-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_7552596-7704539

-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.82920_t
Valid prediction for snap_scaffold_20-snap.1677-T1
Valid prediction for GeneMark_model.82918_t
Valid prediction for GeneMark_model.82946_t
Valid prediction for GlimmerHMM_glimmerT_47479-T1
Valid prediction for GeneMark_model.82939_t
Valid prediction for CodingQuarry_transcript_30494-T1
Valid prediction for Augustus_model.g31668.t1
Valid prediction for GlimmerHMM_glimmerT_47478-T1
Valid prediction for GeneMark_model.82930_t
Valid prediction for GlimmerHMM_glimmerT_47496-T1
Valid prediction for snap_scaffold_20-snap.1684-T1
Valid prediction for GeneMark_model.82923_t
Valid prediction for GlimmerHMM_glimmerT_47497-T1
Valid prediction for GlimmerHMM_glimmerT_47491-T1
Valid prediction for GlimmerHMM_glimmerT_47481-T1
Valid prediction for GeneMark_model.82943_t
Valid prediction for GlimmerHMM_glimmerT_47484-T1
Valid prediction for snap_scaffold_20-snap.1667-T1
Valid prediction for snap_scaffold_20-snap.1703-T1
Valid prediction for snap_scaffold_20-snap.1678-T1
Valid prediction for Augustus_model.g31669.t1
Valid prediction for GeneMark_model.82941_t
Valid prediction for Augustus_model.g31665.t1
Valid prediction for GeneMark_model.82933_t
Valid prediction for GeneMark_model.82938_t
Valid prediction for snap_scaffold_20-snap.1690-T1
Valid prediction for snap_scaffold_20-snap.1679-T1
Valid prediction for snap_scaffold_20-snap.1708-T1
Valid prediction for HiQ_model.g31674.t1
Valid prediction for snap_scaffold_20-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_47490-T1
Valid prediction for Augustus_model.g31671.t1
Valid prediction for snap_scaffold_20-snap.1688-T1
Valid prediction for GeneMark_model.82912_t
Valid prediction for GeneMark_model.82910_t
Valid prediction for GeneMark_model.82914_t
Valid prediction for Augustus_model.g31660.t1
Valid prediction for snap_scaffold_20-snap.1692-T1
Valid prediction for snap_scaffold_20-snap.1687-T1
Valid prediction for GeneMark_model.82948_t
Valid prediction for snap_scaffold_20-snap.1695-T1
Valid prediction for snap_scaffold_20-snap.1674-T1
Valid prediction for GeneMark_model.82916_t
Valid prediction for snap_scaffold_20-snap.1694-T1
Valid prediction for GeneMark_model.82921_t
Valid prediction for snap_scaffold_20-snap.1681-T1
Valid prediction for snap_scaffold_20-snap.1706-T1
Valid prediction for Augustus_model.g31656.t1
Valid prediction for GeneMark_model.82936_t
Valid prediction for GlimmerHMM_glimmerT_47499-T1
Valid prediction for pasa_asmbl_25877.p1
Valid prediction for Augustus_model.g31663.t1
Valid prediction for snap_scaffold_20-snap.1698-T1
Valid prediction for GeneMark_model.82927_t
Valid prediction for GlimmerHMM_glimmerT_47498-T1
Couldn't classify 41220, 41311
Sorry, prediction pasa_asmbl_25875.p1 fails validation.
(ATG)	 AT	35819-35841	GT	TGG
(GTT)	 AG	36502-36601	GT	AGG
(ATC)	 AG	36702-36796	GT	ATG
(AAT)	 AG	37074-37184	GT	AGG
(GTC)	 AG	39950-40080	GT	AGG
(TCC)	 AG	41220-41311	GG	ACG
-recovered pasa_asmbl_25875.p1, initial, 35819, 35841
-recovered pasa_asmbl_25875.p1, internal, 36502, 36601
-recovered pasa_asmbl_25875.p1, internal, 36702, 36796
-recovered pasa_asmbl_25875.p1, internal, 37074, 37184
-recovered pasa_asmbl_25875.p1, internal, 39950, 40080
Valid prediction for snap_scaffold_20-snap.1704-T1
Valid prediction for snap_scaffold_20-snap.1707-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.82926_t
Valid prediction for GlimmerHMM_glimmerT_47485-T1
Valid prediction for snap_scaffold_20-snap.1691-T1
Valid prediction for GeneMark_model.82935_t
Valid prediction for GeneMark_model.82909_t
Valid prediction for snap_scaffold_20-snap.1702-T1
Valid prediction for Augustus_model.g31664.t1
Valid prediction for snap_scaffold_20-snap.1668-T1
Valid prediction for snap_scaffold_20-snap.1682-T1
Valid prediction for GeneMark_model.82924_t
Valid prediction for GlimmerHMM_glimmerT_47473-T1
Valid prediction for snap_scaffold_20-snap.1685-T1
Valid prediction for snap_scaffold_20-snap.1699-T1
Valid prediction for Augustus_model.g31666.t1
Valid prediction for GeneMark_model.82929_t
Valid prediction for GlimmerHMM_glimmerT_47480-T1
Valid prediction for GeneMark_model.82913_t
Valid prediction for GeneMark_model.82931_t
Valid prediction for snap_scaffold_20-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_47483-T1
Valid prediction for GlimmerHMM_glimmerT_47487-T1
Valid prediction for snap_scaffold_20-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_47488-T1
Valid prediction for GlimmerHMM_glimmerT_47474-T1
Valid prediction for GlimmerHMM_glimmerT_47495-T1
Valid prediction for snap_scaffold_20-snap.1697-T1
Valid prediction for GeneMark_model.82944_t
Valid prediction for Augustus_model.g31672.t1
Valid prediction for GeneMark_model.82915_t
Valid prediction for snap_scaffold_20-snap.1686-T1
Valid prediction for GeneMark_model.82937_t
Valid prediction for snap_scaffold_20-snap.1670-T1
Valid prediction for snap_scaffold_20-snap.1705-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47486-T1
Valid prediction for Augustus_model.g31657.t1
Valid prediction for Augustus_model.g31658.t1
Valid prediction for snap_scaffold_20-snap.1673-T1
Valid prediction for snap_scaffold_20-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_47476-T1
Valid prediction for GeneMark_model.82925_t
Valid prediction for snap_scaffold_20-snap.1701-T1
Valid prediction for GeneMark_model.82942_t
Valid prediction for Augustus_model.g31667.t1
Valid prediction for snap_scaffold_20-snap.1680-T1
Valid prediction for GeneMark_model.82911_t
Valid prediction for GlimmerHMM_glimmerT_47492-T1
Valid prediction for GlimmerHMM_glimmerT_47494-T1
Valid prediction for snap_scaffold_20-snap.1683-T1
Valid prediction for GeneMark_model.82940_t
Valid prediction for snap_scaffold_20-snap.1696-T1
Valid prediction for GeneMark_model.82945_t
Valid prediction for GeneMark_model.82919_t
Valid prediction for snap_scaffold_20-snap.1666-T1
Valid prediction for snap_scaffold_20-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_47489-T1
Valid prediction for Augustus_model.g31673.t1
Valid prediction for GeneMark_model.82928_t
Valid prediction for GlimmerHMM_glimmerT_47493-T1
Valid prediction for GeneMark_model.82949_t
Valid prediction for Augustus_model.g31659.t1
Valid prediction for GeneMark_model.82947_t
Valid prediction for GeneMark_model.82922_t
Valid prediction for GlimmerHMM_glimmerT_47477-T1
Valid prediction for Augustus_model.g31662.t1
Valid prediction for GeneMark_model.82908_t
Valid prediction for snap_scaffold_20-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_47482-T1
Valid prediction for Augustus_model.g31670.t1
Valid prediction for Augustus_model.g31661.t1
Valid prediction for GeneMark_model.82932_t
Valid prediction for GeneMark_model.82934_t
Valid prediction for snap_scaffold_20-snap.1672-T1
Valid prediction for GlimmerHMM_glimmerT_47475-T1
Valid prediction for snap_scaffold_20-snap.1693-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19173, rend_intergenic: 10423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75021, rend_intergenic: 71750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81200, rend_intergenic: 79617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98904, rend_intergenic: 93073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105671, rend_intergenic: 103143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112811, rend_intergenic: 109762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120048, rend_intergenic: 114060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135975, rend_intergenic: 132265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144914, rend_intergenic: 140547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151944
-exon list size: 589


building trellis

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96.6    
96.8    
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98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 19173, rend_intergenic: 10423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75021, rend_intergenic: 71750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81200, rend_intergenic: 79617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98904, rend_intergenic: 93073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105671, rend_intergenic: 103143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112811, rend_intergenic: 109762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120048, rend_intergenic: 114060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135975, rend_intergenic: 132265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144914, rend_intergenic: 140547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support