-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_43

-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.106227_t
Valid prediction for GeneMark_model.106232_t
Valid prediction for GlimmerHMM_glimmerT_61028-T1
Valid prediction for GeneMark_model.106237_t
Valid prediction for GeneMark_model.106231_t
Valid prediction for GeneMark_model.106235_t
Valid prediction for Augustus_model.g40596.t1
Valid prediction for GeneMark_model.106229_t
Valid prediction for GeneMark_model.106228_t
Valid prediction for snap_scaffold_43-snap.2-T1
Couldn't classify 26870, 27242
Sorry, prediction snap_scaffold_43-snap.3-T1 fails validation.
(ATG)	 AC	18447-18452	GT	AGG
(GTG)	 AG	18725-18922	GT	TGG
(GCA)	 AG	18993-19140	GT	TGG
(GGT)	 AG	19385-19479	GT	AGG
(AAT)	 AG	25467-25827	GT	GAG
(ACA)	 AG	26870-27242	GT	AAG
-recovered snap_scaffold_43-snap.3-T1, initial, 18447, 18452
-recovered snap_scaffold_43-snap.3-T1, internal, 18725, 18922
-recovered snap_scaffold_43-snap.3-T1, internal, 18993, 19140
-recovered snap_scaffold_43-snap.3-T1, internal, 19385, 19479
-recovered snap_scaffold_43-snap.3-T1, internal, 25467, 25827
-recovered snap_scaffold_43-snap.3-T1, internal, 26870, 27242

-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: -)Couldn't classify 2975, 3129
Sorry, prediction GlimmerHMM_glimmerT_61029-T1 fails validation.
(AGC)	 AG	2975-3129	GT	AGG
(AGG)	 AG	8458-9085	GG	GAG
-recovered GlimmerHMM_glimmerT_61029-T1, terminal, 8458, 9085
-recovered GlimmerHMM_glimmerT_61029-T1, internal, 2975, 3129
Valid prediction for GeneMark_model.106233_t
Valid prediction for GeneMark_model.106236_t
Couldn't classify 2975, 3092
Sorry, prediction snap_scaffold_43-snap.4-T1 fails validation.
(AGC)	 AG	2975-3092	GT	AGG
(GAT)	 AG	4079-4298	GT	TAG
(CTT)	 AG	5190-5198	GT	ATG
(GAA)	 AG	6883-7013	GT	AGG
(ATT)	 AG	7383-7607	GT	AGG
(AAC)	 AG	8282-8289	GT	GTG
(CGG)	 AG	8423-9070	GT	ATG
(CAT)	 AG	10675-10757	GT	TGG
(GGT)	 AG	11114-11582	GA	AGG
add_exon() Sorry, snap_scaffold_43-snap.4-T1 6883-7013-terminal-2 is invalid.
-recovered snap_scaffold_43-snap.4-T1, terminal, 6883, 7013
-recovered snap_scaffold_43-snap.4-T1, terminal, 11114, 11582
-recovered snap_scaffold_43-snap.4-T1, internal, 2975, 3092
-recovered snap_scaffold_43-snap.4-T1, internal, 4079, 4298
-recovered snap_scaffold_43-snap.4-T1, internal, 5190, 5198
-recovered snap_scaffold_43-snap.4-T1, internal, 6883, 7013
-recovered snap_scaffold_43-snap.4-T1, internal, 7383, 7607
-recovered snap_scaffold_43-snap.4-T1, internal, 8282, 8289
-recovered snap_scaffold_43-snap.4-T1, internal, 8423, 9070
-recovered snap_scaffold_43-snap.4-T1, internal, 10675, 10757
Valid prediction for GlimmerHMM_glimmerT_61026-T1
Valid prediction for GeneMark_model.106230_t
Valid prediction for snap_scaffold_43-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_61027-T1
Valid prediction for GeneMark_model.106226_t
Valid prediction for GeneMark_model.106234_t
Valid prediction for Augustus_model.g40595.t1
Couldn't classify 28222, 28459
Couldn't classify 28810, 28940
Sorry, prediction pasa_asmbl_43675.p1 fails validation.
(ATC)	 AG	28222-28459	GT	AGG
(GGG)	 AG	28810-28940	AC	CCA
-recovered pasa_asmbl_43675.p1, internal, 28222, 28459

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15396, rend_intergenic: 2986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27242, rend_intergenic: 20053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 31634
-exon list size: 104


building trellis

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49.1    
50.0    
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62.3    
63.2    
64.2    
65.1    
66.0    
67.0    
67.9    
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73.6    
74.5    
75.5    
76.4    
77.4    
78.3    
79.2    
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81.1    
82.1    
83.0    
84.0    
84.9    
85.8    
86.8    
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89.6    
90.6    
91.5    
92.5    
93.4    
94.3    
95.3    
96.2    
97.2    
98.1    
99.1    
-found 10 predictions from path traversal
Error with prediction: snap lend_intergenic: 15396, rend_intergenic: 2986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27242, rend_intergenic: 20053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support