-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_4653220-4899720

-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 GlimmerHMM_glimmerT_49370-T1
Valid prediction for GlimmerHMM_glimmerT_49369-T1
Valid prediction for Augustus_model.g32946.t1
Valid prediction for GlimmerHMM_glimmerT_49371-T1
Valid prediction for Augustus_model.g32940.t1
Valid prediction for snap_scaffold_22-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_49352-T1
Valid prediction for snap_scaffold_22-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_49361-T1
Valid prediction for Augustus_model.g32943.t1
Valid prediction for snap_scaffold_22-snap.874-T1
Couldn't classify 193418, 193478
Couldn't classify 194043, 194218
Sorry, prediction pasa_asmbl_30449.p1 fails validation.
(GAG)	 AA	193418-193478	GT	AGG
(ATT)	 AG	193708-193872	GT	TGG
(GCC)	 AG	194043-194218	CA	TCC
-recovered pasa_asmbl_30449.p1, internal, 193708, 193872
Valid prediction for GlimmerHMM_glimmerT_49365-T1
Valid prediction for CodingQuarry_transcript_34150-T1
Couldn't classify 183926, 184019
Sorry, prediction pasa_asmbl_30043.p1 fails validation.
(AGC)	 AA	183926-184019	GT	AGG
(GCC)	 AG	184496-184587	GT	AGG
(GAG)	 AG	186704-186797	GT	GGG
(CCA)	 AG	187252-187342	GT	AGG
(GGT)	 AG	188067-188313	AT	AGA
-recovered pasa_asmbl_30043.p1, terminal, 188067, 188313
-recovered pasa_asmbl_30043.p1, internal, 184496, 184587
-recovered pasa_asmbl_30043.p1, internal, 186704, 186797
-recovered pasa_asmbl_30043.p1, internal, 187252, 187342
Valid prediction for snap_scaffold_22-snap.890-T1
Valid prediction for snap_scaffold_22-snap.876-T1
Valid prediction for snap_scaffold_22-snap.900-T1
Valid prediction for snap_scaffold_22-snap.893-T1
Valid prediction for snap_scaffold_22-snap.901-T1
Valid prediction for Augustus_model.g32945.t1
Valid prediction for GlimmerHMM_glimmerT_49362-T1
Valid prediction for snap_scaffold_22-snap.881-T1
Valid prediction for snap_scaffold_22-snap.883-T1
Valid prediction for snap_scaffold_22-snap.895-T1
Valid prediction for snap_scaffold_22-snap.888-T1
Valid prediction for snap_scaffold_22-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_49350-T1
Valid prediction for snap_scaffold_22-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_49363-T1
Valid prediction for snap_scaffold_22-snap.894-T1
Valid prediction for snap_scaffold_22-snap.891-T1
Valid prediction for Augustus_model.g32938.t1
Couldn't classify 126207, 126253
Couldn't classify 128460, 128480
Sorry, prediction pasa_asmbl_30522.p1 fails validation.
(ACC)	 AG	126207-126253	GT	GGG
(CTC)	 AG	127051-127125	GT	AAG
(TGC)	 AG	127421-127514	GT	TGG
(GCG)	 AG	127982-128098	GT	AGG
(GTT)	 AG	128460-128480	GG	GGG
-recovered pasa_asmbl_30522.p1, internal, 126207, 126253
-recovered pasa_asmbl_30522.p1, internal, 127051, 127125
-recovered pasa_asmbl_30522.p1, internal, 127421, 127514
-recovered pasa_asmbl_30522.p1, internal, 127982, 128098
Valid prediction for Augustus_model.g32939.t1
Valid prediction for snap_scaffold_22-snap.898-T1
Couldn't classify 129609, 129647
Sorry, prediction pasa_asmbl_30041.p1 fails validation.
(GAG)	 CA	129609-129647	GT	CGG
(TTC)	 AG	130043-130197	GT	AGG
(GGG)	 AG	130679-130768	GT	AAG
(ACT)	 AG	130998-131128	GT	AGG
(ATC)	 AG	131970-132139	AG	AGA
-recovered pasa_asmbl_30041.p1, terminal, 131970, 132139
-recovered pasa_asmbl_30041.p1, internal, 130043, 130197
-recovered pasa_asmbl_30041.p1, internal, 130679, 130768
-recovered pasa_asmbl_30041.p1, internal, 130998, 131128
Valid prediction for snap_scaffold_22-snap.902-T1
Valid prediction for Augustus_model.g32935.t1
Valid prediction for Augustus_model.g32948.t1
Valid prediction for snap_scaffold_22-snap.887-T1
Valid prediction for snap_scaffold_22-snap.907-T1
Valid prediction for Augustus_model.g32947.t1
Valid prediction for GlimmerHMM_glimmerT_49360-T1
Valid prediction for GlimmerHMM_glimmerT_49367-T1
Valid prediction for snap_scaffold_22-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_49368-T1
Valid prediction for snap_scaffold_22-snap.882-T1
Valid prediction for snap_scaffold_22-snap.905-T1
Valid prediction for snap_scaffold_22-snap.904-T1
Couldn't classify 182267, 182290
Couldn't classify 183597, 183612
Sorry, prediction pasa_asmbl_30042.p1 fails validation.
(GCG)	 AA	182267-182290	GT	AGG
(GGC)	 AG	182461-182615	GT	AGG
(GTT)	 AG	182790-182908	GT	AGG
(GTG)	 AG	183008-183166	GT	AGG
(GGT)	 AG	183296-183449	GT	AGG
(AAT)	 AG	183597-183612	AC	CCA
-recovered pasa_asmbl_30042.p1, internal, 182461, 182615
-recovered pasa_asmbl_30042.p1, internal, 182790, 182908
-recovered pasa_asmbl_30042.p1, internal, 183008, 183166
-recovered pasa_asmbl_30042.p1, internal, 183296, 183449

-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_22-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_49355-T1
Valid prediction for snap_scaffold_22-snap.896-T1
Valid prediction for snap_scaffold_22-snap.879-T1
Valid prediction for snap_scaffold_22-snap.884-T1
Valid prediction for Augustus_model.g32950.t1
Valid prediction for snap_scaffold_22-snap.909-T1
Valid prediction for Augustus_model.g32937.t1
Valid prediction for snap_scaffold_22-snap.911-T1
Valid prediction for Augustus_model.g32944.t1
Valid prediction for GlimmerHMM_glimmerT_49375-T1
Valid prediction for GlimmerHMM_glimmerT_49353-T1
Valid prediction for HiQ_model.g32942.t1
Valid prediction for GlimmerHMM_glimmerT_49372-T1
Valid prediction for CodingQuarry_transcript_34153-T1
Valid prediction for snap_scaffold_22-snap.897-T1
Valid prediction for GlimmerHMM_glimmerT_49366-T1
Valid prediction for Augustus_model.g32936.t1
Valid prediction for CodingQuarry_transcript_34151-T1
Valid prediction for CodingQuarry_transcript_34155-T1
Valid prediction for pasa_asmbl_29275.p1
Valid prediction for HiQ_model.g32951.t1
Valid prediction for pasa_asmbl_29277.p1
Valid prediction for Augustus_model.g32932.t1
Valid prediction for snap_scaffold_22-snap.912-T1
Valid prediction for GlimmerHMM_glimmerT_49356-T1
Valid prediction for Augustus_model.g32949.t1
Valid prediction for GlimmerHMM_glimmerT_49364-T1
Valid prediction for GlimmerHMM_glimmerT_49351-T1
Valid prediction for HiQ_model.g32941.t1
Valid prediction for GlimmerHMM_glimmerT_49354-T1
Valid prediction for Augustus_model.g32931.t1
Valid prediction for snap_scaffold_22-snap.908-T1
Valid prediction for Augustus_model.g32934.t1
Valid prediction for snap_scaffold_22-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_49357-T1
Valid prediction for Augustus_model.g32933.t1
Valid prediction for snap_scaffold_22-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_49373-T1
Valid prediction for GlimmerHMM_glimmerT_49374-T1
Valid prediction for Augustus_model.g32952.t1
Valid prediction for GlimmerHMM_glimmerT_49359-T1
Valid prediction for snap_scaffold_22-snap.906-T1
Valid prediction for snap_scaffold_22-snap.892-T1
Valid prediction for CodingQuarry_transcript_34154-T1
Valid prediction for snap_scaffold_22-snap.899-T1
Valid prediction for pasa_asmbl_29280.p1
Valid prediction for snap_scaffold_22-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_49358-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 59893, rend_intergenic: 59171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198753, rend_intergenic: 196650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209326, rend_intergenic: 201413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 246501
-exon list size: 369


building trellis

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42.9    
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65.8    
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66.3    
66.6    
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67.1    
67.4    
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83.0    
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85.4    
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86.3    
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87.1    
87.3    
87.6    
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88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
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90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 59893, rend_intergenic: 59171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198753, rend_intergenic: 196650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209326, rend_intergenic: 201413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 13403
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support