-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_5652163-5852823

-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_48951-T1
Valid prediction for Augustus_model.g32793.t1
Valid prediction for GeneMark_model.84890_t
Valid prediction for GeneMark_model.84880_t
Valid prediction for GlimmerHMM_glimmerT_48957-T1
Valid prediction for GeneMark_model.84888_t
Valid prediction for GlimmerHMM_glimmerT_48933-T1
Valid prediction for GlimmerHMM_glimmerT_48941-T1
Valid prediction for snap_scaffold_21-snap.1135-T1
Valid prediction for snap_scaffold_21-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_48940-T1
Valid prediction for Augustus_model.g32772.t1
Valid prediction for GlimmerHMM_glimmerT_48939-T1
Valid prediction for pasa_asmbl_29041.p1
Valid prediction for GeneMark_model.84866_t
Valid prediction for snap_scaffold_21-snap.1173-T1
Valid prediction for snap_scaffold_21-snap.1152-T1
Valid prediction for Augustus_model.g32770.t1
Valid prediction for snap_scaffold_21-snap.1164-T1
Valid prediction for snap_scaffold_21-snap.1146-T1
Valid prediction for Augustus_model.g32796.t1
Valid prediction for GlimmerHMM_glimmerT_48935-T1
Valid prediction for snap_scaffold_21-snap.1139-T1
Valid prediction for HiQ_model.g32791.t1
Valid prediction for GeneMark_model.84867_t
Valid prediction for GlimmerHMM_glimmerT_48954-T1
Valid prediction for GeneMark_model.84874_t
Valid prediction for snap_scaffold_21-snap.1147-T1
Valid prediction for snap_scaffold_21-snap.1150-T1
Valid prediction for GeneMark_model.84879_t
Couldn't classify 155063, 155082
Sorry, prediction pasa_asmbl_28609.p1 fails validation.
(AAT)	 AG	155063-155082	GT	GAG
(GGT)	 AG	155399-155476	GT	CAG
(ACG)	 AG	155692-155769	GT	AGG
(TGT)	 AG	155925-156000	GT	TTG
(CGA)	 AG	156118-156231	GT	AGG
(ATT)	 AG	156325-156363	GT	AGG
(GGG)	 AG	156692-156811	GC	TGG
(GAG)	 AG	157000-157053	GT	TGG
(CTC)	 AG	157157-157243	GT	AGG
(GTT)	 AG	157328-157495	AG	GAA
-recovered pasa_asmbl_28609.p1, terminal, 155063, 155082
-recovered pasa_asmbl_28609.p1, terminal, 157328, 157495
-recovered pasa_asmbl_28609.p1, internal, 155063, 155082
-recovered pasa_asmbl_28609.p1, internal, 155399, 155476
-recovered pasa_asmbl_28609.p1, internal, 155692, 155769
-recovered pasa_asmbl_28609.p1, internal, 155925, 156000
-recovered pasa_asmbl_28609.p1, internal, 156118, 156231
-recovered pasa_asmbl_28609.p1, internal, 156325, 156363
-recovered pasa_asmbl_28609.p1, internal, 156692, 156811
-recovered pasa_asmbl_28609.p1, internal, 157000, 157053
-recovered pasa_asmbl_28609.p1, internal, 157157, 157243
Valid prediction for GlimmerHMM_glimmerT_48945-T1
Valid prediction for GlimmerHMM_glimmerT_48953-T1
Valid prediction for GlimmerHMM_glimmerT_48932-T1
Valid prediction for GlimmerHMM_glimmerT_48937-T1
Valid prediction for CodingQuarry_transcript_32505-T1
Valid prediction for snap_scaffold_21-snap.1133-T1
Valid prediction for snap_scaffold_21-snap.1153-T1
Valid prediction for Augustus_model.g32771.t1
Couldn't classify 178175, 178187
Sorry, prediction pasa_asmbl_28610.p1 fails validation.
(ACC)	 AG	178175-178187	GT	GGG
(GGC)	 AG	178308-178385	GT	TGG
(TGA)	 AG	178484-178604	GT	AGG
(CTG)	 AG	178745-178883	GT	AGG
(GGA)	 AG	178983-179107	GT	AGG
(GTA)	 AG	179243-179630	TC	GAT
-recovered pasa_asmbl_28610.p1, terminal, 179243, 179630
-recovered pasa_asmbl_28610.p1, internal, 178175, 178187
-recovered pasa_asmbl_28610.p1, internal, 178308, 178385
-recovered pasa_asmbl_28610.p1, internal, 178484, 178604
-recovered pasa_asmbl_28610.p1, internal, 178745, 178883
-recovered pasa_asmbl_28610.p1, internal, 178983, 179107
Valid prediction for snap_scaffold_21-snap.1165-T1
Valid prediction for GeneMark_model.84877_t
Valid prediction for GlimmerHMM_glimmerT_48956-T1
Valid prediction for snap_scaffold_21-snap.1138-T1
Valid prediction for snap_scaffold_21-snap.1170-T1
Valid prediction for snap_scaffold_21-snap.1160-T1
Valid prediction for GeneMark_model.84872_t
Valid prediction for snap_scaffold_21-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_48947-T1
Valid prediction for HiQ_model.g32787.t1
Valid prediction for GlimmerHMM_glimmerT_48931-T1
Valid prediction for GlimmerHMM_glimmerT_48952-T1
Valid prediction for Augustus_model.g32780.t1
Valid prediction for GlimmerHMM_glimmerT_48928-T1
Valid prediction for GeneMark_model.84889_t
Valid prediction for snap_scaffold_21-snap.1172-T1
Valid prediction for GeneMark_model.84892_t
Valid prediction for snap_scaffold_21-snap.1175-T1
Valid prediction for snap_scaffold_21-snap.1134-T1
Valid prediction for CodingQuarry_transcript_32503-T1
Valid prediction for snap_scaffold_21-snap.1136-T1
Couldn't classify 79449, 79495
Sorry, prediction pasa_asmbl_28606.p1 fails validation.
(GAT)	 GG	79449-79495	GT	ATG
(ATT)	 AG	79658-80393	GC	GAG
-recovered pasa_asmbl_28606.p1, terminal, 79658, 80393
-recovered pasa_asmbl_28606.p1, internal, 79658, 80393
Valid prediction for snap_scaffold_21-snap.1155-T1
Valid prediction for snap_scaffold_21-snap.1167-T1
Valid prediction for Augustus_model.g32795.t1
Valid prediction for Augustus_model.g32778.t1
Valid prediction for GeneMark_model.84868_t
Valid prediction for snap_scaffold_21-snap.1154-T1
Valid prediction for Augustus_model.g32792.t1
Valid prediction for Augustus_model.g32781.t1
Valid prediction for Augustus_model.g32779.t1
Couldn't classify 77522, 77683
Couldn't classify 79037, 79182
Sorry, prediction pasa_asmbl_28605.p1 fails validation.
(CCA)	 CC	77522-77683	GT	AGG
(GAG)	 AG	78589-78775	GT	CGG
(GGA)	 AG	79037-79182	AG	GCA
-recovered pasa_asmbl_28605.p1, internal, 78589, 78775

-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 pasa_asmbl_27727.p1
Valid prediction for GeneMark_model.84883_t
Valid prediction for Augustus_model.g32790.t1
Valid prediction for snap_scaffold_21-snap.1144-T1
Valid prediction for snap_scaffold_21-snap.1166-T1
Valid prediction for snap_scaffold_21-snap.1163-T1
Valid prediction for GeneMark_model.84884_t
Valid prediction for Augustus_model.g32773.t1
Valid prediction for snap_scaffold_21-snap.1157-T1
Valid prediction for GeneMark_model.84878_t
Valid prediction for GeneMark_model.84870_t
Valid prediction for CodingQuarry_transcript_32500-T1
Valid prediction for snap_scaffold_21-snap.1162-T1
Valid prediction for snap_scaffold_21-snap.1141-T1
Valid prediction for GeneMark_model.84869_t
Valid prediction for snap_scaffold_21-snap.1171-T1
Valid prediction for GlimmerHMM_glimmerT_48946-T1
Valid prediction for Augustus_model.g32783.t1
Valid prediction for GlimmerHMM_glimmerT_48944-T1
Valid prediction for snap_scaffold_21-snap.1143-T1
Valid prediction for Augustus_model.g32775.t1
Valid prediction for GeneMark_model.84873_t
Valid prediction for GeneMark_model.84886_t
Valid prediction for pasa_asmbl_27718.p1
Valid prediction for snap_scaffold_21-snap.1168-T1
Valid prediction for Augustus_model.g32776.t1
Valid prediction for GeneMark_model.84891_t
Couldn't classify 91384, 91778
Couldn't classify 91940, 92015
Sorry, prediction pasa_asmbl_27717.p1 fails validation.
(GAG)	 GT	91384-91778	GT	AGG
(GTA)	 AG	91940-92015	CT	AGC
Valid prediction for Augustus_model.g32777.t1
Valid prediction for GeneMark_model.84876_t
Valid prediction for snap_scaffold_21-snap.1148-T1
Valid prediction for GeneMark_model.84882_t
Couldn't classify 138387, 138455
Sorry, prediction pasa_asmbl_27714.p1 fails validation.
(CCA)	 CC	138387-138455	GT	AGG
(GTG)	 AG	139463-139638	GT	ATG
(ACA)	 AG	139845-140640	TG	AGT
-recovered pasa_asmbl_27714.p1, terminal, 139845, 140640
-recovered pasa_asmbl_27714.p1, internal, 139463, 139638
Valid prediction for GeneMark_model.84887_t
Valid prediction for CodingQuarry_transcript_32498-T1
Couldn't classify 70275, 70595
Sorry, prediction pasa_asmbl_28205.p1 fails validation.
(GGG)	 GG	70275-70595	GT	TGG
Valid prediction for GlimmerHMM_glimmerT_48955-T1
Valid prediction for GlimmerHMM_glimmerT_48929-T1
Valid prediction for GeneMark_model.84881_t
Valid prediction for Augustus_model.g32782.t1
Valid prediction for snap_scaffold_21-snap.1149-T1
Valid prediction for Augustus_model.g32774.t1
Valid prediction for snap_scaffold_21-snap.1174-T1
Valid prediction for Augustus_model.g32794.t1
Couldn't classify 138000, 138113
Sorry, prediction pasa_asmbl_27715.p1 fails validation.
(ATG)	 CC	135454-135532	GT	AGG
(GTC)	 AG	135797-135964	GT	TGG
(GTG)	 AG	137498-137784	GT	AGG
(GTG)	 AG	138000-138113	AA	GCA
-recovered pasa_asmbl_27715.p1, initial, 135454, 135532
-recovered pasa_asmbl_27715.p1, internal, 135797, 135964
-recovered pasa_asmbl_27715.p1, internal, 137498, 137784
Valid prediction for Augustus_model.g32788.t1
Valid prediction for GeneMark_model.84871_t
Valid prediction for HiQ_model.g32786.t1
Valid prediction for snap_scaffold_21-snap.1151-T1
Valid prediction for snap_scaffold_21-snap.1158-T1
Valid prediction for GlimmerHMM_glimmerT_48930-T1
Couldn't classify 69346, 70211
Sorry, prediction pasa_asmbl_27726.p1 fails validation.
(ATG)	 GA	60571-60573	GT	TGG
(GAT)	 AG	62607-62708	GT	AGG
(GGC)	 AG	63751-63874	GT	AGG
(GCA)	 AG	65529-65699	GT	AGG
(GGT)	 AG	68584-68709	GT	AGG
(ATG)	 AG	69346-70211	AG	ACA
-recovered pasa_asmbl_27726.p1, initial, 60571, 60573
-recovered pasa_asmbl_27726.p1, internal, 62607, 62708
-recovered pasa_asmbl_27726.p1, internal, 63751, 63874
-recovered pasa_asmbl_27726.p1, internal, 65529, 65699
-recovered pasa_asmbl_27726.p1, internal, 68584, 68709
Valid prediction for CodingQuarry_transcript_32499-T1
Valid prediction for snap_scaffold_21-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_48936-T1
Valid prediction for GlimmerHMM_glimmerT_48943-T1
Valid prediction for CodingQuarry_transcript_32502-T1
Valid prediction for GlimmerHMM_glimmerT_48938-T1
Valid prediction for GlimmerHMM_glimmerT_48949-T1
Valid prediction for snap_scaffold_21-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_48948-T1
Valid prediction for GeneMark_model.84893_t
Valid prediction for Augustus_model.g32785.t1
Valid prediction for snap_scaffold_21-snap.1159-T1
Valid prediction for Augustus_model.g32789.t1
Valid prediction for snap_scaffold_21-snap.1142-T1
Valid prediction for GlimmerHMM_glimmerT_48942-T1
Valid prediction for snap_scaffold_21-snap.1169-T1
Valid prediction for snap_scaffold_21-snap.1145-T1
Valid prediction for CodingQuarry_transcript_32501-T1
Valid prediction for GlimmerHMM_glimmerT_48950-T1
Valid prediction for HiQ_model.g32784.t1
Valid prediction for GlimmerHMM_glimmerT_48934-T1
Valid prediction for GeneMark_model.84875_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18889, rend_intergenic: 17108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42865, rend_intergenic: 38710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64864, rend_intergenic: 60022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127738, rend_intergenic: 124720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131048, rend_intergenic: 128136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169362, rend_intergenic: 165803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191244, rend_intergenic: 186336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200661
-exon list size: 565


building trellis

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97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 18889, rend_intergenic: 17108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42865, rend_intergenic: 38710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64864, rend_intergenic: 60022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127738, rend_intergenic: 124720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131048, rend_intergenic: 128136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169362, rend_intergenic: 165803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191244, rend_intergenic: 186336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support