-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_4860415-5051609

-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.70913_t
Valid prediction for snap_scaffold_17-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_41149-T1
Valid prediction for GlimmerHMM_glimmerT_41139-T1
Valid prediction for GeneMark_model.70906_t
Valid prediction for GeneMark_model.70894_t
Valid prediction for GeneMark_model.70918_t
Valid prediction for GlimmerHMM_glimmerT_41140-T1
Valid prediction for GlimmerHMM_glimmerT_41160-T1
Valid prediction for snap_scaffold_17-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_41142-T1
Valid prediction for GeneMark_model.70891_t
Valid prediction for GeneMark_model.70916_t
Valid prediction for snap_scaffold_17-snap.1027-T1
Valid prediction for snap_scaffold_17-snap.1022-T1
Valid prediction for GeneMark_model.70929_t
Valid prediction for snap_scaffold_17-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_41150-T1
Valid prediction for snap_scaffold_17-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_41143-T1
Valid prediction for GeneMark_model.70889_t
Valid prediction for GeneMark_model.70927_t
Valid prediction for GeneMark_model.70892_t
Valid prediction for GlimmerHMM_glimmerT_41151-T1
Valid prediction for GeneMark_model.70883_t
Valid prediction for GeneMark_model.70903_t
Valid prediction for Augustus_model.g27553.t1
Valid prediction for snap_scaffold_17-snap.1017-T1
Valid prediction for snap_scaffold_17-snap.1015-T1
Valid prediction for GeneMark_model.70896_t
Valid prediction for Augustus_model.g27562.t1
Valid prediction for snap_scaffold_17-snap.1044-T1
Valid prediction for GlimmerHMM_glimmerT_41146-T1
Valid prediction for snap_scaffold_17-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_41148-T1
Valid prediction for GlimmerHMM_glimmerT_41153-T1
Valid prediction for GeneMark_model.70914_t
Valid prediction for GeneMark_model.70904_t
Valid prediction for GeneMark_model.70908_t
Valid prediction for snap_scaffold_17-snap.1028-T1
Valid prediction for GeneMark_model.70911_t
Valid prediction for snap_scaffold_17-snap.1036-T1
Valid prediction for GeneMark_model.70898_t
Valid prediction for GeneMark_model.70921_t
Valid prediction for Augustus_model.g27552.t1
Valid prediction for GeneMark_model.70900_t
Valid prediction for snap_scaffold_17-snap.1046-T1
Valid prediction for snap_scaffold_17-snap.1026-T1
Valid prediction for GeneMark_model.70887_t
Valid prediction for snap_scaffold_17-snap.1024-T1
Valid prediction for snap_scaffold_17-snap.1038-T1
Valid prediction for GeneMark_model.70919_t
Valid prediction for GeneMark_model.70899_t

-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.g27556.t1
Valid prediction for GeneMark_model.70909_t
Valid prediction for GlimmerHMM_glimmerT_41141-T1
Valid prediction for GeneMark_model.70890_t
Valid prediction for GeneMark_model.70895_t
Valid prediction for snap_scaffold_17-snap.1032-T1
Valid prediction for snap_scaffold_17-snap.1041-T1
Valid prediction for GlimmerHMM_glimmerT_41162-T1
Valid prediction for Augustus_model.g27565.t1
Valid prediction for Augustus_model.g27551.t1
Valid prediction for snap_scaffold_17-snap.1018-T1
Couldn't classify 45517, 45573
Sorry, prediction pasa_asmbl_18936.p1 fails validation.
(AGG)	 TG	45517-45573	GT	CGG
(GTT)	 AG	45717-45827	GT	AGG
(TAC)	 AG	47229-47381	GT	ATG
(GAT)	 AG	47688-47819	CA	GAC
-recovered pasa_asmbl_18936.p1, terminal, 47688, 47819
-recovered pasa_asmbl_18936.p1, internal, 45717, 45827
-recovered pasa_asmbl_18936.p1, internal, 47229, 47381
Valid prediction for Augustus_model.g27557.t1
Valid prediction for GeneMark_model.70893_t
Valid prediction for GlimmerHMM_glimmerT_41158-T1
Valid prediction for GeneMark_model.70917_t
Valid prediction for pasa_asmbl_18940.p1
Valid prediction for snap_scaffold_17-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_41138-T1
Valid prediction for snap_scaffold_17-snap.1020-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_21925-T1
Valid prediction for snap_scaffold_17-snap.1042-T1
Valid prediction for GeneMark_model.70884_t
Valid prediction for HiQ_model.g27569.t1
Valid prediction for GeneMark_model.70907_t
Valid prediction for GeneMark_model.70902_t
Valid prediction for GlimmerHMM_glimmerT_41155-T1
Valid prediction for snap_scaffold_17-snap.1034-T1
Couldn't classify 9643, 9769
Sorry, prediction pasa_asmbl_18939.p1 fails validation.
(GAT)	 AT	9643-9769	GT	CGG
(GCA)	 AG	12126-12236	GT	AGG
(TCG)	 AG	12657-12883	AG	AGA
-recovered pasa_asmbl_18939.p1, terminal, 12657, 12883
-recovered pasa_asmbl_18939.p1, internal, 12126, 12236
Valid prediction for Augustus_model.g27555.t1
Valid prediction for snap_scaffold_17-snap.1039-T1
Couldn't classify 16865, 16982
Sorry, prediction pasa_asmbl_18938.p1 fails validation.
(TCG)	 CA	16865-16982	GT	GGG
(CTG)	 AG	17615-17725	GT	AAG
(CCT)	 AG	18010-18230	TC	AAT
-recovered pasa_asmbl_18938.p1, terminal, 18010, 18230
-recovered pasa_asmbl_18938.p1, internal, 17615, 17725
Valid prediction for snap_scaffold_17-snap.1033-T1
Valid prediction for snap_scaffold_17-snap.1052-T1
Valid prediction for GeneMark_model.70897_t
Valid prediction for Augustus_model.g27564.t1
Valid prediction for snap_scaffold_17-snap.1021-T1
Valid prediction for GlimmerHMM_glimmerT_41156-T1
Valid prediction for GeneMark_model.70915_t
Valid prediction for HiQ_model.g27568.t1
Valid prediction for CodingQuarry_transcript_21926-T1
Valid prediction for snap_scaffold_17-snap.1047-T1
Valid prediction for GeneMark_model.70926_t
Valid prediction for Augustus_model.g27563.t1
Valid prediction for GlimmerHMM_glimmerT_41157-T1
Valid prediction for GlimmerHMM_glimmerT_41137-T1
Valid prediction for snap_scaffold_17-snap.1025-T1
Valid prediction for HiQ_model.g27566.t1
Valid prediction for GeneMark_model.70901_t
Valid prediction for GeneMark_model.70888_t
Valid prediction for snap_scaffold_17-snap.1050-T1
Valid prediction for GeneMark_model.70886_t
Valid prediction for snap_scaffold_17-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_41159-T1
Valid prediction for GlimmerHMM_glimmerT_41152-T1
Valid prediction for snap_scaffold_17-snap.1053-T1
Valid prediction for GeneMark_model.70928_t
Valid prediction for CodingQuarry_transcript_21928-T1
Couldn't classify 38903, 38928
Couldn't classify 42474, 42531
Sorry, prediction pasa_asmbl_18937.p1 fails validation.
(CAC)	 GC	38903-38928	GT	GAG
(GTG)	 AG	40719-40888	GT	AGG
(CCT)	 AG	41667-41856	GT	AGG
(GAT)	 AG	42106-42291	GT	AGG
(GTC)	 AG	42474-42531	GG	TGG
add_exon() Sorry, pasa_asmbl_18937.p1 42106-42291-terminal-1 is invalid.
-recovered pasa_asmbl_18937.p1, terminal, 42106, 42291
-recovered pasa_asmbl_18937.p1, internal, 40719, 40888
-recovered pasa_asmbl_18937.p1, internal, 41667, 41856
-recovered pasa_asmbl_18937.p1, internal, 42106, 42291
Valid prediction for snap_scaffold_17-snap.1016-T1
Valid prediction for snap_scaffold_17-snap.1023-T1
Valid prediction for GeneMark_model.70920_t
Valid prediction for GeneMark_model.70885_t
Valid prediction for GeneMark_model.70930_t
Valid prediction for GeneMark_model.70923_t
Valid prediction for GeneMark_model.70924_t
Valid prediction for GeneMark_model.70931_t
Valid prediction for Augustus_model.g27560.t1
Valid prediction for GlimmerHMM_glimmerT_41163-T1
Valid prediction for GlimmerHMM_glimmerT_41145-T1
Valid prediction for Augustus_model.g27567.t1
Valid prediction for snap_scaffold_17-snap.1051-T1
Valid prediction for snap_scaffold_17-snap.1045-T1
Valid prediction for GeneMark_model.70925_t
Valid prediction for GlimmerHMM_glimmerT_41147-T1
Valid prediction for GeneMark_model.70905_t
Valid prediction for snap_scaffold_17-snap.1031-T1
Valid prediction for Augustus_model.g27561.t1
Valid prediction for GeneMark_model.70922_t
Valid prediction for snap_scaffold_17-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_41161-T1
Valid prediction for Augustus_model.g27558.t1
Valid prediction for GeneMark_model.70912_t
Valid prediction for snap_scaffold_17-snap.1043-T1
Valid prediction for GlimmerHMM_glimmerT_41154-T1
Valid prediction for GlimmerHMM_glimmerT_41144-T1
Valid prediction for Augustus_model.g27559.t1
Valid prediction for Augustus_model.g27554.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9491, rend_intergenic: 3764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10474, rend_intergenic: 10005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13061, rend_intergenic: 11217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16303, rend_intergenic: 14591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29287, rend_intergenic: 19611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34153, rend_intergenic: 29315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47997, rend_intergenic: 37980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54797, rend_intergenic: 49362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57897, rend_intergenic: 56307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71703, rend_intergenic: 70345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72742, rend_intergenic: 71753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98893, rend_intergenic: 96279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113184, rend_intergenic: 106486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140155, rend_intergenic: 133527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152629, rend_intergenic: 150858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191195
-exon list size: 576


building trellis

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98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 9491, rend_intergenic: 3764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10474, rend_intergenic: 10005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13061, rend_intergenic: 11217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16303, rend_intergenic: 14591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29287, rend_intergenic: 19611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34153, rend_intergenic: 29315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47997, rend_intergenic: 37980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54797, rend_intergenic: 49362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57897, rend_intergenic: 56307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71703, rend_intergenic: 70345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72742, rend_intergenic: 71753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98893, rend_intergenic: 96279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113184, rend_intergenic: 106486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140155, rend_intergenic: 133527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152629, rend_intergenic: 150858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support