-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_3794462-4010440

-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_42094-T1
Valid prediction for snap_scaffold_18-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_42078-T1
Valid prediction for GlimmerHMM_glimmerT_42086-T1
Valid prediction for Augustus_model.g28027.t1
Valid prediction for snap_scaffold_18-snap.791-T1
Valid prediction for snap_scaffold_18-snap.817-T1
Valid prediction for snap_scaffold_18-snap.786-T1
Valid prediction for snap_scaffold_18-snap.818-T1
Valid prediction for HiQ_model.g28024.t1
Valid prediction for snap_scaffold_18-snap.812-T1
Valid prediction for GlimmerHMM_glimmerT_42075-T1
Valid prediction for Augustus_model.g28038.t1
Valid prediction for HiQ_model.g28021.t1
Valid prediction for Augustus_model.g28032.t1
Valid prediction for GlimmerHMM_glimmerT_42092-T1
Valid prediction for pasa_asmbl_20484.p1
Valid prediction for GlimmerHMM_glimmerT_42074-T1
Valid prediction for Augustus_model.g28035.t1
Valid prediction for snap_scaffold_18-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_42077-T1
Valid prediction for Augustus_model.g28023.t1
Valid prediction for GlimmerHMM_glimmerT_42080-T1
Valid prediction for snap_scaffold_18-snap.798-T1
Valid prediction for snap_scaffold_18-snap.808-T1
Couldn't classify 78216, 78299
Sorry, prediction pasa_asmbl_20486.p1 fails validation.
(GTG)	 CA	78216-78299	GT	AGG
(ATG)	 AG	79609-79720	GT	AGG
(GGC)	 AG	80803-80924	GT	GGG
(ATA)	 AG	83221-83418	GC	GAG
-recovered pasa_asmbl_20486.p1, initial, 79609, 79720
-recovered pasa_asmbl_20486.p1, terminal, 83221, 83418
-recovered pasa_asmbl_20486.p1, internal, 79609, 79720
-recovered pasa_asmbl_20486.p1, internal, 80803, 80924
-recovered pasa_asmbl_20486.p1, internal, 83221, 83418
Valid prediction for Augustus_model.g28036.t1
Valid prediction for snap_scaffold_18-snap.824-T1
Valid prediction for snap_scaffold_18-snap.826-T1
Valid prediction for snap_scaffold_18-snap.822-T1
Couldn't classify 83510, 83851
Sorry, prediction pasa_asmbl_21116.p1 fails validation.
(AGA)	 AC	83510-83851	AG	AAA
Valid prediction for Augustus_model.g28030.t1
Valid prediction for snap_scaffold_18-snap.816-T1
Valid prediction for snap_scaffold_18-snap.811-T1
Valid prediction for GlimmerHMM_glimmerT_42093-T1
Valid prediction for snap_scaffold_18-snap.819-T1
Couldn't classify 141284, 141314
Sorry, prediction pasa_asmbl_20490.p1 fails validation.
(GAG)	 AG	141284-141314	GT	AGG
(ACT)	 AG	141621-141763	GT	AGG
(AAT)	 AG	142232-142332	GT	AGG
(GTT)	 AG	142481-142583	GG	GAG
-recovered pasa_asmbl_20490.p1, terminal, 142481, 142583
-recovered pasa_asmbl_20490.p1, internal, 141284, 141314
-recovered pasa_asmbl_20490.p1, internal, 141621, 141763
-recovered pasa_asmbl_20490.p1, internal, 142232, 142332
Valid prediction for GlimmerHMM_glimmerT_42076-T1
Valid prediction for GlimmerHMM_glimmerT_42088-T1
Valid prediction for GlimmerHMM_glimmerT_42099-T1
Valid prediction for GlimmerHMM_glimmerT_42091-T1
Valid prediction for snap_scaffold_18-snap.789-T1
Valid prediction for snap_scaffold_18-snap.792-T1
Valid prediction for Augustus_model.g28026.t1
Valid prediction for snap_scaffold_18-snap.783-T1
Valid prediction for snap_scaffold_18-snap.797-T1
Valid prediction for snap_scaffold_18-snap.801-T1
Valid prediction for snap_scaffold_18-snap.800-T1
Valid prediction for Augustus_model.g28039.t1
Valid prediction for Augustus_model.g28022.t1
Valid prediction for GlimmerHMM_glimmerT_42084-T1
Valid prediction for snap_scaffold_18-snap.795-T1
Valid prediction for snap_scaffold_18-snap.807-T1
Valid prediction for snap_scaffold_18-snap.820-T1
Valid prediction for pasa_asmbl_20482.p1
Valid prediction for GlimmerHMM_glimmerT_42097-T1
Valid prediction for GlimmerHMM_glimmerT_42083-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_18-snap.821-T1
Valid prediction for snap_scaffold_18-snap.799-T1
Valid prediction for Augustus_model.g28025.t1
Valid prediction for snap_scaffold_18-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_42079-T1
Valid prediction for snap_scaffold_18-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_42101-T1
Valid prediction for pasa_asmbl_19787.p1
Valid prediction for GlimmerHMM_glimmerT_42096-T1
Couldn't classify 97149, 97259
Couldn't classify 98183, 98304
Sorry, prediction pasa_asmbl_19781.p1 fails validation.
(TTC)	 AC	97149-97259	GT	CTG
(GTG)	 AG	97496-97817	GT	GGG
(ACA)	 AG	97981-98031	GT	GGG
(ACA)	 AG	98183-98304	CA	CAC
-recovered pasa_asmbl_19781.p1, internal, 97496, 97817
-recovered pasa_asmbl_19781.p1, internal, 97981, 98031
Valid prediction for Augustus_model.g28040.t1
Valid prediction for snap_scaffold_18-snap.813-T1
Valid prediction for snap_scaffold_18-snap.806-T1
Valid prediction for Augustus_model.g28029.t1
Valid prediction for GlimmerHMM_glimmerT_42095-T1
Valid prediction for snap_scaffold_18-snap.785-T1
Couldn't classify 98806, 99255
Sorry, prediction pasa_asmbl_19780.p1 fails validation.
(TTT)	 AC	98806-99255	GC	CAG
Valid prediction for snap_scaffold_18-snap.784-T1
Valid prediction for Augustus_model.g28033.t1
Valid prediction for CodingQuarry_transcript_23722-T1
Valid prediction for GlimmerHMM_glimmerT_42085-T1
Valid prediction for snap_scaffold_18-snap.825-T1
Valid prediction for Augustus_model.g28031.t1
Valid prediction for snap_scaffold_18-snap.788-T1
Valid prediction for Augustus_model.g28034.t1
Valid prediction for snap_scaffold_18-snap.805-T1
Valid prediction for snap_scaffold_18-snap.787-T1
Valid prediction for snap_scaffold_18-snap.823-T1
Valid prediction for snap_scaffold_18-snap.796-T1
Valid prediction for snap_scaffold_18-snap.814-T1
Valid prediction for Augustus_model.g28037.t1
Couldn't classify 99565, 99972
Sorry, prediction pasa_asmbl_20230.p1 fails validation.
(CTA)	 CT	99565-99972	AA	AAA
Valid prediction for GlimmerHMM_glimmerT_42082-T1
Valid prediction for snap_scaffold_18-snap.803-T1
Valid prediction for snap_scaffold_18-snap.804-T1
Valid prediction for snap_scaffold_18-snap.790-T1
Valid prediction for snap_scaffold_18-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_42087-T1
Valid prediction for GlimmerHMM_glimmerT_42100-T1
Valid prediction for GlimmerHMM_glimmerT_42098-T1
Valid prediction for GlimmerHMM_glimmerT_42081-T1
Valid prediction for GlimmerHMM_glimmerT_42090-T1
Valid prediction for GlimmerHMM_glimmerT_42089-T1
Valid prediction for snap_scaffold_18-snap.794-T1
Valid prediction for Augustus_model.g28028.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23043, rend_intergenic: 20969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50147, rend_intergenic: 47095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113645, rend_intergenic: 89957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134893, rend_intergenic: 129598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139306, rend_intergenic: 137077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142847, rend_intergenic: 139493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152501, rend_intergenic: 148106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181761, rend_intergenic: 179039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215979
-exon list size: 326


building trellis

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31.7    
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32.6    
32.9    
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47.6    
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48.2    
48.5    
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50.6    
50.9    
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86.3    
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88.7    
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93.0    
93.3    
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96.0    
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96.6    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 23043, rend_intergenic: 20969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50147, rend_intergenic: 47095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113645, rend_intergenic: 89957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134893, rend_intergenic: 129598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139306, rend_intergenic: 137077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142847, rend_intergenic: 139493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152501, rend_intergenic: 148106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181761, rend_intergenic: 179039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support