-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_12730349-12905935

-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_19-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_45110-T1
Valid prediction for GlimmerHMM_glimmerT_45118-T1
Valid prediction for HiQ_model.g29948.t1
Valid prediction for GlimmerHMM_glimmerT_45126-T1
Valid prediction for GlimmerHMM_glimmerT_45127-T1
Valid prediction for Augustus_model.g29936.t1
Valid prediction for snap_scaffold_19-snap.2518-T1
Valid prediction for CodingQuarry_transcript_25856-T1
Valid prediction for Augustus_model.g29950.t1
Valid prediction for snap_scaffold_19-snap.2503-T1
Valid prediction for snap_scaffold_19-snap.2500-T1
Valid prediction for snap_scaffold_19-snap.2484-T1
Couldn't classify 96879, 97009
Couldn't classify 97230, 97340
Sorry, prediction CodingQuarry_transcript_25862-T1 fails validation.
(ATG)	 AC	94933-94944	GT	AGG
(GAC)	 AG	95267-95388	GT	AGG
(GAA)	 AG	95823-95919	GT	TGG
(ACA)	 AG	96154-96529	GT	AGG
(TGG)	 AG	96879-97009	GG	CAG
(GAC)	 CG	97230-97340	GT	AGG
(ACA)	 AG	97462-97704	GG	AAG
-recovered CodingQuarry_transcript_25862-T1, initial, 94933, 94944
add_exon() Sorry, CodingQuarry_transcript_25862-T1 96154-96529-terminal-3 is invalid.
-recovered CodingQuarry_transcript_25862-T1, terminal, 96154, 96529
-recovered CodingQuarry_transcript_25862-T1, terminal, 97462, 97704
-recovered CodingQuarry_transcript_25862-T1, internal, 95267, 95388
-recovered CodingQuarry_transcript_25862-T1, internal, 95823, 95919
-recovered CodingQuarry_transcript_25862-T1, internal, 96154, 96529
Valid prediction for snap_scaffold_19-snap.2489-T1
Valid prediction for snap_scaffold_19-snap.2520-T1
Valid prediction for pasa_asmbl_21823.p1
Valid prediction for GlimmerHMM_glimmerT_45120-T1
Valid prediction for snap_scaffold_19-snap.2510-T1
Valid prediction for snap_scaffold_19-snap.2516-T1
Valid prediction for snap_scaffold_19-snap.2513-T1
Valid prediction for snap_scaffold_19-snap.2494-T1
Valid prediction for snap_scaffold_19-snap.2495-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g29937.t1
Valid prediction for GlimmerHMM_glimmerT_45123-T1
Valid prediction for snap_scaffold_19-snap.2511-T1
Valid prediction for pasa_asmbl_21821.p1
Valid prediction for GlimmerHMM_glimmerT_45113-T1
Valid prediction for GlimmerHMM_glimmerT_45128-T1
Valid prediction for snap_scaffold_19-snap.2491-T1
Valid prediction for snap_scaffold_19-snap.2486-T1
Valid prediction for snap_scaffold_19-snap.2496-T1
Valid prediction for snap_scaffold_19-snap.2505-T1
Valid prediction for CodingQuarry_transcript_25861-T1
Valid prediction for GlimmerHMM_glimmerT_45112-T1
Valid prediction for Augustus_model.g29943.t1
Valid prediction for GlimmerHMM_glimmerT_45129-T1
Valid prediction for Augustus_model.g29951.t1
Valid prediction for snap_scaffold_19-snap.2508-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 GlimmerHMM_glimmerT_45116-T1
Couldn't classify 27181, 27316
Sorry, prediction pasa_asmbl_22557.p1 fails validation.
(CTG)	 AG	27181-27316	GT	AGG
(AAC)	 AG	29020-29154	GT	GGG
(CTC)	 AG	29372-29526	GT	ACG
(GAG)	 AG	29667-29792	AG	AGA
-recovered pasa_asmbl_22557.p1, terminal, 27181, 27316
-recovered pasa_asmbl_22557.p1, terminal, 29667, 29792
-recovered pasa_asmbl_22557.p1, internal, 27181, 27316
-recovered pasa_asmbl_22557.p1, internal, 29020, 29154
-recovered pasa_asmbl_22557.p1, internal, 29372, 29526
Valid prediction for snap_scaffold_19-snap.2515-T1
Valid prediction for Augustus_model.g29945.t1
Couldn't classify 124555, 124863
Sorry, prediction pasa_asmbl_22538.p3 fails validation.
(TAC)	 AC	124555-124863	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_45122-T1
Valid prediction for snap_scaffold_19-snap.2506-T1
Valid prediction for snap_scaffold_19-snap.2493-T1
Valid prediction for snap_scaffold_19-snap.2507-T1
Valid prediction for snap_scaffold_19-snap.2492-T1
Valid prediction for Augustus_model.g29941.t1
Valid prediction for Augustus_model.g29939.t1
Valid prediction for Augustus_model.g29944.t1
Valid prediction for snap_scaffold_19-snap.2512-T1
Valid prediction for pasa_asmbl_22534.p1
Valid prediction for snap_scaffold_19-snap.2499-T1
Valid prediction for snap_scaffold_19-snap.2502-T1
Valid prediction for Augustus_model.g29946.t1
Valid prediction for snap_scaffold_19-snap.2487-T1
Valid prediction for snap_scaffold_19-snap.2509-T1
Valid prediction for snap_scaffold_19-snap.2519-T1
Valid prediction for Augustus_model.g29940.t1
Valid prediction for snap_scaffold_19-snap.2504-T1
Valid prediction for snap_scaffold_19-snap.2517-T1
Valid prediction for GlimmerHMM_glimmerT_45117-T1
Valid prediction for snap_scaffold_19-snap.2488-T1
Valid prediction for CodingQuarry_transcript_25860-T1
Valid prediction for GlimmerHMM_glimmerT_45130-T1
Valid prediction for pasa_asmbl_22548.p1
Valid prediction for snap_scaffold_19-snap.2514-T1
Valid prediction for Augustus_model.g29952.t1
Valid prediction for snap_scaffold_19-snap.2490-T1
Valid prediction for snap_scaffold_19-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_45114-T1
Valid prediction for CodingQuarry_transcript_25857-T1
Valid prediction for Augustus_model.g29949.t1
Valid prediction for snap_scaffold_19-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_45124-T1
Valid prediction for snap_scaffold_19-snap.2501-T1
Couldn't classify 137818, 137825
Sorry, prediction pasa_asmbl_22536.p1 fails validation.
(CAT)	 AC	137818-137825	GT	AGG
(ATG)	 AG	137902-138571	GT	AGG
(AGC)	 AG	139464-139499	TG	GAT
add_exon() Sorry, pasa_asmbl_22536.p1 137902-138571-initial-1 is invalid.
-recovered pasa_asmbl_22536.p1, initial, 137902, 138571
-recovered pasa_asmbl_22536.p1, terminal, 139464, 139499
-recovered pasa_asmbl_22536.p1, internal, 137902, 138571
Valid prediction for GlimmerHMM_glimmerT_45119-T1
Valid prediction for Augustus_model.g29947.t1
Couldn't classify 95138, 95236
Couldn't classify 97351, 97605
Sorry, prediction pasa_asmbl_22540.p1 fails validation.
(AAG)	 TG	95138-95236	GT	GAG
(GAC)	 AG	97351-97605	GG	AAG
Valid prediction for Augustus_model.g29953.t1
Valid prediction for GlimmerHMM_glimmerT_45121-T1
Valid prediction for GlimmerHMM_glimmerT_45111-T1
Valid prediction for Augustus_model.g29942.t1
Valid prediction for GlimmerHMM_glimmerT_45125-T1
Valid prediction for HiQ_model.g29938.t1
Valid prediction for GlimmerHMM_glimmerT_45115-T1
Valid prediction for CodingQuarry_transcript_25863-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12749, rend_intergenic: 5841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17040, rend_intergenic: 14215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41324, rend_intergenic: 33904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48310, rend_intergenic: 41719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81718, rend_intergenic: 78491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83958, rend_intergenic: 82046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106606, rend_intergenic: 103678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107620, rend_intergenic: 106681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116214, rend_intergenic: 110373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119452, rend_intergenic: 117063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130697, rend_intergenic: 119948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132260, rend_intergenic: 131143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158076, rend_intergenic: 149870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163718, rend_intergenic: 160041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169147, rend_intergenic: 164673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175587
-exon list size: 379


building trellis

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18.9    
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27.6    
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28.6    
28.9    
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31.8    
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32.3    
32.5    
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33.3    
33.6    
33.9    
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34.4    
34.6    
34.9    
35.2    
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35.7    
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38.6    
38.8    
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39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
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42.0    
42.3    
42.5    
42.8    
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43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
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47.0    
47.2    
47.5    
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48.0    
48.3    
48.6    
48.8    
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49.3    
49.6    
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50.4    
50.7    
50.9    
51.2    
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51.7    
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55.4    
55.6    
55.9    
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56.7    
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58.3    
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85.3    
85.6    
85.8    
86.1    
86.4    
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87.1    
87.4    
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87.9    
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88.7    
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89.2    
89.5    
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90.3    
90.6    
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91.6    
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92.4    
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95.5    
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96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 12749, rend_intergenic: 5841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17040, rend_intergenic: 14215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41324, rend_intergenic: 33904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48310, rend_intergenic: 41719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81718, rend_intergenic: 78491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83958, rend_intergenic: 82046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106606, rend_intergenic: 103678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107620, rend_intergenic: 106681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116214, rend_intergenic: 110373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119452, rend_intergenic: 117063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130697, rend_intergenic: 119948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132260, rend_intergenic: 131143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158076, rend_intergenic: 149870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163718, rend_intergenic: 160041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169147, rend_intergenic: 164673  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