-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_4986904-5177421

-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_44073-T1
Valid prediction for HiQ_model.g29207.t1
Valid prediction for Augustus_model.g29200.t1
Valid prediction for CodingQuarry_transcript_25645-T1
Valid prediction for snap_scaffold_19-snap.1066-T1
Valid prediction for snap_scaffold_19-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_44088-T1
Valid prediction for GlimmerHMM_glimmerT_44077-T1
Valid prediction for GlimmerHMM_glimmerT_44082-T1
Valid prediction for snap_scaffold_19-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_44070-T1
Valid prediction for GlimmerHMM_glimmerT_44083-T1
Valid prediction for Augustus_model.g29197.t1
Valid prediction for snap_scaffold_19-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_44078-T1
Valid prediction for CodingQuarry_transcript_25648-T1
Valid prediction for snap_scaffold_19-snap.1059-T1
Valid prediction for pasa_asmbl_21348.p1
Valid prediction for Augustus_model.g29213.t1
Valid prediction for Augustus_model.g29215.t1
Valid prediction for snap_scaffold_19-snap.1061-T1
Valid prediction for snap_scaffold_19-snap.1068-T1
Couldn't classify 153471, 153523
Couldn't classify 154748, 154838
Sorry, prediction pasa_asmbl_21967.p1 fails validation.
(GAC)	 TG	153471-153523	GT	GGG
(GCG)	 AG	153775-153951	GT	CAG
(GAA)	 AG	154057-154114	GT	AGG
(GTT)	 AG	154268-154329	GT	AGG
(CAC)	 AG	154413-154562	GT	CGG
(AAT)	 AG	154748-154838	TG	CCT
-recovered pasa_asmbl_21967.p1, internal, 153775, 153951
-recovered pasa_asmbl_21967.p1, internal, 154057, 154114
-recovered pasa_asmbl_21967.p1, internal, 154268, 154329
-recovered pasa_asmbl_21967.p1, internal, 154413, 154562
Couldn't classify 171695, 171817
Sorry, prediction pasa_asmbl_21359.p1 fails validation.
(GGC)	 CC	171695-171817	GT	AGG
(ACA)	 AG	172198-172339	GT	GGG
(GAC)	 AG	172451-172584	GT	TGG
(GGT)	 AG	172787-172888	GA	GAG
-recovered pasa_asmbl_21359.p1, terminal, 172787, 172888
-recovered pasa_asmbl_21359.p1, internal, 172198, 172339
-recovered pasa_asmbl_21359.p1, internal, 172451, 172584
Valid prediction for Augustus_model.g29199.t1
Valid prediction for CodingQuarry_transcript_25647-T1
Couldn't classify 149970, 150040
Couldn't classify 152808, 152817
Sorry, prediction pasa_asmbl_21351.p1 fails validation.
(TTC)	 AG	149970-150040	GT	CAG
(GTA)	 AG	150143-150209	GT	AGG
(ACC)	 AG	150375-150577	GT	AGG
(GGG)	 AG	150797-150862	GT	GGG
(GTA)	 AG	150967-151065	GT	AGG
(GTA)	 AG	151292-151568	GT	TGG
(GGC)	 AG	151828-151905	GT	AGG
(GGG)	 AG	152067-152200	GT	GTG
(TAA)	 AG	152404-152568	GT	AGG
(CCC)	 AG	152808-152817	GG	TGG
-recovered pasa_asmbl_21351.p1, internal, 149970, 150040
-recovered pasa_asmbl_21351.p1, internal, 150143, 150209
-recovered pasa_asmbl_21351.p1, internal, 150375, 150577
-recovered pasa_asmbl_21351.p1, internal, 150797, 150862
-recovered pasa_asmbl_21351.p1, internal, 150967, 151065
-recovered pasa_asmbl_21351.p1, internal, 151292, 151568
-recovered pasa_asmbl_21351.p1, internal, 151828, 151905
-recovered pasa_asmbl_21351.p1, internal, 152067, 152200
-recovered pasa_asmbl_21351.p1, internal, 152404, 152568
Valid prediction for GlimmerHMM_glimmerT_44079-T1
Valid prediction for snap_scaffold_19-snap.1070-T1
Valid prediction for snap_scaffold_19-snap.1079-T1
Valid prediction for Augustus_model.g29205.t1
Valid prediction for GlimmerHMM_glimmerT_44087-T1
Valid prediction for Augustus_model.g29214.t1
Valid prediction for snap_scaffold_19-snap.1077-T1
Valid prediction for snap_scaffold_19-snap.1050-T1
Valid prediction for GlimmerHMM_glimmerT_44089-T1
Valid prediction for Augustus_model.g29206.t1
Valid prediction for snap_scaffold_19-snap.1078-T1
Valid prediction for snap_scaffold_19-snap.1069-T1
Valid prediction for snap_scaffold_19-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_44076-T1
Valid prediction for snap_scaffold_19-snap.1048-T1
Valid prediction for Augustus_model.g29212.t1
Valid prediction for snap_scaffold_19-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_44071-T1
Valid prediction for GlimmerHMM_glimmerT_44074-T1
Valid prediction for snap_scaffold_19-snap.1044-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 snap_scaffold_19-snap.1071-T1
Valid prediction for snap_scaffold_19-snap.1054-T1
Valid prediction for Augustus_model.g29220.t1
Valid prediction for Augustus_model.g29210.t1
Valid prediction for snap_scaffold_19-snap.1060-T1
Valid prediction for GlimmerHMM_glimmerT_44085-T1
Valid prediction for Augustus_model.g29203.t1
Valid prediction for Augustus_model.g29208.t1
Valid prediction for Augustus_model.g29204.t1
Valid prediction for snap_scaffold_19-snap.1076-T1
Valid prediction for snap_scaffold_19-snap.1043-T1
Valid prediction for GlimmerHMM_glimmerT_44072-T1
Valid prediction for GlimmerHMM_glimmerT_44091-T1
Valid prediction for snap_scaffold_19-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_44093-T1
Valid prediction for GlimmerHMM_glimmerT_44090-T1
Valid prediction for Augustus_model.g29218.t1
Valid prediction for Augustus_model.g29209.t1
Valid prediction for Augustus_model.g29217.t1
Valid prediction for snap_scaffold_19-snap.1055-T1
Valid prediction for snap_scaffold_19-snap.1082-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.1051-T1
Valid prediction for Augustus_model.g29211.t1
Valid prediction for snap_scaffold_19-snap.1083-T1
Couldn't classify 56350, 56493
Couldn't classify 59738, 59800
Sorry, prediction pasa_asmbl_22143.p1 fails validation.
(CTG)	 AG	56350-56493	GT	GGG
(AAG)	 AG	56693-56787	GT	CGG
(GAT)	 AG	57380-57459	GT	AGG
(CCT)	 AG	57558-57652	GT	TGG
(CAA)	 AG	57797-57859	GT	GGG
(ATC)	 AG	58134-58257	GT	TGG
(GCC)	 AG	58500-58620	GT	TGG
(GGG)	 AG	59463-59556	GT	CCG
(GTT)	 AG	59738-59800	GG	CAG
-recovered pasa_asmbl_22143.p1, internal, 56350, 56493
-recovered pasa_asmbl_22143.p1, internal, 56693, 56787
-recovered pasa_asmbl_22143.p1, internal, 57380, 57459
-recovered pasa_asmbl_22143.p1, internal, 57558, 57652
-recovered pasa_asmbl_22143.p1, internal, 57797, 57859
-recovered pasa_asmbl_22143.p1, internal, 58134, 58257
-recovered pasa_asmbl_22143.p1, internal, 58500, 58620
-recovered pasa_asmbl_22143.p1, internal, 59463, 59556
Valid prediction for snap_scaffold_19-snap.1058-T1
Valid prediction for snap_scaffold_19-snap.1065-T1
Valid prediction for snap_scaffold_19-snap.1046-T1
Valid prediction for Augustus_model.g29202.t1
Valid prediction for Augustus_model.g29201.t1
Valid prediction for snap_scaffold_19-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_44080-T1
Valid prediction for snap_scaffold_19-snap.1080-T1
Valid prediction for snap_scaffold_19-snap.1067-T1
Valid prediction for snap_scaffold_19-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_44092-T1
Valid prediction for snap_scaffold_19-snap.1072-T1
Valid prediction for snap_scaffold_19-snap.1084-T1
Valid prediction for snap_scaffold_19-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_44069-T1
Valid prediction for GlimmerHMM_glimmerT_44084-T1
Valid prediction for snap_scaffold_19-snap.1062-T1
Valid prediction for snap_scaffold_19-snap.1049-T1
Valid prediction for snap_scaffold_19-snap.1063-T1
Valid prediction for Augustus_model.g29216.t1
Valid prediction for snap_scaffold_19-snap.1047-T1
Valid prediction for Augustus_model.g29219.t1
Valid prediction for Augustus_model.g29198.t1
Valid prediction for snap_scaffold_19-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_44075-T1
Valid prediction for GlimmerHMM_glimmerT_44086-T1
Valid prediction for GlimmerHMM_glimmerT_44068-T1
Valid prediction for snap_scaffold_19-snap.1056-T1
Valid prediction for GlimmerHMM_glimmerT_44081-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19196, rend_intergenic: 12429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84871, rend_intergenic: 80424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91901, rend_intergenic: 87034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115828, rend_intergenic: 112512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133253, rend_intergenic: 115891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136801, rend_intergenic: 133330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140702, rend_intergenic: 137162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155997, rend_intergenic: 142898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174993, rend_intergenic: 171910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 34041, rend_intergenic: 34038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190518
-exon list size: 461


building trellis

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97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 19196, rend_intergenic: 12429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84871, rend_intergenic: 80424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91901, rend_intergenic: 87034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115828, rend_intergenic: 112512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133253, rend_intergenic: 115891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136801, rend_intergenic: 133330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140702, rend_intergenic: 137162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155997, rend_intergenic: 142898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174993, rend_intergenic: 171910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 34041, rend_intergenic: 34038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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