-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5530762-5743885

-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_17-snap.1156-T1
Valid prediction for snap_scaffold_17-snap.1163-T1
Valid prediction for snap_scaffold_17-snap.1175-T1
Valid prediction for GeneMark_model.71044_t
Valid prediction for GlimmerHMM_glimmerT_41252-T1
Valid prediction for GlimmerHMM_glimmerT_41256-T1
Valid prediction for snap_scaffold_17-snap.1146-T1
Valid prediction for CodingQuarry_transcript_21944-T1
Valid prediction for snap_scaffold_17-snap.1164-T1
Couldn't classify 162493, 162544
Sorry, prediction CodingQuarry_transcript_21943-T1 fails validation.
(ATG)	 TT	161298-161420	GT	CCG
(GAT)	 CT	162493-162544	GT	AGG
(ACT)	 AG	163075-163131	GT	AAG
(GAC)	 AG	163246-163313	GT	AGG
(ACT)	 AG	163491-163613	GT	AGG
(GAT)	 AG	163863-163949	GC	AAG
-recovered CodingQuarry_transcript_21943-T1, initial, 161298, 161420
-recovered CodingQuarry_transcript_21943-T1, terminal, 163863, 163949
-recovered CodingQuarry_transcript_21943-T1, internal, 163075, 163131
-recovered CodingQuarry_transcript_21943-T1, internal, 163246, 163313
-recovered CodingQuarry_transcript_21943-T1, internal, 163491, 163613
-recovered CodingQuarry_transcript_21943-T1, internal, 163863, 163949
Valid prediction for GlimmerHMM_glimmerT_41234-T1
Valid prediction for GlimmerHMM_glimmerT_41244-T1
Valid prediction for snap_scaffold_17-snap.1150-T1
Valid prediction for GlimmerHMM_glimmerT_41243-T1
Valid prediction for GeneMark_model.71046_t
Valid prediction for snap_scaffold_17-snap.1162-T1
Valid prediction for GeneMark_model.71042_t
Valid prediction for snap_scaffold_17-snap.1157-T1
Valid prediction for GeneMark_model.71047_t
Valid prediction for GeneMark_model.71053_t
Valid prediction for GeneMark_model.71058_t
Valid prediction for GlimmerHMM_glimmerT_41260-T1
Valid prediction for GeneMark_model.71035_t
Valid prediction for GeneMark_model.71032_t
Valid prediction for snap_scaffold_17-snap.1153-T1
Valid prediction for GeneMark_model.71039_t
Valid prediction for snap_scaffold_17-snap.1167-T1
Valid prediction for snap_scaffold_17-snap.1170-T1
Valid prediction for Augustus_model.g27627.t1
Valid prediction for snap_scaffold_17-snap.1160-T1
Valid prediction for GeneMark_model.71037_t
Valid prediction for Augustus_model.g27631.t1
Valid prediction for snap_scaffold_17-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_41236-T1
Valid prediction for GlimmerHMM_glimmerT_41259-T1
Valid prediction for pasa_asmbl_17954.p1
Valid prediction for GeneMark_model.71030_t
Valid prediction for snap_scaffold_17-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_41248-T1
Valid prediction for GeneMark_model.71049_t
Valid prediction for GlimmerHMM_glimmerT_41233-T1
Valid prediction for snap_scaffold_17-snap.1165-T1
Valid prediction for Augustus_model.g27635.t1
Valid prediction for Augustus_model.g27629.t1
Valid prediction for GlimmerHMM_glimmerT_41251-T1
Valid prediction for GeneMark_model.71055_t
Valid prediction for GlimmerHMM_glimmerT_41249-T1
Valid prediction for GlimmerHMM_glimmerT_41246-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 GeneMark_model.71040_t
Valid prediction for GeneMark_model.71061_t
Valid prediction for GeneMark_model.71045_t
Valid prediction for GlimmerHMM_glimmerT_41238-T1
Valid prediction for GlimmerHMM_glimmerT_41245-T1
Valid prediction for GeneMark_model.71038_t
Valid prediction for Augustus_model.g27621.t1
Valid prediction for GlimmerHMM_glimmerT_41241-T1
Valid prediction for snap_scaffold_17-snap.1151-T1
Valid prediction for CodingQuarry_transcript_21947-T1
Valid prediction for snap_scaffold_17-snap.1158-T1
Valid prediction for HiQ_model.g27634.t1
Valid prediction for GeneMark_model.71034_t
Valid prediction for GlimmerHMM_glimmerT_41253-T1
Valid prediction for GeneMark_model.71057_t
Couldn't classify 11842, 11931
Sorry, prediction pasa_asmbl_18994.p1 fails validation.
(CAA)	 GT	11842-11931	GT	TGG
(GCA)	 AG	14832-14901	GT	AGG
(GTA)	 AG	15337-15416	GT	AGG
(AAA)	 AG	16422-16514	GT	TGG
(ATC)	 AG	17605-17787	GT	AGG
(CTC)	 AG	18579-18655	GT	TCG
(CCC)	 AG	18806-18963	GT	AGG
(ACA)	 AG	19193-19413	GC	GAG
-recovered pasa_asmbl_18994.p1, terminal, 19193, 19413
-recovered pasa_asmbl_18994.p1, internal, 14832, 14901
-recovered pasa_asmbl_18994.p1, internal, 15337, 15416
-recovered pasa_asmbl_18994.p1, internal, 16422, 16514
-recovered pasa_asmbl_18994.p1, internal, 17605, 17787
-recovered pasa_asmbl_18994.p1, internal, 18579, 18655
-recovered pasa_asmbl_18994.p1, internal, 18806, 18963
-recovered pasa_asmbl_18994.p1, internal, 19193, 19413
Valid prediction for GlimmerHMM_glimmerT_41258-T1
Valid prediction for GlimmerHMM_glimmerT_41257-T1
Valid prediction for Augustus_model.g27623.t1
Valid prediction for GlimmerHMM_glimmerT_41239-T1
Valid prediction for GeneMark_model.71052_t
Valid prediction for GeneMark_model.71056_t
Valid prediction for snap_scaffold_17-snap.1149-T1
Valid prediction for GeneMark_model.71051_t
Valid prediction for snap_scaffold_17-snap.1171-T1
Valid prediction for snap_scaffold_17-snap.1174-T1
Valid prediction for GeneMark_model.71033_t
Valid prediction for Augustus_model.g27624.t1
Valid prediction for GeneMark_model.71036_t
Valid prediction for GlimmerHMM_glimmerT_41254-T1
Valid prediction for GlimmerHMM_glimmerT_41242-T1
Couldn't classify 54109, 54247
Sorry, prediction pasa_asmbl_18985.p1 fails validation.
(GAC)	 AG	54109-54247	GT	GGG
(GTG)	 AG	55221-55399	GT	CGG
(AGT)	 AG	55867-55983	GT	TGG
(ACA)	 AG	56082-56132	TA	GAT
-recovered pasa_asmbl_18985.p1, terminal, 56082, 56132
-recovered pasa_asmbl_18985.p1, internal, 54109, 54247
-recovered pasa_asmbl_18985.p1, internal, 55221, 55399
-recovered pasa_asmbl_18985.p1, internal, 55867, 55983
Valid prediction for GlimmerHMM_glimmerT_41250-T1
Valid prediction for Augustus_model.g27626.t1
Valid prediction for GeneMark_model.71043_t
Valid prediction for Augustus_model.g27622.t1
Valid prediction for GlimmerHMM_glimmerT_41237-T1
Valid prediction for GeneMark_model.71031_t
Valid prediction for snap_scaffold_17-snap.1172-T1
Valid prediction for pasa_asmbl_18992.p1
Valid prediction for GlimmerHMM_glimmerT_41240-T1
Valid prediction for GlimmerHMM_glimmerT_41247-T1
Valid prediction for CodingQuarry_transcript_21945-T1
Valid prediction for GeneMark_model.71059_t
Valid prediction for HiQ_model.g27630.t1
Valid prediction for Augustus_model.g27633.t1
Valid prediction for Augustus_model.g27628.t1
Valid prediction for GeneMark_model.71060_t
Valid prediction for GlimmerHMM_glimmerT_41235-T1
Valid prediction for CodingQuarry_transcript_21946-T1
Valid prediction for Augustus_model.g27625.t1
Valid prediction for snap_scaffold_17-snap.1176-T1
Valid prediction for snap_scaffold_17-snap.1152-T1
Valid prediction for snap_scaffold_17-snap.1147-T1
Valid prediction for GeneMark_model.71041_t
Valid prediction for snap_scaffold_17-snap.1148-T1
Valid prediction for GeneMark_model.71050_t
Valid prediction for GeneMark_model.71054_t
Valid prediction for snap_scaffold_17-snap.1173-T1
Valid prediction for snap_scaffold_17-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_41255-T1
Valid prediction for snap_scaffold_17-snap.1161-T1
Valid prediction for GeneMark_model.71048_t
Valid prediction for HiQ_model.g27632.t1
Valid prediction for snap_scaffold_17-snap.1166-T1
Valid prediction for snap_scaffold_17-snap.1168-T1
Valid prediction for snap_scaffold_17-snap.1155-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69762, rend_intergenic: 63834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80373, rend_intergenic: 75130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100024, rend_intergenic: 85494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111998, rend_intergenic: 108735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142300, rend_intergenic: 134533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159357, rend_intergenic: 157682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213124
-exon list size: 492


building trellis

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37.9    
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38.3    
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38.9    
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39.5    
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40.1    
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40.9    
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82.8    
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83.4    
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85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
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87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
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94.3    
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94.9    
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95.3    
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97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 69762, rend_intergenic: 63834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80373, rend_intergenic: 75130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100024, rend_intergenic: 85494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111998, rend_intergenic: 108735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142300, rend_intergenic: 134533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159357, rend_intergenic: 157682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support