-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_1831114-2210359

-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_11522-T1
Valid prediction for GlimmerHMM_glimmerT_11517-T1
Valid prediction for GlimmerHMM_glimmerT_11514-T1
Valid prediction for snap_scaffold_5-snap.427-T1
Valid prediction for snap_scaffold_5-snap.417-T1
Valid prediction for snap_scaffold_5-snap.401-T1
Valid prediction for snap_scaffold_5-snap.378-T1
Valid prediction for snap_scaffold_5-snap.415-T1
Valid prediction for snap_scaffold_5-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_11541-T1
Valid prediction for GlimmerHMM_glimmerT_11549-T1
Valid prediction for snap_scaffold_5-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_11526-T1
Valid prediction for snap_scaffold_5-snap.419-T1
Valid prediction for snap_scaffold_5-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_11534-T1
Valid prediction for GlimmerHMM_glimmerT_11531-T1
Valid prediction for snap_scaffold_5-snap.366-T1
Valid prediction for snap_scaffold_5-snap.408-T1
Valid prediction for snap_scaffold_5-snap.428-T1
Valid prediction for Augustus_model.g7534.t1
Valid prediction for GlimmerHMM_glimmerT_11518-T1
Valid prediction for Augustus_model.g7530.t1
Valid prediction for GlimmerHMM_glimmerT_11532-T1
Valid prediction for snap_scaffold_5-snap.379-T1
Valid prediction for snap_scaffold_5-snap.424-T1
Valid prediction for snap_scaffold_5-snap.388-T1
Valid prediction for snap_scaffold_5-snap.411-T1
Valid prediction for Augustus_model.g7533.t1
Valid prediction for snap_scaffold_5-snap.382-T1
Valid prediction for snap_scaffold_5-snap.392-T1
Valid prediction for pasa_asmbl_45155.p1
Valid prediction for GlimmerHMM_glimmerT_11523-T1
Valid prediction for GlimmerHMM_glimmerT_11527-T1
Valid prediction for snap_scaffold_5-snap.400-T1
Valid prediction for snap_scaffold_5-snap.399-T1
Valid prediction for snap_scaffold_5-snap.364-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g7539.t1
Valid prediction for snap_scaffold_5-snap.371-T1
Valid prediction for Augustus_model.g7547.t1
Valid prediction for snap_scaffold_5-snap.376-T1
Valid prediction for snap_scaffold_5-snap.416-T1
Valid prediction for snap_scaffold_5-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_11528-T1
Valid prediction for snap_scaffold_5-snap.409-T1
Couldn't classify 205878, 206327
Sorry, prediction pasa_asmbl_45154.p1 fails validation.
(AGC)	 AC	205878-206327	AT	GAA
Valid prediction for Augustus_model.g7541.t1
Valid prediction for GlimmerHMM_glimmerT_11544-T1
Valid prediction for GlimmerHMM_glimmerT_11546-T1
Valid prediction for snap_scaffold_5-snap.383-T1
Valid prediction for snap_scaffold_5-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_11548-T1
Valid prediction for snap_scaffold_5-snap.420-T1
Valid prediction for Augustus_model.g7535.t1
Valid prediction for snap_scaffold_5-snap.374-T1
Valid prediction for snap_scaffold_5-snap.375-T1
Valid prediction for snap_scaffold_5-snap.410-T1
Valid prediction for Augustus_model.g7532.t1
Valid prediction for GlimmerHMM_glimmerT_11539-T1
Valid prediction for snap_scaffold_5-snap.394-T1
Valid prediction for snap_scaffold_5-snap.391-T1
Valid prediction for snap_scaffold_5-snap.386-T1
Valid prediction for snap_scaffold_5-snap.384-T1
Valid prediction for snap_scaffold_5-snap.429-T1
Valid prediction for snap_scaffold_5-snap.402-T1
Valid prediction for Augustus_model.g7529.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 Augustus_model.g7545.t1
Valid prediction for snap_scaffold_5-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_11536-T1
Valid prediction for snap_scaffold_5-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_11516-T1
Valid prediction for snap_scaffold_5-snap.406-T1
Valid prediction for Augustus_model.g7540.t1
Valid prediction for snap_scaffold_5-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_11538-T1
Couldn't classify 165588, 165692
Sorry, prediction pasa_asmbl_44958.p2 fails validation.
(GGG)	 TG	165588-165692	GT	AGG
(GAG)	 AG	166127-166208	GT	TGG
(GAC)	 AG	166777-166915	GT	AGG
(CCT)	 AG	168161-168203	AA	AGA
-recovered pasa_asmbl_44958.p2, terminal, 168161, 168203
-recovered pasa_asmbl_44958.p2, internal, 166127, 166208
-recovered pasa_asmbl_44958.p2, internal, 166777, 166915
Valid prediction for GlimmerHMM_glimmerT_11535-T1
Valid prediction for snap_scaffold_5-snap.389-T1
Valid prediction for snap_scaffold_5-snap.380-T1
Valid prediction for Augustus_model.g7531.t1
Valid prediction for Augustus_model.g7542.t1
Valid prediction for snap_scaffold_5-snap.407-T1
Valid prediction for snap_scaffold_5-snap.387-T1
Valid prediction for Augustus_model.g7536.t1
Valid prediction for GlimmerHMM_glimmerT_11525-T1
Valid prediction for GlimmerHMM_glimmerT_11545-T1
Valid prediction for GlimmerHMM_glimmerT_11520-T1
Valid prediction for snap_scaffold_5-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_11519-T1
Couldn't classify 34196, 34261
Couldn't classify 43964, 44005
Sorry, prediction pasa_asmbl_43876.p1 fails validation.
(GCA)	 CA	34196-34261	GT	AGG
(GGG)	 AG	34632-34752	GT	CGG
(GAA)	 AG	36798-36905	GT	TGG
(AGA)	 AG	37314-37426	GT	AGG
(CTA)	 AG	38195-38286	GT	AAG
(GAG)	 AG	39361-39487	GT	CAG
(CTC)	 AG	40690-40843	GT	GGG
(TCT)	 AG	41552-41612	GT	AAG
(GTG)	 AG	42152-42218	GT	TGG
(GTG)	 AG	43382-43600	GT	AGG
(GGT)	 AG	43964-44005	GT	AGG
-recovered pasa_asmbl_43876.p1, internal, 34632, 34752
-recovered pasa_asmbl_43876.p1, internal, 36798, 36905
-recovered pasa_asmbl_43876.p1, internal, 37314, 37426
-recovered pasa_asmbl_43876.p1, internal, 38195, 38286
-recovered pasa_asmbl_43876.p1, internal, 39361, 39487
-recovered pasa_asmbl_43876.p1, internal, 40690, 40843
-recovered pasa_asmbl_43876.p1, internal, 41552, 41612
-recovered pasa_asmbl_43876.p1, internal, 42152, 42218
-recovered pasa_asmbl_43876.p1, internal, 43382, 43600
-recovered pasa_asmbl_43876.p1, internal, 43964, 44005
Valid prediction for snap_scaffold_5-snap.413-T1
Valid prediction for snap_scaffold_5-snap.418-T1
Valid prediction for snap_scaffold_5-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_11530-T1
Valid prediction for Augustus_model.g7528.t1
Valid prediction for snap_scaffold_5-snap.412-T1
Valid prediction for snap_scaffold_5-snap.423-T1
Valid prediction for snap_scaffold_5-snap.372-T1
Valid prediction for snap_scaffold_5-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_11543-T1
Valid prediction for snap_scaffold_5-snap.426-T1
Valid prediction for snap_scaffold_5-snap.390-T1
Valid prediction for snap_scaffold_5-snap.393-T1
Valid prediction for snap_scaffold_5-snap.373-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g7544.t1
Couldn't classify 157038, 157093
Couldn't classify 161801, 161895
Sorry, prediction pasa_asmbl_45029.p1 fails validation.
(AAT)	 AG	157038-157093	GT	ATG
(GGG)	 AG	158042-158129	GT	GGG
(GAT)	 AG	158264-158383	GT	AGG
(GTG)	 AG	158782-158879	GT	AGG
(GAC)	 AG	160994-161112	GT	ATG
(GTT)	 AG	161801-161895	GC	ACG
-recovered pasa_asmbl_45029.p1, internal, 157038, 157093
-recovered pasa_asmbl_45029.p1, internal, 158042, 158129
-recovered pasa_asmbl_45029.p1, internal, 158264, 158383
-recovered pasa_asmbl_45029.p1, internal, 158782, 158879
-recovered pasa_asmbl_45029.p1, internal, 160994, 161112
-recovered pasa_asmbl_45029.p1, internal, 161801, 161895
Valid prediction for GlimmerHMM_glimmerT_11515-T1
Valid prediction for Augustus_model.g7538.t1
Valid prediction for GlimmerHMM_glimmerT_11540-T1
Valid prediction for snap_scaffold_5-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_11521-T1
Couldn't classify 47879, 48238
Sorry, prediction pasa_asmbl_43873.p1 fails validation.
(GAT)	 AA	47879-48238	CA	GAC
Valid prediction for snap_scaffold_5-snap.368-T1
Valid prediction for snap_scaffold_5-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_11542-T1
Valid prediction for snap_scaffold_5-snap.421-T1
Valid prediction for snap_scaffold_5-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_11537-T1
Valid prediction for GlimmerHMM_glimmerT_11524-T1
Valid prediction for snap_scaffold_5-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_11533-T1
Valid prediction for GlimmerHMM_glimmerT_11529-T1
Valid prediction for snap_scaffold_5-snap.363-T1
Valid prediction for snap_scaffold_5-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_11547-T1
Valid prediction for CodingQuarry_transcript_51988-T1
Valid prediction for Augustus_model.g7537.t1
Valid prediction for snap_scaffold_5-snap.381-T1
Valid prediction for Augustus_model.g7543.t1
Valid prediction for snap_scaffold_5-snap.403-T1
Valid prediction for Augustus_model.g7546.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7235, rend_intergenic: 3263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27970, rend_intergenic: 22738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40872, rend_intergenic: 36670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51603, rend_intergenic: 47713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78751, rend_intergenic: 51870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84293, rend_intergenic: 80710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99345, rend_intergenic: 89509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115689, rend_intergenic: 106855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134012, rend_intergenic: 115714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 137782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144834, rend_intergenic: 139419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162336, rend_intergenic: 145162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163544, rend_intergenic: 163301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191133, rend_intergenic: 165856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198758, rend_intergenic: 198550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201481, rend_intergenic: 201021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203693, rend_intergenic: 202754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208443, rend_intergenic: 205537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224923, rend_intergenic: 210431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229724, rend_intergenic: 226076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231588, rend_intergenic: 229803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236151, rend_intergenic: 231597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258832, rend_intergenic: 236162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272579, rend_intergenic: 264600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 292684, rend_intergenic: 275212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296731, rend_intergenic: 294283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 311182, rend_intergenic: 303105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 339114, rend_intergenic: 335185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 347444, rend_intergenic: 339821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 370293, rend_intergenic: 361093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 379246
-exon list size: 518


building trellis

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92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 7235, rend_intergenic: 3263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27970, rend_intergenic: 22738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40872, rend_intergenic: 36670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51603, rend_intergenic: 47713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78751, rend_intergenic: 51870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84293, rend_intergenic: 80710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99345, rend_intergenic: 89509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115689, rend_intergenic: 106855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134012, rend_intergenic: 115714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 137782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144834, rend_intergenic: 139419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162336, rend_intergenic: 145162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163544, rend_intergenic: 163301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191133, rend_intergenic: 165856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198758, rend_intergenic: 198550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201481, rend_intergenic: 201021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203693, rend_intergenic: 202754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208443, rend_intergenic: 205537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224923, rend_intergenic: 210431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229724, rend_intergenic: 226076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231588, rend_intergenic: 229803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236151, rend_intergenic: 231597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258832, rend_intergenic: 236162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272579, rend_intergenic: 264600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 292684, rend_intergenic: 275212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296731, rend_intergenic: 294283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 311182, rend_intergenic: 303105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 339114, rend_intergenic: 335185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 347444, rend_intergenic: 339821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 370293, rend_intergenic: 361093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support