-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_1721093-1878571

-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 GeneMark_model.73925_t
Valid prediction for CodingQuarry_transcript_23622-T1
Valid prediction for snap_scaffold_18-snap.371-T1
Valid prediction for GeneMark_model.73956_t
Valid prediction for GeneMark_model.73944_t
Valid prediction for GlimmerHMM_glimmerT_42790-T1
Valid prediction for GlimmerHMM_glimmerT_42771-T1
Valid prediction for GeneMark_model.73948_t
Valid prediction for Augustus_model.g28628.t1
Valid prediction for snap_scaffold_18-snap.378-T1
Valid prediction for HiQ_model.g28614.t1
Valid prediction for GlimmerHMM_glimmerT_42788-T1
Valid prediction for snap_scaffold_18-snap.363-T1
Valid prediction for Augustus_model.g28616.t1
Valid prediction for GeneMark_model.73942_t
Valid prediction for Augustus_model.g28624.t1
Valid prediction for snap_scaffold_18-snap.353-T1
Valid prediction for GeneMark_model.73936_t
Valid prediction for GeneMark_model.73934_t
Valid prediction for Augustus_model.g28618.t1
Couldn't classify 153004, 153062
Couldn't classify 154170, 154242
Sorry, prediction pasa_asmbl_20414.p1 fails validation.
(GTC)	 AA	153004-153062	GT	ATG
(GTT)	 AG	153198-153417	GT	AGG
(GAT)	 AG	153567-153680	GT	TGG
(CCT)	 AG	153789-153874	GT	AAG
(GTT)	 AG	153960-154058	GT	AGG
(GAA)	 AG	154170-154242	GA	GGG
-recovered pasa_asmbl_20414.p1, terminal, 153789, 153874
-recovered pasa_asmbl_20414.p1, internal, 153198, 153417
-recovered pasa_asmbl_20414.p1, internal, 153567, 153680
-recovered pasa_asmbl_20414.p1, internal, 153789, 153874
-recovered pasa_asmbl_20414.p1, internal, 153960, 154058
Valid prediction for snap_scaffold_18-snap.358-T1
Valid prediction for snap_scaffold_18-snap.356-T1
Valid prediction for snap_scaffold_18-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_42782-T1
Valid prediction for snap_scaffold_18-snap.354-T1
Valid prediction for Augustus_model.g28615.t1
Valid prediction for snap_scaffold_18-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_42783-T1
Valid prediction for snap_scaffold_18-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_42774-T1
Valid prediction for GlimmerHMM_glimmerT_42791-T1
Valid prediction for pasa_asmbl_20410.p1
Valid prediction for GeneMark_model.73929_t
Valid prediction for GeneMark_model.73950_t
Valid prediction for GlimmerHMM_glimmerT_42778-T1
Valid prediction for Augustus_model.g28626.t1
Valid prediction for snap_scaffold_18-snap.351-T1
Couldn't classify 152182, 152682
Sorry, prediction pasa_asmbl_20413.p1 fails validation.
(GCT)	 TG	152182-152682	AG	ACA
Valid prediction for snap_scaffold_18-snap.372-T1
Valid prediction for CodingQuarry_transcript_23623-T1
Valid prediction for snap_scaffold_18-snap.355-T1
Couldn't classify 146132, 146246
Couldn't classify 146556, 146690
Sorry, prediction pasa_asmbl_21113.p1 fails validation.
(GAG)	 AG	146132-146246	GT	TGG
(CTG)	 AG	146373-146437	GT	TGG
(ACA)	 AG	146556-146690	GT	AGG
-recovered pasa_asmbl_21113.p1, internal, 146132, 146246
-recovered pasa_asmbl_21113.p1, internal, 146373, 146437
-recovered pasa_asmbl_21113.p1, internal, 146556, 146690
Valid prediction for snap_scaffold_18-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_42776-T1
Valid prediction for CodingQuarry_transcript_23621-T1
Couldn't classify 150455, 150601
Couldn't classify 151247, 151287
Sorry, prediction pasa_asmbl_21154.p1 fails validation.
(TTC)	 GC	150455-150601	GT	AGG
(GAT)	 AG	150738-150908	GT	AGG
(GTT)	 AG	151034-151157	GT	GGG
(GAG)	 AG	151247-151287	GG	CAG
-recovered pasa_asmbl_21154.p1, internal, 150738, 150908
-recovered pasa_asmbl_21154.p1, internal, 151034, 151157
Valid prediction for GeneMark_model.73927_t
Valid prediction for GeneMark_model.73946_t
Valid prediction for Augustus_model.g28623.t1
Valid prediction for GeneMark_model.73939_t
Valid prediction for GlimmerHMM_glimmerT_42779-T1
Valid prediction for GeneMark_model.73955_t
Valid prediction for GlimmerHMM_glimmerT_42773-T1
Valid prediction for Augustus_model.g28631.t1
Couldn't classify 114560, 114602
Sorry, prediction pasa_asmbl_20408.p1 fails validation.
(GGG)	 TC	114560-114602	GT	AGG
(AGG)	 AG	115181-115482	AC	GAA
-recovered pasa_asmbl_20408.p1, terminal, 115181, 115482
Valid prediction for snap_scaffold_18-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_42786-T1
Valid prediction for snap_scaffold_18-snap.377-T1
Valid prediction for snap_scaffold_18-snap.367-T1
Valid prediction for Augustus_model.g28633.t1
Valid prediction for Augustus_model.g28622.t1
Couldn't classify 89346, 89386
Sorry, prediction pasa_asmbl_20407.p1 fails validation.
(TAC)	 AG	89346-89386	GT	CCG
(GGA)	 AG	89497-89566	GT	AGG
(GAA)	 AG	89694-89750	GT	CGG
(GTC)	 AG	89859-89954	GT	AGG
(TAC)	 AG	90584-90717	GT	GGG
(GAA)	 AG	90841-90956	GT	TGG
(GTG)	 AG	91220-91263	AA	AAA
-recovered pasa_asmbl_20407.p1, terminal, 91220, 91263
-recovered pasa_asmbl_20407.p1, internal, 89346, 89386
-recovered pasa_asmbl_20407.p1, internal, 89497, 89566
-recovered pasa_asmbl_20407.p1, internal, 89694, 89750
-recovered pasa_asmbl_20407.p1, internal, 89859, 89954
-recovered pasa_asmbl_20407.p1, internal, 90584, 90717
-recovered pasa_asmbl_20407.p1, internal, 90841, 90956
Valid prediction for GeneMark_model.73926_t

-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 GeneMark_model.73940_t
Valid prediction for Augustus_model.g28632.t1
Valid prediction for GlimmerHMM_glimmerT_42787-T1
Valid prediction for GeneMark_model.73933_t
Valid prediction for snap_scaffold_18-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_42780-T1
Valid prediction for snap_scaffold_18-snap.364-T1
Valid prediction for Augustus_model.g28621.t1
Valid prediction for snap_scaffold_18-snap.352-T1
Valid prediction for HiQ_model.g28617.t1
Valid prediction for Augustus_model.g28619.t1
Valid prediction for Augustus_model.g28620.t1
Valid prediction for Augustus_model.g28625.t1
Valid prediction for snap_scaffold_18-snap.379-T1
Valid prediction for snap_scaffold_18-snap.370-T1
Valid prediction for snap_scaffold_18-snap.375-T1
Valid prediction for snap_scaffold_18-snap.374-T1
Valid prediction for snap_scaffold_18-snap.361-T1
Valid prediction for GeneMark_model.73935_t
Valid prediction for CodingQuarry_transcript_23620-T1
Valid prediction for GeneMark_model.73952_t
Valid prediction for GeneMark_model.73930_t
Valid prediction for GeneMark_model.73941_t
Valid prediction for Augustus_model.g28629.t1
Valid prediction for GeneMark_model.73938_t
Valid prediction for snap_scaffold_18-snap.357-T1
Valid prediction for GeneMark_model.73937_t
Valid prediction for GeneMark_model.73945_t
Valid prediction for GlimmerHMM_glimmerT_42789-T1
Valid prediction for GeneMark_model.73928_t
Valid prediction for GlimmerHMM_glimmerT_42781-T1
Valid prediction for GeneMark_model.73953_t
Valid prediction for GeneMark_model.73947_t
Valid prediction for GeneMark_model.73943_t
Valid prediction for snap_scaffold_18-snap.359-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42777-T1
Valid prediction for GlimmerHMM_glimmerT_42775-T1
Valid prediction for GeneMark_model.73954_t
Valid prediction for snap_scaffold_18-snap.368-T1
Valid prediction for Augustus_model.g28630.t1
Valid prediction for snap_scaffold_18-snap.376-T1
Valid prediction for snap_scaffold_18-snap.362-T1
Valid prediction for GeneMark_model.73931_t
Valid prediction for Augustus_model.g28627.t1
Valid prediction for snap_scaffold_18-snap.380-T1
Valid prediction for GeneMark_model.73951_t
Valid prediction for pasa_asmbl_19680.p1
Couldn't classify 53549, 53644
Sorry, prediction pasa_asmbl_19681.p1 fails validation.
(ATG)	 CA	51158-51313	GT	AGG
(GAG)	 AG	51408-51532	GT	AGG
(ATT)	 AG	52963-53035	GT	AGG
(GTT)	 AG	53549-53644	TC	GGT
-recovered pasa_asmbl_19681.p1, initial, 51158, 51313
-recovered pasa_asmbl_19681.p1, internal, 51408, 51532
-recovered pasa_asmbl_19681.p1, internal, 52963, 53035
Valid prediction for pasa_asmbl_19677.p1
Valid prediction for GlimmerHMM_glimmerT_42784-T1
Valid prediction for GlimmerHMM_glimmerT_42785-T1
Valid prediction for GlimmerHMM_glimmerT_42772-T1
Valid prediction for GeneMark_model.73949_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48535, rend_intergenic: 47145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52301, rend_intergenic: 50018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60275, rend_intergenic: 59524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69698, rend_intergenic: 61010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72329, rend_intergenic: 70515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157479
-exon list size: 458


building trellis

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32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
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34.6    
34.8    
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35.9    
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37.8    
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39.8    
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40.9    
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42.8    
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45.9    
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64.1    
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64.6    
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80.0    
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80.9    
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82.8    
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83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
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94.6    
94.8    
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95.4    
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95.9    
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96.5    
96.7    
97.0    
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97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 48535, rend_intergenic: 47145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52301, rend_intergenic: 50018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60275, rend_intergenic: 59524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69698, rend_intergenic: 61010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72329, rend_intergenic: 70515  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