-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_5659084-5882802

-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: +)Couldn't classify 207851, 208719
Sorry, prediction pasa_asmbl_40044.p1 fails validation.
(ATG)	 CA	206909-206936	GT	AGG
(GCG)	 AG	207120-207330	GT	AGG
(TGC)	 AG	207561-207643	GT	AGG
(ATC)	 AG	207851-208719	AG	CCA
-recovered pasa_asmbl_40044.p1, initial, 206909, 206936
-recovered pasa_asmbl_40044.p1, internal, 207120, 207330
-recovered pasa_asmbl_40044.p1, internal, 207561, 207643
Valid prediction for GeneMark_model.11127_t
Couldn't classify 19778, 19913
Sorry, prediction pasa_asmbl_40035.p1 fails validation.
(CCC)	 AA	19778-19913	GT	GGG
(TCC)	 AG	20115-20272	GT	GCG
(CTT)	 AG	20400-20570	GT	AGG
(AGC)	 AG	20705-20775	GT	AGG
(CAT)	 AG	20989-21034	GC	GAG
-recovered pasa_asmbl_40035.p1, terminal, 20989, 21034
-recovered pasa_asmbl_40035.p1, internal, 20115, 20272
-recovered pasa_asmbl_40035.p1, internal, 20400, 20570
-recovered pasa_asmbl_40035.p1, internal, 20705, 20775
-recovered pasa_asmbl_40035.p1, internal, 20989, 21034
Valid prediction for GeneMark_model.11121_t
Valid prediction for GlimmerHMM_glimmerT_6726-T1
Valid prediction for Augustus_model.g4408.t1
Valid prediction for GlimmerHMM_glimmerT_6727-T1
Valid prediction for Augustus_model.g4392.t1
Valid prediction for GeneMark_model.11143_t
Valid prediction for Augustus_model.g4405.t1
Valid prediction for snap_scaffold_3-snap.1203-T1
Valid prediction for GeneMark_model.11140_t
Valid prediction for pasa_asmbl_40041.p1
Valid prediction for snap_scaffold_3-snap.1215-T1
Valid prediction for snap_scaffold_3-snap.1202-T1
Valid prediction for GeneMark_model.11138_t
Valid prediction for GlimmerHMM_glimmerT_6737-T1
Valid prediction for GeneMark_model.11136_t
Valid prediction for GeneMark_model.11114_t
Valid prediction for Augustus_model.g4393.t1
Valid prediction for snap_scaffold_3-snap.1210-T1
Couldn't classify 1679, 1735
Couldn't classify 2289, 2365
Sorry, prediction CodingQuarry_transcript_46052-T1 fails validation.
(ATG)	 TC	188-209	GT	CAG
(ACT)	 AG	307-426	GT	GGG
(ATA)	 AG	801-935	GT	TGG
(ATA)	 AG	1043-1165	GT	AGG
(TCA)	 AG	1679-1735	AC	CAA
(AGC)	 GC	2289-2365	CC	GAC
-recovered CodingQuarry_transcript_46052-T1, initial, 188, 209
-recovered CodingQuarry_transcript_46052-T1, internal, 307, 426
-recovered CodingQuarry_transcript_46052-T1, internal, 801, 935
-recovered CodingQuarry_transcript_46052-T1, internal, 1043, 1165
Valid prediction for GlimmerHMM_glimmerT_6733-T1
Valid prediction for GeneMark_model.11117_t
Valid prediction for GeneMark_model.11147_t
Valid prediction for Augustus_model.g4397.t1
Valid prediction for GeneMark_model.11146_t
Valid prediction for GeneMark_model.11132_t
Valid prediction for Augustus_model.g4398.t1
Valid prediction for Augustus_model.g4400.t1
Valid prediction for snap_scaffold_3-snap.1204-T1
Valid prediction for GlimmerHMM_glimmerT_6729-T1
Valid prediction for snap_scaffold_3-snap.1211-T1
Couldn't classify 17174, 17488
Sorry, prediction pasa_asmbl_40034.p1 fails validation.
(GTG)	 AG	17174-17488	AT	ACA
Valid prediction for snap_scaffold_3-snap.1189-T1
Valid prediction for snap_scaffold_3-snap.1216-T1
Valid prediction for GeneMark_model.11131_t
Valid prediction for snap_scaffold_3-snap.1206-T1
Valid prediction for snap_scaffold_3-snap.1194-T1
Valid prediction for GeneMark_model.11123_t
Valid prediction for CodingQuarry_transcript_46055-T1
Valid prediction for snap_scaffold_3-snap.1190-T1
Valid prediction for Augustus_model.g4390.t1
Valid prediction for snap_scaffold_3-snap.1198-T1
Valid prediction for GlimmerHMM_glimmerT_6739-T1
Valid prediction for GlimmerHMM_glimmerT_6731-T1
Valid prediction for snap_scaffold_3-snap.1214-T1
Valid prediction for Augustus_model.g4394.t1
Valid prediction for Augustus_model.g4403.t1
Valid prediction for Augustus_model.g4407.t1
Valid prediction for GeneMark_model.11109_t
Couldn't classify 208864, 209975
Sorry, prediction pasa_asmbl_40046.p1 fails validation.
(CTC)	 GG	208864-209975	GT	AGG
(GTC)	 AG	210128-210585	GT	CGG
(ACA)	 AG	210774-211249	GT	AGG
(AAG)	 AG	211372-211446	TG	AGT
-recovered pasa_asmbl_40046.p1, terminal, 211372, 211446
-recovered pasa_asmbl_40046.p1, internal, 210128, 210585
-recovered pasa_asmbl_40046.p1, internal, 210774, 211249
Valid prediction for pasa_asmbl_40036.p1
Valid prediction for GlimmerHMM_glimmerT_6716-T1
Valid prediction for GlimmerHMM_glimmerT_6738-T1
Valid prediction for GlimmerHMM_glimmerT_6715-T1
Valid prediction for GlimmerHMM_glimmerT_6734-T1
Valid prediction for GeneMark_model.11125_t
Valid prediction for CodingQuarry_transcript_46054-T1
Valid prediction for GeneMark_model.11130_t
Valid prediction for Augustus_model.g4388.t1
Couldn't classify 155, 209
Sorry, prediction pasa_asmbl_40032.p1 fails validation.
(TAC)	 GC	155-209	GT	CAG
(ACT)	 AG	307-426	GT	GGG
(ATA)	 AG	801-935	GT	TGG
(ATA)	 AG	1043-1165	GT	AGG
(TCA)	 AG	1679-1738	GT	CGG
(CCA)	 AG	2291-2524	GT	TGG
(TTC)	 AG	5062-5136	GT	AGG
(ATT)	 AG	5225-5320	GT	TGG
(GTC)	 AG	5434-5696	GT	CTG
(GTC)	 AG	5911-6015	AG	AAA
-recovered pasa_asmbl_40032.p1, terminal, 5911, 6015
-recovered pasa_asmbl_40032.p1, internal, 307, 426
-recovered pasa_asmbl_40032.p1, internal, 801, 935
-recovered pasa_asmbl_40032.p1, internal, 1043, 1165
-recovered pasa_asmbl_40032.p1, internal, 1679, 1738
-recovered pasa_asmbl_40032.p1, internal, 2291, 2524
-recovered pasa_asmbl_40032.p1, internal, 5062, 5136
-recovered pasa_asmbl_40032.p1, internal, 5225, 5320
-recovered pasa_asmbl_40032.p1, internal, 5434, 5696
Valid prediction for GeneMark_model.11142_t
Valid prediction for GeneMark_model.11119_t
Valid prediction for GeneMark_model.11148_t
Couldn't classify 112401, 112599
Sorry, prediction pasa_asmbl_40042.p1 fails validation.
(GGC)	 CG	112401-112599	GT	AGG
(GTT)	 AG	113577-113680	CT	AGC
-recovered pasa_asmbl_40042.p1, terminal, 113577, 113680
Valid prediction for snap_scaffold_3-snap.1195-T1
Valid prediction for GeneMark_model.11120_t
Valid prediction for snap_scaffold_3-snap.1197-T1
Valid prediction for GeneMark_model.11145_t
Valid prediction for GeneMark_model.11112_t
Valid prediction for Augustus_model.g4402.t1
Valid prediction for snap_scaffold_3-snap.1218-T1
Valid prediction for Augustus_model.g4404.t1
Valid prediction for GeneMark_model.11110_t
Valid prediction for snap_scaffold_3-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_6721-T1
Valid prediction for GeneMark_model.11118_t
Valid prediction for snap_scaffold_3-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_6717-T1
Valid prediction for CodingQuarry_transcript_46056-T1
Valid prediction for GlimmerHMM_glimmerT_6722-T1
Valid prediction for GlimmerHMM_glimmerT_6723-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 GeneMark_model.11126_t
Valid prediction for GeneMark_model.11128_t
Valid prediction for snap_scaffold_3-snap.1213-T1
Valid prediction for GeneMark_model.11122_t
Valid prediction for GeneMark_model.11133_t
Valid prediction for GlimmerHMM_glimmerT_6720-T1
Valid prediction for CodingQuarry_transcript_46057-T1
Valid prediction for pasa_asmbl_38816.p1
Valid prediction for GeneMark_model.11135_t
Couldn't classify 195076, 195263
Sorry, prediction pasa_asmbl_38811.p1 fails validation.
(GGT)	 CA	195076-195263	GT	ATG
(AGT)	 AG	196164-196320	GT	TGG
(TTT)	 AG	196429-196597	GT	CGG
(GAA)	 AG	197235-197308	GT	AGG
(TTC)	 AG	197459-197524	GT	TGG
(CTG)	 AG	197989-198069	TT	AAT
-recovered pasa_asmbl_38811.p1, terminal, 197989, 198069
-recovered pasa_asmbl_38811.p1, internal, 196164, 196320
-recovered pasa_asmbl_38811.p1, internal, 196429, 196597
-recovered pasa_asmbl_38811.p1, internal, 197235, 197308
-recovered pasa_asmbl_38811.p1, internal, 197459, 197524
Valid prediction for snap_scaffold_3-snap.1191-T1
Valid prediction for GlimmerHMM_glimmerT_6730-T1
Valid prediction for GlimmerHMM_glimmerT_6736-T1
Valid prediction for GlimmerHMM_glimmerT_6724-T1
Valid prediction for snap_scaffold_3-snap.1193-T1
Valid prediction for GeneMark_model.11141_t
Valid prediction for GlimmerHMM_glimmerT_6735-T1
Valid prediction for Augustus_model.g4399.t1
Valid prediction for snap_scaffold_3-snap.1219-T1
Valid prediction for GeneMark_model.11116_t
Valid prediction for snap_scaffold_3-snap.1205-T1
Valid prediction for Augustus_model.g4396.t1
Valid prediction for GeneMark_model.11124_t
Valid prediction for GeneMark_model.11113_t
Couldn't classify 140746, 140866
Sorry, prediction pasa_asmbl_38813.p1 fails validation.
(GGC)	 AG	140746-140866	GT	AGG
(ACA)	 AG	141032-141272	GT	AGG
(CCC)	 AG	141447-141861	TC	GAT
-recovered pasa_asmbl_38813.p1, terminal, 141447, 141861
-recovered pasa_asmbl_38813.p1, internal, 140746, 140866
-recovered pasa_asmbl_38813.p1, internal, 141032, 141272
Valid prediction for snap_scaffold_3-snap.1199-T1
Valid prediction for GeneMark_model.11139_t
Valid prediction for Augustus_model.g4406.t1
Valid prediction for snap_scaffold_3-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_6732-T1
Valid prediction for snap_scaffold_3-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_6718-T1
Valid prediction for GlimmerHMM_glimmerT_6728-T1
Valid prediction for snap_scaffold_3-snap.1207-T1
Valid prediction for Augustus_model.g4395.t1
Valid prediction for GeneMark_model.11129_t
Valid prediction for snap_scaffold_3-snap.1201-T1
Valid prediction for snap_scaffold_3-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_6725-T1
Valid prediction for GeneMark_model.11144_t
Valid prediction for GlimmerHMM_glimmerT_6719-T1
Valid prediction for HiQ_model.g4389.t1
Valid prediction for snap_scaffold_3-snap.1217-T1
Valid prediction for snap_scaffold_3-snap.1209-T1
Valid prediction for snap_scaffold_3-snap.1200-T1
Valid prediction for Augustus_model.g4391.t1
Valid prediction for HiQ_model.g4401.t1
Valid prediction for GeneMark_model.11115_t
Valid prediction for snap_scaffold_3-snap.1208-T1
Couldn't classify 138100, 138150
Couldn't classify 140463, 140592
Sorry, prediction pasa_asmbl_38814.p1 fails validation.
(AAT)	 AT	138100-138150	GT	CAG
(TGT)	 AG	138298-138387	GT	AGG
(AGC)	 AG	138526-138654	GT	AAG
(GAA)	 AG	138805-138977	GT	CTG
(ACC)	 AG	140463-140592	GA	CAG
-recovered pasa_asmbl_38814.p1, internal, 138298, 138387
-recovered pasa_asmbl_38814.p1, internal, 138526, 138654
-recovered pasa_asmbl_38814.p1, internal, 138805, 138977

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36046, rend_intergenic: 32455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167614, rend_intergenic: 160699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216738, rend_intergenic: 214769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223719
-exon list size: 499


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 36046, rend_intergenic: 32455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167614, rend_intergenic: 160699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216738, rend_intergenic: 214769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support