-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_3189754-3435427

-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_3-snap.711-T1
Valid prediction for snap_scaffold_3-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_6269-T1
Valid prediction for snap_scaffold_3-snap.703-T1
Valid prediction for snap_scaffold_3-snap.700-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_6255-T1
Valid prediction for snap_scaffold_3-snap.702-T1
Valid prediction for snap_scaffold_3-snap.744-T1
Valid prediction for snap_scaffold_3-snap.707-T1
Valid prediction for Augustus_model.g4079.t1
Valid prediction for Augustus_model.g4065.t1
Valid prediction for pasa_asmbl_39938.p1
Valid prediction for snap_scaffold_3-snap.736-T1
Valid prediction for pasa_asmbl_39943.p1
Valid prediction for snap_scaffold_3-snap.710-T1
Valid prediction for CodingQuarry_transcript_46108-T1
Valid prediction for snap_scaffold_3-snap.733-T1
Valid prediction for snap_scaffold_3-snap.738-T1
Valid prediction for snap_scaffold_3-snap.727-T1
Valid prediction for snap_scaffold_3-snap.698-T1
Valid prediction for snap_scaffold_3-snap.724-T1
Valid prediction for GlimmerHMM_glimmerT_6276-T1
Valid prediction for GlimmerHMM_glimmerT_6253-T1
Valid prediction for pasa_asmbl_39947.p1
Valid prediction for snap_scaffold_3-snap.747-T1
Valid prediction for CodingQuarry_transcript_46109-T1
Valid prediction for GlimmerHMM_glimmerT_6249-T1
Valid prediction for CodingQuarry_transcript_46107-T1
Valid prediction for Augustus_model.g4067.t1
Valid prediction for snap_scaffold_3-snap.709-T1
Valid prediction for snap_scaffold_3-snap.730-T1
Valid prediction for snap_scaffold_3-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_6250-T1
Valid prediction for GlimmerHMM_glimmerT_6267-T1
Valid prediction for snap_scaffold_3-snap.715-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_3-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_6273-T1
Valid prediction for GlimmerHMM_glimmerT_6261-T1
Valid prediction for snap_scaffold_3-snap.717-T1
Valid prediction for pasa_asmbl_38769.p1
Couldn't classify 243264, 243572
Sorry, prediction pasa_asmbl_38758.p1 fails validation.
(GAC)	 CA	243264-243572	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_6262-T1
Valid prediction for GlimmerHMM_glimmerT_6271-T1
Valid prediction for GlimmerHMM_glimmerT_6260-T1
Valid prediction for GlimmerHMM_glimmerT_6268-T1
Valid prediction for snap_scaffold_3-snap.705-T1
Valid prediction for CodingQuarry_transcript_46116-T1
Valid prediction for snap_scaffold_3-snap.737-T1
Valid prediction for snap_scaffold_3-snap.728-T1
Valid prediction for snap_scaffold_3-snap.739-T1
Valid prediction for Augustus_model.g4072.t1
Valid prediction for Augustus_model.g4066.t1
Valid prediction for Augustus_model.g4068.t1
Valid prediction for snap_scaffold_3-snap.740-T1
Valid prediction for snap_scaffold_3-snap.722-T1
Valid prediction for CodingQuarry_transcript_46111-T1
Valid prediction for snap_scaffold_3-snap.714-T1
Valid prediction for Augustus_model.g4076.t1
Valid prediction for pasa_asmbl_38775.p2
Valid prediction for snap_scaffold_3-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_6259-T1
Valid prediction for HiQ_model.g4070.t1
Valid prediction for snap_scaffold_3-snap.742-T1
Couldn't classify 116470, 117535
Couldn't classify 117608, 117623
Sorry, prediction CodingQuarry_transcript_46115-T1 fails validation.
(ATG)	 AT	115888-115894	GT	AGG
(ATC)	 AG	116470-117535	CT	ACC
(CTC)	 AC	117608-117623	TC	AAT
-recovered CodingQuarry_transcript_46115-T1, initial, 115888, 115894
Valid prediction for snap_scaffold_3-snap.729-T1
Valid prediction for CodingQuarry_transcript_46110-T1
Valid prediction for HiQ_model.g4073.t1
Valid prediction for GlimmerHMM_glimmerT_6257-T1
Valid prediction for snap_scaffold_3-snap.723-T1
Valid prediction for snap_scaffold_3-snap.712-T1
Valid prediction for snap_scaffold_3-snap.721-T1
Valid prediction for snap_scaffold_3-snap.697-T1
Valid prediction for snap_scaffold_3-snap.706-T1
Valid prediction for GlimmerHMM_glimmerT_6275-T1
Valid prediction for snap_scaffold_3-snap.704-T1
Valid prediction for snap_scaffold_3-snap.718-T1
Valid prediction for snap_scaffold_3-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_6270-T1
Valid prediction for Augustus_model.g4064.t1
Valid prediction for Augustus_model.g4080.t1
Valid prediction for Augustus_model.g4077.t1
Valid prediction for Augustus_model.g4069.t1
Valid prediction for GlimmerHMM_glimmerT_6252-T1
Valid prediction for CodingQuarry_transcript_46112-T1
Valid prediction for Augustus_model.g4078.t1
Valid prediction for pasa_asmbl_38761.p1
Valid prediction for snap_scaffold_3-snap.716-T1
Valid prediction for GlimmerHMM_glimmerT_6264-T1
Valid prediction for GlimmerHMM_glimmerT_6263-T1
Valid prediction for GlimmerHMM_glimmerT_6265-T1
Couldn't classify 232090, 232419
Sorry, prediction pasa_asmbl_38759.p1 fails validation.
(CTG)	 TG	232090-232419	GG	CTG
Valid prediction for snap_scaffold_3-snap.743-T1
Valid prediction for HiQ_model.g4074.t1
Valid prediction for Augustus_model.g4071.t1
Valid prediction for GlimmerHMM_glimmerT_6272-T1
Valid prediction for GlimmerHMM_glimmerT_6274-T1
Valid prediction for snap_scaffold_3-snap.748-T1
Valid prediction for snap_scaffold_3-snap.699-T1
Valid prediction for snap_scaffold_3-snap.746-T1
Valid prediction for snap_scaffold_3-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_6256-T1
Valid prediction for GlimmerHMM_glimmerT_6266-T1
Valid prediction for GlimmerHMM_glimmerT_6251-T1
Valid prediction for snap_scaffold_3-snap.719-T1
Valid prediction for snap_scaffold_3-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_6254-T1
Valid prediction for snap_scaffold_3-snap.734-T1
Valid prediction for snap_scaffold_3-snap.732-T1
Valid prediction for Augustus_model.g4075.t1
Couldn't classify 153073, 153086
Couldn't classify 153688, 153818
Sorry, prediction pasa_asmbl_38768.p1 fails validation.
(TAT)	 CA	153073-153086	GT	AGG
(GTC)	 AG	153253-153560	GT	GGG
(TTC)	 AG	153688-153818	GA	AGG
-recovered pasa_asmbl_38768.p1, internal, 153253, 153560
Valid prediction for pasa_asmbl_38771.p2
Valid prediction for GlimmerHMM_glimmerT_6258-T1
Valid prediction for snap_scaffold_3-snap.731-T1
Valid prediction for snap_scaffold_3-snap.726-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13561, rend_intergenic: 9018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28949, rend_intergenic: 21423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144970, rend_intergenic: 137775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151183, rend_intergenic: 148515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157406, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163805, rend_intergenic: 159598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167320, rend_intergenic: 163855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177586, rend_intergenic: 171368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181720, rend_intergenic: 178950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187727, rend_intergenic: 184198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203557, rend_intergenic: 197647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237390, rend_intergenic: 230849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240108, rend_intergenic: 239419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243590, rend_intergenic: 241253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245674
-exon list size: 392


building trellis

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25.4    
25.6    
25.9    
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26.6    
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27.7    
27.9    
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28.7    
28.9    
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30.7    
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33.8    
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34.8    
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35.5    
35.8    
36.0    
36.3    
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37.3    
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38.8    
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39.6    
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40.4    
40.6    
40.9    
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42.9    
43.1    
43.4    
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44.2    
44.4    
44.7    
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45.4    
45.7    
45.9    
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96.4    
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97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 13561, rend_intergenic: 9018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28949, rend_intergenic: 21423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144970, rend_intergenic: 137775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151183, rend_intergenic: 148515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157406, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163805, rend_intergenic: 159598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167320, rend_intergenic: 163855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177586, rend_intergenic: 171368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181720, rend_intergenic: 178950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187727, rend_intergenic: 184198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203557, rend_intergenic: 197647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237390, rend_intergenic: 230849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240108, rend_intergenic: 239419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243590, rend_intergenic: 241253  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