-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_4950316-5138479

-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_15-snap.1105-T1
Valid prediction for snap_scaffold_15-snap.1095-T1
Valid prediction for snap_scaffold_15-snap.1117-T1
Valid prediction for GeneMark_model.63482_t
Valid prediction for Augustus_model.g24762.t1
Valid prediction for snap_scaffold_15-snap.1089-T1
Valid prediction for GeneMark_model.63504_t
Valid prediction for snap_scaffold_15-snap.1112-T1
Valid prediction for GlimmerHMM_glimmerT_36894-T1
Couldn't classify 18098, 18523
Sorry, prediction pasa_asmbl_15181.p1 fails validation.
(ATC)	 CC	18098-18523	AG	AAA
Valid prediction for GeneMark_model.63500_t
Couldn't classify 45759, 46139
Sorry, prediction pasa_asmbl_14128.p1 fails validation.
(CCT)	 GC	45759-46139	AG	GAA
Valid prediction for GeneMark_model.63494_t
Valid prediction for snap_scaffold_15-snap.1094-T1
Valid prediction for snap_scaffold_15-snap.1090-T1
Valid prediction for GeneMark_model.63511_t
Valid prediction for GeneMark_model.63491_t
Valid prediction for GeneMark_model.63509_t
Valid prediction for GlimmerHMM_glimmerT_36887-T1
Valid prediction for GeneMark_model.63484_t
Valid prediction for Augustus_model.g24770.t1
Valid prediction for snap_scaffold_15-snap.1100-T1
Valid prediction for GeneMark_model.63498_t
Valid prediction for snap_scaffold_15-snap.1111-T1
Valid prediction for pasa_asmbl_14120.p1
Valid prediction for snap_scaffold_15-snap.1087-T1
Valid prediction for snap_scaffold_15-snap.1119-T1
Valid prediction for GeneMark_model.63488_t
Valid prediction for GlimmerHMM_glimmerT_36902-T1
Valid prediction for GeneMark_model.63496_t
Valid prediction for Augustus_model.g24772.t1
Valid prediction for GeneMark_model.63476_t
Valid prediction for snap_scaffold_15-snap.1096-T1
Valid prediction for Augustus_model.g24768.t1
Couldn't classify 56240, 56798
Sorry, prediction pasa_asmbl_14129.p1 fails validation.
(ACG)	 CA	56240-56798	GT	GGG
(GCC)	 AG	56935-57140	GT	TGG
(GTC)	 AG	57284-57892	CA	AAC
-recovered pasa_asmbl_14129.p1, terminal, 57284, 57892
-recovered pasa_asmbl_14129.p1, internal, 56935, 57140
Valid prediction for Augustus_model.g24758.t1
Valid prediction for GlimmerHMM_glimmerT_36913-T1
Valid prediction for GlimmerHMM_glimmerT_36895-T1
Valid prediction for GeneMark_model.63505_t
Valid prediction for snap_scaffold_15-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_36912-T1
Valid prediction for snap_scaffold_15-snap.1109-T1
Valid prediction for GeneMark_model.63479_t
Valid prediction for snap_scaffold_15-snap.1108-T1
Valid prediction for GeneMark_model.63507_t
Valid prediction for pasa_asmbl_14121.p1
Valid prediction for GlimmerHMM_glimmerT_36893-T1
Valid prediction for snap_scaffold_15-snap.1097-T1
Valid prediction for snap_scaffold_15-snap.1107-T1
Valid prediction for Augustus_model.g24764.t1
Valid prediction for HiQ_model.g24761.t1
Valid prediction for GlimmerHMM_glimmerT_36896-T1
Valid prediction for GeneMark_model.63502_t
Valid prediction for GlimmerHMM_glimmerT_36898-T1
Valid prediction for snap_scaffold_15-snap.1098-T1
Valid prediction for GeneMark_model.63512_t
Valid prediction for GlimmerHMM_glimmerT_36889-T1
Valid prediction for snap_scaffold_15-snap.1116-T1
Valid prediction for snap_scaffold_15-snap.1115-T1
Valid prediction for GlimmerHMM_glimmerT_36904-T1
Valid prediction for GeneMark_model.63486_t
Valid prediction for GeneMark_model.63481_t
Valid prediction for snap_scaffold_15-snap.1101-T1
Valid prediction for GeneMark_model.63475_t
Valid prediction for HiQ_model.g24756.t1
Valid prediction for CodingQuarry_transcript_17950-T1
Valid prediction for GlimmerHMM_glimmerT_36890-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 GlimmerHMM_glimmerT_36911-T1
Valid prediction for Augustus_model.g24757.t1
Valid prediction for Augustus_model.g24769.t1
Valid prediction for GeneMark_model.63499_t
Valid prediction for Augustus_model.g24763.t1
Valid prediction for snap_scaffold_15-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_36903-T1
Valid prediction for GeneMark_model.63480_t
Valid prediction for pasa_asmbl_15187.p1
Valid prediction for GeneMark_model.63490_t
Valid prediction for GlimmerHMM_glimmerT_36908-T1
Valid prediction for CodingQuarry_transcript_17954-T1
Valid prediction for Augustus_model.g24771.t1
Valid prediction for snap_scaffold_15-snap.1093-T1
Valid prediction for snap_scaffold_15-snap.1110-T1
Valid prediction for snap_scaffold_15-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_36907-T1
Valid prediction for snap_scaffold_15-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_36892-T1
Valid prediction for GeneMark_model.63497_t
Valid prediction for GeneMark_model.63483_t
Valid prediction for CodingQuarry_transcript_17952-T1
Valid prediction for GeneMark_model.63508_t
Valid prediction for snap_scaffold_15-snap.1113-T1
Valid prediction for GeneMark_model.63492_t
Valid prediction for GeneMark_model.63506_t
Valid prediction for GeneMark_model.63477_t
Valid prediction for GlimmerHMM_glimmerT_36906-T1
Valid prediction for GeneMark_model.63493_t
Valid prediction for snap_scaffold_15-snap.1085-T1
Valid prediction for GeneMark_model.63489_t
Valid prediction for snap_scaffold_15-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_36910-T1
Valid prediction for GeneMark_model.63487_t
Valid prediction for GeneMark_model.63474_t
Valid prediction for Augustus_model.g24765.t1
Valid prediction for GeneMark_model.63478_t
Valid prediction for GeneMark_model.63503_t
Valid prediction for GeneMark_model.63501_t
Valid prediction for Augustus_model.g24755.t1
Valid prediction for GeneMark_model.63510_t
Valid prediction for snap_scaffold_15-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_36891-T1
Valid prediction for GeneMark_model.63495_t
Valid prediction for snap_scaffold_15-snap.1102-T1
Valid prediction for HiQ_model.g24759.t1
Valid prediction for GlimmerHMM_glimmerT_36900-T1
Valid prediction for CodingQuarry_transcript_17953-T1
Valid prediction for Augustus_model.g24767.t1
Couldn't classify 148536, 148734
Sorry, prediction pasa_asmbl_15194.p1 fails validation.
(CCA)	 GT	148536-148734	GT	CGG
(TGT)	 AG	148824-149018	GT	AGG
(ACA)	 AG	149137-149275	GT	AGG
(GAG)	 AG	149759-150171	GT	CGG
(ATA)	 AG	150285-150310	AG	GAA
-recovered pasa_asmbl_15194.p1, terminal, 150285, 150310
-recovered pasa_asmbl_15194.p1, internal, 148824, 149018
-recovered pasa_asmbl_15194.p1, internal, 149137, 149275
-recovered pasa_asmbl_15194.p1, internal, 149759, 150171
Valid prediction for GeneMark_model.63485_t
Couldn't classify 82113, 82163
Sorry, prediction pasa_asmbl_15199.p1 fails validation.
(GGC)	 CT	82113-82163	GT	AGG
(GTG)	 AG	82472-82690	GT	AGG
(GAC)	 AG	82919-83026	GT	GGG
(GAC)	 AG	83527-83686	GT	TGG
(GAA)	 AG	84162-84280	GT	AGG
(GTG)	 AG	85319-85553	GT	TGG
(GTG)	 AG	85708-85935	GT	TGG
(GTT)	 AG	86208-86479	GT	AGG
(GTG)	 AG	86590-86687	GT	AGG
(AGT)	 AG	86816-86955	GT	AGG
(ATG)	 AG	87229-87236	AT	AAA
-recovered pasa_asmbl_15199.p1, terminal, 87229, 87236
-recovered pasa_asmbl_15199.p1, internal, 82472, 82690
-recovered pasa_asmbl_15199.p1, internal, 82919, 83026
-recovered pasa_asmbl_15199.p1, internal, 83527, 83686
-recovered pasa_asmbl_15199.p1, internal, 84162, 84280
-recovered pasa_asmbl_15199.p1, internal, 85319, 85553
-recovered pasa_asmbl_15199.p1, internal, 85708, 85935
-recovered pasa_asmbl_15199.p1, internal, 86208, 86479
-recovered pasa_asmbl_15199.p1, internal, 86590, 86687
-recovered pasa_asmbl_15199.p1, internal, 86816, 86955
Valid prediction for GlimmerHMM_glimmerT_36901-T1
Valid prediction for Augustus_model.g24766.t1
Valid prediction for snap_scaffold_15-snap.1092-T1
Valid prediction for Augustus_model.g24760.t1
Valid prediction for GlimmerHMM_glimmerT_36897-T1
Valid prediction for snap_scaffold_15-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_36888-T1
Valid prediction for snap_scaffold_15-snap.1114-T1
Valid prediction for snap_scaffold_15-snap.1106-T1
Valid prediction for pasa_asmbl_15186.p1
Valid prediction for GlimmerHMM_glimmerT_36909-T1
Valid prediction for CodingQuarry_transcript_17951-T1
Valid prediction for GlimmerHMM_glimmerT_36905-T1
Valid prediction for GlimmerHMM_glimmerT_36899-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4050, rend_intergenic: 2244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52897, rend_intergenic: 38877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117976, rend_intergenic: 116780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148100, rend_intergenic: 145274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164875, rend_intergenic: 163200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184372, rend_intergenic: 179851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188164
-exon list size: 583


building trellis

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92.3    
92.5    
92.6    
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98.3    
98.5    
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: 4050, rend_intergenic: 2244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52897, rend_intergenic: 38877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117976, rend_intergenic: 116780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148100, rend_intergenic: 145274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164875, rend_intergenic: 163200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184372, rend_intergenic: 179851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support