-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_2669543-2936189

-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_25-snap.559-T1
Valid prediction for snap_scaffold_25-snap.552-T1
Valid prediction for pasa_asmbl_33399.p1
Valid prediction for snap_scaffold_25-snap.553-T1
Valid prediction for snap_scaffold_25-snap.554-T1
Valid prediction for snap_scaffold_25-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_53779-T1
Valid prediction for GlimmerHMM_glimmerT_53776-T1
Valid prediction for GlimmerHMM_glimmerT_53780-T1
Valid prediction for CodingQuarry_transcript_38655-T1
Valid prediction for GlimmerHMM_glimmerT_53785-T1
Valid prediction for snap_scaffold_25-snap.560-T1
Couldn't classify 21631, 21728
Sorry, prediction pasa_asmbl_33403.p1 fails validation.
(ATG)	 GG	17866-17985	GT	AGG
(GCG)	 AG	18352-18454	GT	CGG
(AGG)	 AG	18562-18677	GT	CGG
(GTT)	 AG	19277-19342	GT	CCG
(GGA)	 AG	19779-19892	GT	AGG
(GAT)	 AG	20790-20907	GT	AGG
(GTC)	 AG	21631-21728	GG	AAG
-recovered pasa_asmbl_33403.p1, initial, 17866, 17985
-recovered pasa_asmbl_33403.p1, internal, 18352, 18454
-recovered pasa_asmbl_33403.p1, internal, 18562, 18677
-recovered pasa_asmbl_33403.p1, internal, 19277, 19342
-recovered pasa_asmbl_33403.p1, internal, 19779, 19892
-recovered pasa_asmbl_33403.p1, internal, 20790, 20907
Valid prediction for snap_scaffold_25-snap.550-T1
Valid prediction for snap_scaffold_25-snap.555-T1
Valid prediction for Augustus_model.g35703.t1
Valid prediction for snap_scaffold_25-snap.544-T1
Valid prediction for snap_scaffold_25-snap.548-T1
Valid prediction for snap_scaffold_25-snap.592-T1
Valid prediction for snap_scaffold_25-snap.593-T1
Valid prediction for snap_scaffold_25-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_53769-T1
Valid prediction for Augustus_model.g35701.t1
Valid prediction for snap_scaffold_25-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_53772-T1
Valid prediction for snap_scaffold_25-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_53791-T1
Valid prediction for snap_scaffold_25-snap.563-T1
Valid prediction for snap_scaffold_25-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_53783-T1
Valid prediction for GlimmerHMM_glimmerT_53800-T1
Valid prediction for Augustus_model.g35702.t1
Valid prediction for snap_scaffold_25-snap.572-T1
Valid prediction for GlimmerHMM_glimmerT_53787-T1
Valid prediction for GlimmerHMM_glimmerT_53799-T1
Valid prediction for GlimmerHMM_glimmerT_53777-T1
Valid prediction for Augustus_model.g35705.t1
Valid prediction for snap_scaffold_25-snap.584-T1
Valid prediction for GlimmerHMM_glimmerT_53784-T1
Valid prediction for Augustus_model.g35704.t1
Valid prediction for snap_scaffold_25-snap.557-T1
Valid prediction for CodingQuarry_transcript_38656-T1
Valid prediction for snap_scaffold_25-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_53778-T1
Valid prediction for GlimmerHMM_glimmerT_53775-T1
Valid prediction for GlimmerHMM_glimmerT_53773-T1
Valid prediction for snap_scaffold_25-snap.549-T1
Valid prediction for snap_scaffold_25-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_53801-T1
Valid prediction for snap_scaffold_25-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_53792-T1
Valid prediction for Augustus_model.g35706.t1
Valid prediction for snap_scaffold_25-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_53797-T1
Couldn't classify 225951, 226079
Sorry, prediction pasa_asmbl_33405.p1 fails validation.
(CAG)	 AT	225951-226079	GT	AGG
(GAG)	 AG	226241-226383	GT	AGG
(GAT)	 AG	226774-226950	GT	GTG
(CTG)	 AG	227485-227559	GT	GAG
(AGG)	 AG	227711-227881	GT	GTG
(GGT)	 AG	228856-229054	GC	GAG
-recovered pasa_asmbl_33405.p1, terminal, 227485, 227559
-recovered pasa_asmbl_33405.p1, terminal, 228856, 229054
-recovered pasa_asmbl_33405.p1, internal, 226241, 226383
-recovered pasa_asmbl_33405.p1, internal, 226774, 226950
-recovered pasa_asmbl_33405.p1, internal, 227485, 227559
-recovered pasa_asmbl_33405.p1, internal, 227711, 227881
-recovered pasa_asmbl_33405.p1, internal, 228856, 229054
Valid prediction for CodingQuarry_transcript_38654-T1
Valid prediction for GlimmerHMM_glimmerT_53793-T1
Valid prediction for snap_scaffold_25-snap.578-T1
Valid prediction for Augustus_model.g35699.t1
Valid prediction for Augustus_model.g35700.t1
Valid prediction for snap_scaffold_25-snap.589-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53782-T1
Valid prediction for snap_scaffold_25-snap.588-T1
Valid prediction for HiQ_model.g35697.t1
Valid prediction for GlimmerHMM_glimmerT_53790-T1
Couldn't classify 23138, 23356
Sorry, prediction pasa_asmbl_33922.p1 fails validation.
(TCC)	 TC	23138-23356	GT	AGG
(GCA)	 AG	23562-23675	GT	AGG
(AAG)	 AG	23811-23867	GT	CGG
(GCG)	 AG	23992-24120	GT	AGG
(GTT)	 AG	24351-24438	GT	AGG
(ATA)	 AG	24592-24602	AC	GAA
-recovered pasa_asmbl_33922.p1, terminal, 24592, 24602
-recovered pasa_asmbl_33922.p1, internal, 23562, 23675
-recovered pasa_asmbl_33922.p1, internal, 23811, 23867
-recovered pasa_asmbl_33922.p1, internal, 23992, 24120
-recovered pasa_asmbl_33922.p1, internal, 24351, 24438

-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 GlimmerHMM_glimmerT_53788-T1
Valid prediction for snap_scaffold_25-snap.543-T1
Valid prediction for snap_scaffold_25-snap.591-T1
Valid prediction for snap_scaffold_25-snap.558-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.545-T1
Valid prediction for snap_scaffold_25-snap.570-T1
Valid prediction for snap_scaffold_25-snap.585-T1
Valid prediction for snap_scaffold_25-snap.581-T1
Valid prediction for snap_scaffold_25-snap.561-T1
Valid prediction for snap_scaffold_25-snap.574-T1
Valid prediction for snap_scaffold_25-snap.551-T1
Valid prediction for snap_scaffold_25-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_53770-T1
Valid prediction for snap_scaffold_25-snap.590-T1
Valid prediction for snap_scaffold_25-snap.569-T1
Valid prediction for snap_scaffold_25-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_53794-T1
Valid prediction for snap_scaffold_25-snap.573-T1
Valid prediction for GlimmerHMM_glimmerT_53774-T1
Valid prediction for GlimmerHMM_glimmerT_53786-T1
Valid prediction for snap_scaffold_25-snap.562-T1
Valid prediction for snap_scaffold_25-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_53796-T1
Valid prediction for GlimmerHMM_glimmerT_53789-T1
Valid prediction for snap_scaffold_25-snap.547-T1
Valid prediction for Augustus_model.g35698.t1
Valid prediction for GlimmerHMM_glimmerT_53781-T1
Valid prediction for GlimmerHMM_glimmerT_53798-T1
Valid prediction for snap_scaffold_25-snap.583-T1
Valid prediction for snap_scaffold_25-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_53771-T1
Valid prediction for snap_scaffold_25-snap.586-T1
Valid prediction for snap_scaffold_25-snap.556-T1
Valid prediction for snap_scaffold_25-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_53795-T1
Valid prediction for snap_scaffold_25-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_53802-T1
Valid prediction for snap_scaffold_25-snap.587-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17072, rend_intergenic: 11763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21737, rend_intergenic: 19526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41349, rend_intergenic: 22813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46710, rend_intergenic: 45688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50383, rend_intergenic: 47548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55563, rend_intergenic: 50396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61810, rend_intergenic: 57144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69125, rend_intergenic: 61964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73829, rend_intergenic: 69174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76338, rend_intergenic: 74262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133974, rend_intergenic: 85610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159578, rend_intergenic: 136970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174485, rend_intergenic: 160804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182825, rend_intergenic: 177867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183725, rend_intergenic: 182885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185664, rend_intergenic: 183992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190249, rend_intergenic: 185982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210448, rend_intergenic: 192137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230743, rend_intergenic: 214509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262437, rend_intergenic: 235610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266647
-exon list size: 430


building trellis

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24.8    
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29.4    
29.6    
29.9    
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30.6    
30.8    
31.0    
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31.9    
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32.4    
32.6    
32.9    
33.1    
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33.8    
34.0    
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36.1    
36.3    
36.6    
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39.1    
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39.6    
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40.0    
40.3    
40.5    
40.7    
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41.7    
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42.1    
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42.6    
42.8    
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44.9    
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83.6    
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86.1    
86.3    
86.6    
86.8    
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87.3    
87.5    
87.7    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
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94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
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97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 17072, rend_intergenic: 11763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21737, rend_intergenic: 19526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41349, rend_intergenic: 22813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46710, rend_intergenic: 45688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50383, rend_intergenic: 47548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55563, rend_intergenic: 50396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61810, rend_intergenic: 57144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69125, rend_intergenic: 61964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73829, rend_intergenic: 69174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76338, rend_intergenic: 74262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133974, rend_intergenic: 85610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159578, rend_intergenic: 136970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174485, rend_intergenic: 160804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182825, rend_intergenic: 177867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183725, rend_intergenic: 182885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185664, rend_intergenic: 183992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190249, rend_intergenic: 185982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210448, rend_intergenic: 192137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230743, rend_intergenic: 214509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262437, rend_intergenic: 235610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support