-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_5046441-5230017

-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 snap_scaffold_12-snap.1066-T1
Valid prediction for snap_scaffold_12-snap.1051-T1
Valid prediction for snap_scaffold_12-snap.1054-T1
Valid prediction for Augustus_model.g19932.t1
Valid prediction for GlimmerHMM_glimmerT_29941-T1
Valid prediction for GeneMark_model.51774_t
Valid prediction for Augustus_model.g19925.t1
Valid prediction for GeneMark_model.51751_t
Valid prediction for snap_scaffold_12-snap.1070-T1
Valid prediction for GeneMark_model.51773_t
Valid prediction for GlimmerHMM_glimmerT_29932-T1
Valid prediction for snap_scaffold_12-snap.1048-T1
Valid prediction for Augustus_model.g19926.t1
Valid prediction for GeneMark_model.51759_t
Valid prediction for snap_scaffold_12-snap.1058-T1
Valid prediction for snap_scaffold_12-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_29934-T1
Valid prediction for GeneMark_model.51780_t
Valid prediction for GlimmerHMM_glimmerT_29939-T1
Valid prediction for snap_scaffold_12-snap.1063-T1
Valid prediction for GeneMark_model.51753_t
Valid prediction for snap_scaffold_12-snap.1045-T1
Valid prediction for GeneMark_model.51745_t
Valid prediction for Augustus_model.g19929.t1
Valid prediction for GeneMark_model.51782_t
Valid prediction for snap_scaffold_12-snap.1061-T1
Valid prediction for GeneMark_model.51754_t
Valid prediction for snap_scaffold_12-snap.1065-T1
Valid prediction for GeneMark_model.51747_t
Valid prediction for GlimmerHMM_glimmerT_29933-T1
Valid prediction for GeneMark_model.51750_t
Valid prediction for GeneMark_model.51776_t
Valid prediction for GeneMark_model.51752_t
Valid prediction for GeneMark_model.51741_t
Valid prediction for GeneMark_model.51763_t
Valid prediction for GeneMark_model.51766_t
Valid prediction for GeneMark_model.51756_t
Valid prediction for GeneMark_model.51748_t
Valid prediction for GeneMark_model.51762_t
Valid prediction for GlimmerHMM_glimmerT_29937-T1
Valid prediction for GlimmerHMM_glimmerT_29943-T1
Couldn't classify 33998, 34054
Sorry, prediction pasa_asmbl_8600.p1 fails validation.
(TCC)	 GC	33998-34054	GT	AGG
(GCC)	 AG	34172-34272	GT	AAG
(AAA)	 AG	34352-34459	GT	ATG
(GGC)	 AG	34879-34942	GT	AGG
(GTG)	 AG	35319-35393	GT	TTG
(CCC)	 AG	35802-35885	GT	AGG
(GAG)	 AG	36133-36301	GT	AGG
(CGA)	 AG	36458-36507	AG	AGA
-recovered pasa_asmbl_8600.p1, terminal, 36458, 36507
-recovered pasa_asmbl_8600.p1, internal, 34172, 34272
-recovered pasa_asmbl_8600.p1, internal, 34352, 34459
-recovered pasa_asmbl_8600.p1, internal, 34879, 34942
-recovered pasa_asmbl_8600.p1, internal, 35319, 35393
-recovered pasa_asmbl_8600.p1, internal, 35802, 35885
-recovered pasa_asmbl_8600.p1, internal, 36133, 36301
Valid prediction for Augustus_model.g19933.t1
Valid prediction for GeneMark_model.51778_t
Valid prediction for GlimmerHMM_glimmerT_29952-T1
Valid prediction for GeneMark_model.51743_t
Valid prediction for GlimmerHMM_glimmerT_29944-T1
Valid prediction for GeneMark_model.51757_t
Valid prediction for snap_scaffold_12-snap.1071-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_12-snap.1050-T1
Valid prediction for GeneMark_model.51749_t
Valid prediction for GlimmerHMM_glimmerT_29942-T1
Valid prediction for GeneMark_model.51760_t
Valid prediction for Augustus_model.g19934.t1
Valid prediction for Augustus_model.g19928.t1
Valid prediction for CodingQuarry_transcript_10188-T1
Couldn't classify 133813, 134019
Couldn't classify 137054, 137443
Sorry, prediction pasa_asmbl_7613.p1 fails validation.
(CTC)	 CT	133813-134019	GT	AGG
(ATA)	 AG	134610-134801	GT	TAG
(CTG)	 AG	136616-136738	GT	AGG
(AAC)	 AG	137054-137443	GC	GGG
-recovered pasa_asmbl_7613.p1, internal, 134610, 134801
-recovered pasa_asmbl_7613.p1, internal, 136616, 136738
-recovered pasa_asmbl_7613.p1, internal, 137054, 137443
Valid prediction for GlimmerHMM_glimmerT_29953-T1
Valid prediction for GeneMark_model.51740_t
Valid prediction for snap_scaffold_12-snap.1056-T1
Valid prediction for snap_scaffold_12-snap.1073-T1
Valid prediction for snap_scaffold_12-snap.1053-T1
Valid prediction for GeneMark_model.51775_t
Valid prediction for GlimmerHMM_glimmerT_29938-T1
Valid prediction for snap_scaffold_12-snap.1067-T1
Valid prediction for HiQ_model.g19930.t1
Couldn't classify 85607, 85805
Sorry, prediction pasa_asmbl_7617.p1 fails validation.
(CAG)	 CG	85607-85805	GT	AGG
(GTC)	 AG	86290-86456	GT	AGG
(GTG)	 AG	88078-88299	GG	AAG
-recovered pasa_asmbl_7617.p1, terminal, 88078, 88299
-recovered pasa_asmbl_7617.p1, internal, 86290, 86456
Valid prediction for GeneMark_model.51758_t
Valid prediction for Augustus_model.g19935.t1
Valid prediction for GlimmerHMM_glimmerT_29948-T1
Valid prediction for GlimmerHMM_glimmerT_29946-T1
Valid prediction for GlimmerHMM_glimmerT_29954-T1
Valid prediction for GlimmerHMM_glimmerT_29945-T1
Valid prediction for GeneMark_model.51764_t
Valid prediction for GeneMark_model.51767_t
Valid prediction for snap_scaffold_12-snap.1057-T1
Valid prediction for snap_scaffold_12-snap.1049-T1
Valid prediction for GeneMark_model.51769_t
Valid prediction for GeneMark_model.51742_t
Couldn't classify 138751, 138859
Sorry, prediction pasa_asmbl_7612.p1 fails validation.
(CTC)	 GC	138751-138859	GT	AGG
(GCC)	 AG	139246-139855	GT	AGG
(CTG)	 AG	140051-140123	GT	AGG
(GAC)	 AG	140258-140376	GT	GAG
(GGA)	 AG	140760-140893	GT	AGG
(ATG)	 AG	141166-141257	CT	GAC
add_exon() Sorry, pasa_asmbl_7612.p1 140258-140376-terminal-2 is invalid.
-recovered pasa_asmbl_7612.p1, terminal, 140258, 140376
add_exon() Sorry, pasa_asmbl_7612.p1 140760-140893-terminal-2 is invalid.
-recovered pasa_asmbl_7612.p1, terminal, 140760, 140893
-recovered pasa_asmbl_7612.p1, terminal, 141166, 141257
-recovered pasa_asmbl_7612.p1, internal, 139246, 139855
-recovered pasa_asmbl_7612.p1, internal, 140051, 140123
-recovered pasa_asmbl_7612.p1, internal, 140258, 140376
-recovered pasa_asmbl_7612.p1, internal, 140760, 140893
Valid prediction for snap_scaffold_12-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_29940-T1
Valid prediction for GeneMark_model.51755_t
Valid prediction for GeneMark_model.51770_t
Valid prediction for Augustus_model.g19937.t1
Couldn't classify 162245, 162314
Sorry, prediction pasa_asmbl_7608.p1 fails validation.
(CAC)	 CT	162245-162314	GT	TGG
(ATA)	 AG	162633-162743	GT	AGG
(AAG)	 AG	163749-163996	CA	AAC
-recovered pasa_asmbl_7608.p1, terminal, 163749, 163996
-recovered pasa_asmbl_7608.p1, internal, 162633, 162743
Valid prediction for GlimmerHMM_glimmerT_29949-T1
Valid prediction for GeneMark_model.51765_t
Valid prediction for snap_scaffold_12-snap.1062-T1
Valid prediction for snap_scaffold_12-snap.1069-T1
Valid prediction for GeneMark_model.51771_t
Valid prediction for snap_scaffold_12-snap.1047-T1
Valid prediction for GeneMark_model.51783_t
Valid prediction for GeneMark_model.51779_t
Valid prediction for Augustus_model.g19936.t1
Valid prediction for snap_scaffold_12-snap.1060-T1
Valid prediction for snap_scaffold_12-snap.1064-T1
Valid prediction for snap_scaffold_12-snap.1068-T1
Valid prediction for GeneMark_model.51781_t
Valid prediction for GeneMark_model.51744_t
Couldn't classify 84673, 84777
Sorry, prediction pasa_asmbl_8353.p1 fails validation.
(ATG)	 AC	78872-79291	GT	AGG
(CCT)	 AG	80459-80588	GT	CTG
(GTG)	 AG	80764-80911	GT	GCG
(GCC)	 AG	81328-81527	GT	GGG
(CGG)	 AG	81800-81930	GT	AGG
(CTA)	 AG	82690-82794	GT	AAG
(AGG)	 AG	83148-83261	GT	TTG
(GAG)	 AG	83640-83809	GT	AGG
(GAC)	 AG	84216-84363	GT	AGG
(CTT)	 AG	84673-84777	CA	ATC
-recovered pasa_asmbl_8353.p1, initial, 78872, 79291
-recovered pasa_asmbl_8353.p1, internal, 80459, 80588
-recovered pasa_asmbl_8353.p1, internal, 80764, 80911
-recovered pasa_asmbl_8353.p1, internal, 81328, 81527
-recovered pasa_asmbl_8353.p1, internal, 81800, 81930
-recovered pasa_asmbl_8353.p1, internal, 82690, 82794
-recovered pasa_asmbl_8353.p1, internal, 83148, 83261
-recovered pasa_asmbl_8353.p1, internal, 83640, 83809
-recovered pasa_asmbl_8353.p1, internal, 84216, 84363
Valid prediction for snap_scaffold_12-snap.1046-T1
Valid prediction for GeneMark_model.51777_t
Valid prediction for GlimmerHMM_glimmerT_29947-T1
Valid prediction for GeneMark_model.51772_t
Valid prediction for GeneMark_model.51746_t
Valid prediction for Augustus_model.g19927.t1
Valid prediction for GlimmerHMM_glimmerT_29950-T1
Valid prediction for GlimmerHMM_glimmerT_29936-T1
Valid prediction for snap_scaffold_12-snap.1072-T1
Valid prediction for GeneMark_model.51768_t
Valid prediction for GlimmerHMM_glimmerT_29951-T1
Valid prediction for HiQ_model.g19931.t1
Valid prediction for snap_scaffold_12-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_29935-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16969, rend_intergenic: 13202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63680, rend_intergenic: 60218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141943, rend_intergenic: 131885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146663, rend_intergenic: 143440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153275, rend_intergenic: 149037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155208, rend_intergenic: 154292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161547, rend_intergenic: 159088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170027, rend_intergenic: 165845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179822, rend_intergenic: 172096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183577
-exon list size: 480


building trellis

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98.1    
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99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 16969, rend_intergenic: 13202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63680, rend_intergenic: 60218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141943, rend_intergenic: 131885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146663, rend_intergenic: 143440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153275, rend_intergenic: 149037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155208, rend_intergenic: 154292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161547, rend_intergenic: 159088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170027, rend_intergenic: 165845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179822, rend_intergenic: 172096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10785
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support