-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_769623-952135

-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: +)Couldn't classify 161883, 162186
Sorry, prediction pasa_asmbl_37297.p1 fails validation.
(ATG)	 CC	160810-161270	GT	CGG
(AGT)	 AG	161883-162186	CC	CCC
-recovered pasa_asmbl_37297.p1, initial, 160810, 161270
Valid prediction for GlimmerHMM_glimmerT_58061-T1
Valid prediction for GlimmerHMM_glimmerT_58059-T1
Valid prediction for snap_scaffold_28-snap.179-T1
Valid prediction for snap_scaffold_28-snap.205-T1
Valid prediction for Augustus_model.g38436.t1
Valid prediction for snap_scaffold_28-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_58064-T1
Valid prediction for snap_scaffold_28-snap.169-T1
Valid prediction for Augustus_model.g38438.t1
Valid prediction for snap_scaffold_28-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_58063-T1
Valid prediction for snap_scaffold_28-snap.200-T1
Valid prediction for snap_scaffold_28-snap.172-T1
Valid prediction for snap_scaffold_28-snap.170-T1
Valid prediction for snap_scaffold_28-snap.208-T1
Valid prediction for Augustus_model.g38432.t1
Valid prediction for snap_scaffold_28-snap.193-T1
Valid prediction for HiQ_model.g38433.t1
Valid prediction for Augustus_model.g38431.t1
Valid prediction for snap_scaffold_28-snap.166-T1
Valid prediction for snap_scaffold_28-snap.197-T1
Valid prediction for GlimmerHMM_glimmerT_58046-T1
Valid prediction for snap_scaffold_28-snap.203-T1
Valid prediction for snap_scaffold_28-snap.168-T1
Valid prediction for snap_scaffold_28-snap.173-T1
Valid prediction for snap_scaffold_28-snap.183-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g38423.t1
Valid prediction for snap_scaffold_28-snap.201-T1
Valid prediction for snap_scaffold_28-snap.196-T1
Valid prediction for snap_scaffold_28-snap.194-T1
Valid prediction for pasa_asmbl_37296.p1
Couldn't classify 143494, 144516
Sorry, prediction pasa_asmbl_37293.p1 fails validation.
(ATG)	 AG	142649-142894	GT	AGG
(TTG)	 AG	143494-144516	CC	ACC
-recovered pasa_asmbl_37293.p1, initial, 142649, 142894
-recovered pasa_asmbl_37293.p1, internal, 142649, 142894
Valid prediction for snap_scaffold_28-snap.176-T1
Valid prediction for CodingQuarry_transcript_43523-T1
Valid prediction for GlimmerHMM_glimmerT_58041-T1
Valid prediction for GlimmerHMM_glimmerT_58053-T1
Valid prediction for HiQ_model.g38435.t1
Valid prediction for snap_scaffold_28-snap.187-T1
Valid prediction for GlimmerHMM_glimmerT_58067-T1
Valid prediction for Augustus_model.g38430.t1
Valid prediction for GlimmerHMM_glimmerT_58049-T1
Valid prediction for Augustus_model.g38427.t1
Valid prediction for snap_scaffold_28-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_58051-T1
Valid prediction for GlimmerHMM_glimmerT_58058-T1
Valid prediction for snap_scaffold_28-snap.202-T1
Valid prediction for GlimmerHMM_glimmerT_58060-T1
Valid prediction for snap_scaffold_28-snap.207-T1
Valid prediction for snap_scaffold_28-snap.191-T1
Valid prediction for Augustus_model.g38434.t1
Valid prediction for GlimmerHMM_glimmerT_58043-T1
Valid prediction for GlimmerHMM_glimmerT_58055-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_28-snap.167-T1
Valid prediction for snap_scaffold_28-snap.186-T1
Valid prediction for HiQ_model.g38424.t1
Valid prediction for Augustus_model.g38426.t1
Valid prediction for GlimmerHMM_glimmerT_58045-T1
Valid prediction for GlimmerHMM_glimmerT_58062-T1
Valid prediction for snap_scaffold_28-snap.171-T1
Valid prediction for snap_scaffold_28-snap.185-T1
Valid prediction for snap_scaffold_28-snap.206-T1
Valid prediction for snap_scaffold_28-snap.190-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_43519-T1
Valid prediction for snap_scaffold_28-snap.180-T1
Valid prediction for Augustus_model.g38428.t1
Valid prediction for GlimmerHMM_glimmerT_58065-T1
Valid prediction for GlimmerHMM_glimmerT_58054-T1
Valid prediction for snap_scaffold_28-snap.174-T1
Valid prediction for snap_scaffold_28-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_58066-T1
Valid prediction for GlimmerHMM_glimmerT_58050-T1
Valid prediction for GlimmerHMM_glimmerT_58047-T1
Valid prediction for GlimmerHMM_glimmerT_58044-T1
Valid prediction for snap_scaffold_28-snap.204-T1
Valid prediction for Augustus_model.g38437.t1
Valid prediction for snap_scaffold_28-snap.184-T1
Valid prediction for CodingQuarry_transcript_43520-T1
Valid prediction for snap_scaffold_28-snap.199-T1
Couldn't classify 2753, 2783
Couldn't classify 6146, 6204
Sorry, prediction pasa_asmbl_37948.p1 fails validation.
(AGC)	 TC	2753-2783	GT	CAG
(CGC)	 AG	4884-5086	GT	AGG
(GGA)	 AG	5473-5560	GT	ACG
(GCA)	 AG	5739-5852	GT	AGG
(TGT)	 AG	6146-6204	GT	TGG
-recovered pasa_asmbl_37948.p1, internal, 4884, 5086
-recovered pasa_asmbl_37948.p1, internal, 5473, 5560
-recovered pasa_asmbl_37948.p1, internal, 5739, 5852
-recovered pasa_asmbl_37948.p1, internal, 6146, 6204
Valid prediction for snap_scaffold_28-snap.195-T1
Valid prediction for snap_scaffold_28-snap.188-T1
Couldn't classify 148091, 148189
Sorry, prediction pasa_asmbl_37939.p1 fails validation.
(ATG)	 AG	136714-136875	GT	AGG
(TGG)	 AG	139580-139649	GT	TGG
(CCA)	 AG	139736-140036	GT	AGG
(GGT)	 AG	142056-142130	GT	AGG
(GAT)	 AG	142260-142349	GT	AGG
(TGA)	 AG	144147-144240	GT	TGG
(GTT)	 AG	144493-144608	GT	AGG
(ATT)	 AG	144713-144768	GT	GGG
(GTA)	 AG	144884-144969	GT	AGG
(TAC)	 AG	145099-145227	GT	AGG
(CAC)	 AG	148091-148189	CC	CCC
-recovered pasa_asmbl_37939.p1, initial, 136714, 136875
-recovered pasa_asmbl_37939.p1, internal, 136714, 136875
-recovered pasa_asmbl_37939.p1, internal, 139580, 139649
-recovered pasa_asmbl_37939.p1, internal, 139736, 140036
-recovered pasa_asmbl_37939.p1, internal, 142056, 142130
-recovered pasa_asmbl_37939.p1, internal, 142260, 142349
-recovered pasa_asmbl_37939.p1, internal, 144147, 144240
-recovered pasa_asmbl_37939.p1, internal, 144493, 144608
-recovered pasa_asmbl_37939.p1, internal, 144713, 144768
-recovered pasa_asmbl_37939.p1, internal, 144884, 144969
-recovered pasa_asmbl_37939.p1, internal, 145099, 145227
Couldn't classify 158554, 158617
Sorry, prediction pasa_asmbl_38600.p1 fails validation.
(GCT)	 AG	158554-158617	GT	CGG
(CTA)	 AG	159269-159372	GT	ATG
(TCC)	 AG	160445-160497	GT	CAG
(AGG)	 AG	160976-161095	GT	AGG
(GAT)	 AG	161230-161314	GT	AAG
(AAA)	 AG	161501-161593	GT	AGG
(GTC)	 AG	161892-161966	GT	CGG
(CTG)	 AG	162168-162241	GT	AGG
(CTA)	 AG	162412-162523	GT	GGG
(GGA)	 AG	162722-162790	GT	AGG
(CCT)	 AG	162874-162937	GT	CTG
(ATA)	 AG	163721-163830	CC	AAC
-recovered pasa_asmbl_38600.p1, terminal, 163721, 163830
-recovered pasa_asmbl_38600.p1, internal, 158554, 158617
-recovered pasa_asmbl_38600.p1, internal, 159269, 159372
-recovered pasa_asmbl_38600.p1, internal, 160445, 160497
-recovered pasa_asmbl_38600.p1, internal, 160976, 161095
-recovered pasa_asmbl_38600.p1, internal, 161230, 161314
-recovered pasa_asmbl_38600.p1, internal, 161501, 161593
-recovered pasa_asmbl_38600.p1, internal, 161892, 161966
-recovered pasa_asmbl_38600.p1, internal, 162168, 162241
-recovered pasa_asmbl_38600.p1, internal, 162412, 162523
-recovered pasa_asmbl_38600.p1, internal, 162722, 162790
-recovered pasa_asmbl_38600.p1, internal, 162874, 162937
Valid prediction for GlimmerHMM_glimmerT_58052-T1
Valid prediction for pasa_asmbl_37944.p1
Couldn't classify 7072, 7161
Couldn't classify 8608, 9138
Sorry, prediction pasa_asmbl_37947.p1 fails validation.
(CTG)	 AC	7072-7161	GT	CAG
(GGT)	 AG	7325-7398	GT	AGG
(GTT)	 AG	7524-7645	GT	AGG
(CCA)	 AG	8173-8327	GT	AGG
(TGT)	 AG	8608-9138	CA	AAC
-recovered pasa_asmbl_37947.p1, internal, 7325, 7398
-recovered pasa_asmbl_37947.p1, internal, 7524, 7645
-recovered pasa_asmbl_37947.p1, internal, 8173, 8327
Valid prediction for snap_scaffold_28-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_58048-T1
Valid prediction for Augustus_model.g38425.t1
Valid prediction for snap_scaffold_28-snap.177-T1
Valid prediction for pasa_asmbl_37942.p1
Valid prediction for GlimmerHMM_glimmerT_58042-T1
Valid prediction for snap_scaffold_28-snap.175-T1
Valid prediction for Augustus_model.g38439.t1
Valid prediction for Augustus_model.g38422.t1
Valid prediction for Augustus_model.g38429.t1
Valid prediction for CodingQuarry_transcript_43521-T1
Valid prediction for GlimmerHMM_glimmerT_58057-T1
Valid prediction for GlimmerHMM_glimmerT_58056-T1
Valid prediction for snap_scaffold_28-snap.178-T1
Valid prediction for CodingQuarry_transcript_43522-T1
Valid prediction for GlimmerHMM_glimmerT_58068-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21459, rend_intergenic: 18343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25279, rend_intergenic: 22120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44616, rend_intergenic: 39393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57647, rend_intergenic: 51519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66346, rend_intergenic: 64305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113669, rend_intergenic: 66356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117617, rend_intergenic: 115074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119567, rend_intergenic: 117832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120498, rend_intergenic: 119813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137669, rend_intergenic: 120502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154032, rend_intergenic: 150660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170023, rend_intergenic: 169698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174378, rend_intergenic: 172936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179981, rend_intergenic: 174877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182513
-exon list size: 403


building trellis

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25.9    
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32.6    
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34.6    
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35.6    
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37.3    
37.5    
37.8    
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38.5    
38.8    
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39.5    
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40.0    
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41.2    
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42.5    
42.7    
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44.4    
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44.9    
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98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 21459, rend_intergenic: 18343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25279, rend_intergenic: 22120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44616, rend_intergenic: 39393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57647, rend_intergenic: 51519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66346, rend_intergenic: 64305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113669, rend_intergenic: 66356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117617, rend_intergenic: 115074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119567, rend_intergenic: 117832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120498, rend_intergenic: 119813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137669, rend_intergenic: 120502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154032, rend_intergenic: 150660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170023, rend_intergenic: 169698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174378, rend_intergenic: 172936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179981, rend_intergenic: 174877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support