-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_16674190-16837043

-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_1-snap.2963-T1
Couldn't classify 55968, 56077
Couldn't classify 62680, 62814
Sorry, prediction pasa_asmbl_2501.p1 fails validation.
(AGA)	 GC	55968-56077	GT	CGG
(GAC)	 AG	56763-56900	GT	AAG
(AGA)	 AG	57125-57203	GT	TGG
(GCT)	 AG	57312-57335	GT	AGG
(GAG)	 AG	57442-57495	GT	AGG
(GTG)	 AG	57797-57946	GT	AGG
(GAC)	 AG	58249-58312	GT	AGG
(GAC)	 AG	58537-58580	GT	AGG
(GTG)	 AG	58805-58930	GT	AGG
(GTG)	 AG	59171-59316	GT	AAG
(TCC)	 AG	61090-61219	GT	TGG
(TCC)	 AG	62680-62814	AG	CCA
-recovered pasa_asmbl_2501.p1, internal, 56763, 56900
-recovered pasa_asmbl_2501.p1, internal, 57125, 57203
-recovered pasa_asmbl_2501.p1, internal, 57312, 57335
-recovered pasa_asmbl_2501.p1, internal, 57442, 57495
-recovered pasa_asmbl_2501.p1, internal, 57797, 57946
-recovered pasa_asmbl_2501.p1, internal, 58249, 58312
-recovered pasa_asmbl_2501.p1, internal, 58537, 58580
-recovered pasa_asmbl_2501.p1, internal, 58805, 58930
-recovered pasa_asmbl_2501.p1, internal, 59171, 59316
-recovered pasa_asmbl_2501.p1, internal, 61090, 61219
Valid prediction for snap_scaffold_1-snap.2962-T1
Valid prediction for snap_scaffold_1-snap.2996-T1
Couldn't classify 125423, 126115
Sorry, prediction pasa_asmbl_2507.p1 fails validation.
(CCA)	 CT	125423-126115	GT	AGG
(ATT)	 AG	127780-128217	AC	GAA
-recovered pasa_asmbl_2507.p1, terminal, 127780, 128217
Valid prediction for snap_scaffold_1-snap.2976-T1
Valid prediction for GlimmerHMM_glimmerT_2227-T1
Valid prediction for snap_scaffold_1-snap.2977-T1
Valid prediction for GlimmerHMM_glimmerT_2207-T1
Valid prediction for snap_scaffold_1-snap.2988-T1
Valid prediction for snap_scaffold_1-snap.2972-T1
Valid prediction for Augustus_model.g1651.t1
Valid prediction for Augustus_model.g1643.t1
Valid prediction for HiQ_model.g1641.t1
Valid prediction for GlimmerHMM_glimmerT_2222-T1
Valid prediction for snap_scaffold_1-snap.2981-T1
Valid prediction for Augustus_model.g1647.t1
Valid prediction for GlimmerHMM_glimmerT_2202-T1
Valid prediction for GlimmerHMM_glimmerT_2201-T1
Valid prediction for HiQ_model.g1656.t1
Valid prediction for GlimmerHMM_glimmerT_2224-T1
Valid prediction for GlimmerHMM_glimmerT_2211-T1
Valid prediction for GlimmerHMM_glimmerT_2215-T1
Valid prediction for snap_scaffold_1-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_2216-T1
Valid prediction for GlimmerHMM_glimmerT_2223-T1
Valid prediction for GlimmerHMM_glimmerT_2203-T1
Valid prediction for GlimmerHMM_glimmerT_2210-T1
Valid prediction for GlimmerHMM_glimmerT_2226-T1
Valid prediction for pasa_asmbl_2508.p1
Valid prediction for GlimmerHMM_glimmerT_2231-T1
Valid prediction for Augustus_model.g1645.t1
Valid prediction for snap_scaffold_1-snap.2978-T1
Valid prediction for snap_scaffold_1-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_2205-T1
Valid prediction for HiQ_model.g1640.t1
Valid prediction for snap_scaffold_1-snap.2966-T1
Valid prediction for Augustus_model.g1648.t1
Valid prediction for snap_scaffold_1-snap.2975-T1
Valid prediction for snap_scaffold_1-snap.2982-T1
Valid prediction for Augustus_model.g1650.t1
Valid prediction for Augustus_model.g1652.t1
Valid prediction for GlimmerHMM_glimmerT_2218-T1
Valid prediction for snap_scaffold_1-snap.2967-T1
Valid prediction for snap_scaffold_1-snap.3000-T1
Valid prediction for snap_scaffold_1-snap.2994-T1
Couldn't classify 48447, 48800
Sorry, prediction pasa_asmbl_2499.p3 fails validation.
(GAG)	 GA	48447-48800	GA	GAG
Valid prediction for snap_scaffold_1-snap.2971-T1
Valid prediction for snap_scaffold_1-snap.2999-T1
Valid prediction for GlimmerHMM_glimmerT_2209-T1
Valid prediction for snap_scaffold_1-snap.2990-T1
Valid prediction for snap_scaffold_1-snap.2985-T1
Valid prediction for Augustus_model.g1638.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_1-snap.2989-T1
Valid prediction for snap_scaffold_1-snap.2983-T1
Valid prediction for Augustus_model.g1649.t1
Valid prediction for GlimmerHMM_glimmerT_2206-T1
Valid prediction for snap_scaffold_1-snap.2960-T1
Valid prediction for GlimmerHMM_glimmerT_2208-T1
Valid prediction for GlimmerHMM_glimmerT_2230-T1
Valid prediction for snap_scaffold_1-snap.2979-T1
Valid prediction for snap_scaffold_1-snap.2987-T1
Valid prediction for GlimmerHMM_glimmerT_2217-T1
Valid prediction for GlimmerHMM_glimmerT_2213-T1
Valid prediction for snap_scaffold_1-snap.2991-T1
Valid prediction for Augustus_model.g1635.t1
Valid prediction for pasa_asmbl_1017.p1
Valid prediction for pasa_asmbl_1012.p1
Valid prediction for GlimmerHMM_glimmerT_2219-T1
Valid prediction for snap_scaffold_1-snap.2964-T1
Valid prediction for CodingQuarry_transcript_2963-T1
Valid prediction for CodingQuarry_transcript_2965-T1
Valid prediction for HiQ_model.g1644.t1
Valid prediction for Augustus_model.g1642.t1
Valid prediction for snap_scaffold_1-snap.2965-T1
Valid prediction for CodingQuarry_transcript_2962-T1
Valid prediction for CodingQuarry_transcript_2967-T1
Valid prediction for GlimmerHMM_glimmerT_2229-T1
Valid prediction for HiQ_model.g1639.t1
Valid prediction for snap_scaffold_1-snap.2997-T1
Valid prediction for snap_scaffold_1-snap.2970-T1
Valid prediction for snap_scaffold_1-snap.2968-T1
Valid prediction for GlimmerHMM_glimmerT_2221-T1
Valid prediction for GlimmerHMM_glimmerT_2214-T1
Valid prediction for GlimmerHMM_glimmerT_2228-T1
Valid prediction for GlimmerHMM_glimmerT_2225-T1
Valid prediction for CodingQuarry_transcript_2964-T1
Valid prediction for snap_scaffold_1-snap.2959-T1
Valid prediction for snap_scaffold_1-snap.2980-T1
Valid prediction for Augustus_model.g1655.t1
Valid prediction for snap_scaffold_1-snap.2995-T1
Valid prediction for GlimmerHMM_glimmerT_2220-T1
Valid prediction for snap_scaffold_1-snap.2993-T1
Couldn't classify 153713, 153895
Sorry, prediction pasa_asmbl_1008.p1 fails validation.
(ATG)	 TC	149237-149500	GT	AGG
(GAT)	 AG	149742-149854	GT	AGG
(GAC)	 AG	151023-151182	GT	AGG
(CTC)	 AG	151424-151573	GT	AGG
(GAG)	 AG	153264-153386	GT	AGG
(GTG)	 AG	153713-153895	TA	GGT
-recovered pasa_asmbl_1008.p1, initial, 149237, 149500
-recovered pasa_asmbl_1008.p1, internal, 149742, 149854
-recovered pasa_asmbl_1008.p1, internal, 151023, 151182
-recovered pasa_asmbl_1008.p1, internal, 151424, 151573
-recovered pasa_asmbl_1008.p1, internal, 153264, 153386
Valid prediction for snap_scaffold_1-snap.2973-T1
Valid prediction for Augustus_model.g1636.t1
Valid prediction for Augustus_model.g1654.t1
Valid prediction for snap_scaffold_1-snap.2961-T1
Valid prediction for snap_scaffold_1-snap.2969-T1
Valid prediction for Augustus_model.g1637.t1
Valid prediction for snap_scaffold_1-snap.2998-T1
Valid prediction for snap_scaffold_1-snap.2986-T1
Valid prediction for Augustus_model.g1653.t1
Valid prediction for snap_scaffold_1-snap.2974-T1
Valid prediction for GlimmerHMM_glimmerT_2204-T1
Valid prediction for Augustus_model.g1646.t1
Valid prediction for GlimmerHMM_glimmerT_2212-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13016, rend_intergenic: 6618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24725, rend_intergenic: 22918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35977, rend_intergenic: 29962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54639, rend_intergenic: 48153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59341, rend_intergenic: 54774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61777, rend_intergenic: 60020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80682, rend_intergenic: 72645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87412, rend_intergenic: 84481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96298, rend_intergenic: 90174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119684, rend_intergenic: 108621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126166, rend_intergenic: 123371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134465, rend_intergenic: 132686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137317, rend_intergenic: 134955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147557, rend_intergenic: 137658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162854
-exon list size: 391


building trellis

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34.6    
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35.4    
35.6    
35.9    
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36.9    
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37.4    
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37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
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42.5    
42.7    
43.0    
43.3    
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43.8    
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44.3    
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44.8    
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45.3    
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46.1    
46.3    
46.6    
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47.6    
47.8    
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48.3    
48.6    
48.9    
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49.4    
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55.0    
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58.3    
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97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 13016, rend_intergenic: 6618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24725, rend_intergenic: 22918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35977, rend_intergenic: 29962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54639, rend_intergenic: 48153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59341, rend_intergenic: 54774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61777, rend_intergenic: 60020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80682, rend_intergenic: 72645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87412, rend_intergenic: 84481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96298, rend_intergenic: 90174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119684, rend_intergenic: 108621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126166, rend_intergenic: 123371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134465, rend_intergenic: 132686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137317, rend_intergenic: 134955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147557, rend_intergenic: 137658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support