
-recovered pasa_asmbl_44043.p1, internal, 208602, 208788
-recovered pasa_asmbl_44043.p1, internal, 209191, 209332
-recovered pasa_asmbl_44043.p1, internal, 209492, 209581
-recovered pasa_asmbl_44043.p1, internal, 209683, 209812
Valid prediction for CodingQuarry_transcript_51949-T1
Valid prediction for HiQ_model.g8087.t1
Valid prediction for snap_scaffold_5-snap.1157-T1
Valid prediction for HiQ_model.g8100.t1
Valid prediction for snap_scaffold_5-snap.1160-T1
Valid prediction for Augustus_model.g8096.t1
Valid prediction for Augustus_model.g8092.t1
Valid prediction for GeneMark_model.20801_t
Valid prediction for GlimmerHMM_glimmerT_12247-T1
Valid prediction for snap_scaffold_5-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_12271-T1
Couldn't classify 211627, 211628
Sorry, prediction CodingQuarry_transcript_51951-T1 fails validation.
(ATG)	 TG	211627-211628	GT	ATG
(GCA)	 AG	211777-211897	GT	AGG
(GCC)	 AG	212249-212422	GT	AGG
(GAG)	 AG	212687-212797	GT	AGG
(GTA)	 AG	212971-213186	GG	GAG
-recovered CodingQuarry_transcript_51951-T1, terminal, 212971, 213186
-recovered CodingQuarry_transcript_51951-T1, internal, 211777, 211897
-recovered CodingQuarry_transcript_51951-T1, internal, 212249, 212422
-recovered CodingQuarry_transcript_51951-T1, internal, 212687, 212797
Valid prediction for GlimmerHMM_glimmerT_12245-T1
Valid prediction for Augustus_model.g8098.t1
Valid prediction for GeneMark_model.20787_t
Valid prediction for pasa_asmbl_44047.p1
Valid prediction for GeneMark_model.20793_t
Couldn't classify 130561, 130641
Couldn't classify 131287, 131425
Sorry, prediction pasa_asmbl_44040.p1 fails validation.
(AAA)	 AG	130561-130641	GT	ATG
(ATC)	 AG	130962-131179	GT	AGG
(ATC)	 AG	131287-131425	GA	AGG
-recovered pasa_asmbl_44040.p1, internal, 130561, 130641
-recovered pasa_asmbl_44040.p1, internal, 130962, 131179
Valid prediction for snap_scaffold_5-snap.1178-T1
Valid prediction for GeneMark_model.20786_t
Valid prediction for pasa_asmbl_44039.p1
Valid prediction for Augustus_model.g8099.t1
Valid prediction for GeneMark_model.20775_t
Valid prediction for Augustus_model.g8080.t1
Valid prediction for snap_scaffold_5-snap.1183-T1
Valid prediction for GeneMark_model.20792_t
Valid prediction for GeneMark_model.20804_t
Valid prediction for CodingQuarry_transcript_51952-T1
Valid prediction for GlimmerHMM_glimmerT_12261-T1
Valid prediction for GlimmerHMM_glimmerT_12270-T1
Valid prediction for GeneMark_model.20782_t
Valid prediction for GlimmerHMM_glimmerT_12256-T1
Valid prediction for GeneMark_model.20795_t
Valid prediction for GlimmerHMM_glimmerT_12268-T1
Valid prediction for Augustus_model.g8090.t1
Valid prediction for snap_scaffold_5-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_12264-T1
Valid prediction for GeneMark_model.20769_t
Valid prediction for snap_scaffold_5-snap.1179-T1
Valid prediction for CodingQuarry_transcript_51950-T1
Valid prediction for snap_scaffold_5-snap.1174-T1
Valid prediction for pasa_asmbl_44044.p2
Valid prediction for GlimmerHMM_glimmerT_12248-T1
Valid prediction for snap_scaffold_5-snap.1159-T1
Valid prediction for HiQ_model.g8089.t1
Valid prediction for GlimmerHMM_glimmerT_12259-T1
Valid prediction for snap_scaffold_5-snap.1187-T1
Valid prediction for snap_scaffold_5-snap.1176-T1
Valid prediction for GeneMark_model.20800_t
Valid prediction for GeneMark_model.20771_t
Valid prediction for GeneMark_model.20798_t
Valid prediction for GeneMark_model.20773_t
Valid prediction for GeneMark_model.20784_t
Valid prediction for snap_scaffold_5-snap.1177-T1
Valid prediction for snap_scaffold_5-snap.1173-T1
Valid prediction for GlimmerHMM_glimmerT_12260-T1
Valid prediction for Augustus_model.g8093.t1
Valid prediction for pasa_asmbl_44036.p1
Couldn't classify 132419, 132712
Sorry, prediction pasa_asmbl_44041.p2 fails validation.
(AAG)	 GG	132419-132712	GT	GAG
(CCA)	 AG	132907-132948	AA	GAA
-recovered pasa_asmbl_44041.p2, terminal, 132907, 132948
Valid prediction for Augustus_model.g8094.t1
Valid prediction for snap_scaffold_5-snap.1180-T1
Valid prediction for snap_scaffold_5-snap.1170-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 GlimmerHMM_glimmerT_12266-T1
Valid prediction for GlimmerHMM_glimmerT_12244-T1
Valid prediction for GeneMark_model.20768_t
Valid prediction for GlimmerHMM_glimmerT_12250-T1
Valid prediction for GeneMark_model.20796_t
Valid prediction for GeneMark_model.20803_t
Valid prediction for GlimmerHMM_glimmerT_12257-T1
Valid prediction for snap_scaffold_5-snap.1168-T1
Valid prediction for snap_scaffold_5-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_12253-T1
Valid prediction for snap_scaffold_5-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_12272-T1
Valid prediction for GlimmerHMM_glimmerT_12258-T1
Valid prediction for snap_scaffold_5-snap.1186-T1
Valid prediction for GeneMark_model.20797_t
Couldn't classify 32808, 32898
Couldn't classify 34279, 34367
Sorry, prediction pasa_asmbl_46314.p1 fails validation.
(GTT)	 GC	32808-32898	GT	AGG
(TTC)	 AG	33075-33223	GT	AGG
(CTC)	 AG	33465-33560	GT	AGG
(GAT)	 AG	34109-34175	GT	AGG
(GGC)	 AG	34279-34367	AC	CCA
-recovered pasa_asmbl_46314.p1, internal, 33075, 33223
-recovered pasa_asmbl_46314.p1, internal, 33465, 33560
-recovered pasa_asmbl_46314.p1, internal, 34109, 34175
Valid prediction for snap_scaffold_5-snap.1158-T1
Valid prediction for snap_scaffold_5-snap.1166-T1
Valid prediction for CodingQuarry_transcript_51947-T1
Valid prediction for Augustus_model.g8078.t1
Valid prediction for GeneMark_model.20799_t
Valid prediction for GlimmerHMM_glimmerT_12269-T1
Valid prediction for snap_scaffold_5-snap.1165-T1
Valid prediction for snap_scaffold_5-snap.1156-T1
Valid prediction for HiQ_model.g8088.t1
Valid prediction for snap_scaffold_5-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_12254-T1
Valid prediction for GlimmerHMM_glimmerT_12246-T1
Valid prediction for GeneMark_model.20780_t
Valid prediction for GlimmerHMM_glimmerT_12255-T1
Valid prediction for snap_scaffold_5-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_12252-T1
Valid prediction for GeneMark_model.20785_t
Valid prediction for snap_scaffold_5-snap.1154-T1
Valid prediction for Augustus_model.g8077.t1
Valid prediction for GeneMark_model.20767_t
Valid prediction for GlimmerHMM_glimmerT_12249-T1
Valid prediction for Augustus_model.g8082.t1
Valid prediction for snap_scaffold_5-snap.1184-T1
Valid prediction for snap_scaffold_5-snap.1152-T1
Valid prediction for Augustus_model.g8097.t1
Valid prediction for GeneMark_model.20774_t
Valid prediction for GlimmerHMM_glimmerT_12265-T1
Valid prediction for CodingQuarry_transcript_51948-T1
Valid prediction for Augustus_model.g8079.t1
Valid prediction for GeneMark_model.20772_t
Valid prediction for snap_scaffold_5-snap.1188-T1
Valid prediction for snap_scaffold_5-snap.1163-T1
Valid prediction for Augustus_model.g8091.t1
Valid prediction for snap_scaffold_5-snap.1171-T1
Valid prediction for pasa_asmbl_45454.p1
Valid prediction for GeneMark_model.20794_t
Couldn't classify 137165, 137929
Sorry, prediction pasa_asmbl_45450.p1 fails validation.
(GAT)	 GT	137165-137929	GA	GAG
Valid prediction for Augustus_model.g8081.t1
Valid prediction for GeneMark_model.20783_t
Valid prediction for GeneMark_model.20776_t
Valid prediction for Augustus_model.g8085.t1
Couldn't classify 34588, 34699
Sorry, prediction pasa_asmbl_45458.p1 fails validation.
(AGT)	 AG	34588-34699	GT	CAG
(CTT)	 AG	34948-35031	GT	AAG
(TTG)	 AG	35148-35183	GT	AGG
(AGC)	 AG	35332-35948	CT	AAC
-recovered pasa_asmbl_45458.p1, terminal, 35332, 35948
-recovered pasa_asmbl_45458.p1, internal, 34588, 34699
-recovered pasa_asmbl_45458.p1, internal, 34948, 35031
-recovered pasa_asmbl_45458.p1, internal, 35148, 35183
Valid prediction for snap_scaffold_5-snap.1175-T1
Valid prediction for snap_scaffold_5-snap.1189-T1
Valid prediction for snap_scaffold_5-snap.1151-T1
Valid prediction for GeneMark_model.20790_t
Valid prediction for GeneMark_model.20777_t
Valid prediction for GeneMark_model.20789_t
Valid prediction for snap_scaffold_5-snap.1182-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g8095.t1
Valid prediction for HiQ_model.g8086.t1
Valid prediction for GeneMark_model.20781_t
Valid prediction for snap_scaffold_5-snap.1164-T1
Valid prediction for Augustus_model.g8084.t1
Valid prediction for GlimmerHMM_glimmerT_12251-T1
Valid prediction for snap_scaffold_5-snap.1153-T1
Valid prediction for Augustus_model.g8083.t1
Valid prediction for GlimmerHMM_glimmerT_12262-T1
Valid prediction for GeneMark_model.20770_t
Valid prediction for snap_scaffold_5-snap.1162-T1
Valid prediction for snap_scaffold_5-snap.1169-T1
Couldn't classify 138026, 138331
Sorry, prediction pasa_asmbl_46374.p1 fails validation.
(TCC)	 GC	138026-138331	GT	AGG
(GTG)	 AG	139319-139927	AC	AAA
-recovered pasa_asmbl_46374.p1, terminal, 139319, 139927
Valid prediction for GlimmerHMM_glimmerT_12267-T1
Couldn't classify 105030, 105049
Sorry, prediction pasa_asmbl_45456.p1 fails validation.
(CAG)	 GC	105030-105049	GT	AGG
(CGG)	 AG	105162-105264	GT	AGG
(GTC)	 AG	105567-105728	GT	CTG
(AAT)	 AG	105995-106068	GT	TGG
(GGG)	 AG	107652-107701	GT	CAG
(ATG)	 AG	107823-107950	GT	AGG
(GAC)	 AG	108230-108374	GT	GGG
(ACA)	 AG	108544-108699	GT	GGG
(ATC)	 AG	109602-109708	GT	AGG
(TGC)	 AG	110156-110258	GT	CGG
(GAA)	 AG	110508-110679	GT	AAG
(GTT)	 AG	110898-111088	GT	CTG
(GCG)	 AG	111348-111537	GT	TGG
(TGA)	 AG	111764-111880	GT	GGG
(TTA)	 AG	112182-112290	GT	TGG
(ACT)	 AG	112545-112657	GT	CGG
(GTT)	 AG	112864-112993	GT	AGG
(GAC)	 AG	113111-113125	CT	AGC
add_exon() Sorry, pasa_asmbl_45456.p1 107823-107950-initial-1 is invalid.
-recovered pasa_asmbl_45456.p1, initial, 107823, 107950
-recovered pasa_asmbl_45456.p1, terminal, 113111, 113125
-recovered pasa_asmbl_45456.p1, internal, 105162, 105264
-recovered pasa_asmbl_45456.p1, internal, 105567, 105728
-recovered pasa_asmbl_45456.p1, internal, 105995, 106068
-recovered pasa_asmbl_45456.p1, internal, 107652, 107701
-recovered pasa_asmbl_45456.p1, internal, 107823, 107950
-recovered pasa_asmbl_45456.p1, internal, 108230, 108374
-recovered pasa_asmbl_45456.p1, internal, 108544, 108699
-recovered pasa_asmbl_45456.p1, internal, 109602, 109708
-recovered pasa_asmbl_45456.p1, internal, 110156, 110258
-recovered pasa_asmbl_45456.p1, internal, 110508, 110679
-recovered pasa_asmbl_45456.p1, internal, 110898, 111088
-recovered pasa_asmbl_45456.p1, internal, 111348, 111537
-recovered pasa_asmbl_45456.p1, internal, 111764, 111880
-recovered pasa_asmbl_45456.p1, internal, 112182, 112290
-recovered pasa_asmbl_45456.p1, internal, 112545, 112657
-recovered pasa_asmbl_45456.p1, internal, 112864, 112993
Valid prediction for Augustus_model.g8101.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24678, rend_intergenic: 21761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40456, rend_intergenic: 37719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213186, rend_intergenic: 206082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224940
-exon list size: 476


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 24678, rend_intergenic: 21761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40456, rend_intergenic: 37719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213186, rend_intergenic: 206082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support