-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_249

-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 Augustus_model.g40946.t1
Valid prediction for GlimmerHMM_glimmerT_61576-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61576-T1 243-564-terminal-1 is invalid.
Valid prediction for GeneMark_model.107076_t
add_exon() Sorry, GeneMark_model.107076_t 243-564-terminal-1 is invalid.
Valid prediction for Augustus_model.g40945.t1
add_exon() Sorry, Augustus_model.g40945.t1 243-564-terminal-1 is invalid.
Valid prediction for GeneMark_model.107077_t
Couldn't classify 243, 556
Couldn't classify 8987, 9054
Sorry, prediction snap_scaffold_249-snap.1-T1 fails validation.
(GGA)	 AG	243-556	GT	CTG
(GTG)	 AG	2640-2695	GT	AAG
(GCG)	 AG	4212-4294	GT	CGG
(ACA)	 AG	4483-4627	GT	AAG
(AAC)	 AG	5007-5096	GT	AGG
(AGC)	 AG	5229-5348	GT	TGG
(GCG)	 AG	5692-5820	GT	GGG
(TCA)	 AG	8987-9054	GT	AAG
-recovered snap_scaffold_249-snap.1-T1, internal, 243, 556
-recovered snap_scaffold_249-snap.1-T1, internal, 2640, 2695
-recovered snap_scaffold_249-snap.1-T1, internal, 4212, 4294
-recovered snap_scaffold_249-snap.1-T1, internal, 4483, 4627
-recovered snap_scaffold_249-snap.1-T1, internal, 5007, 5096
-recovered snap_scaffold_249-snap.1-T1, internal, 5229, 5348
-recovered snap_scaffold_249-snap.1-T1, internal, 5692, 5820
-recovered snap_scaffold_249-snap.1-T1, internal, 8987, 9054
Couldn't classify 5692, 5820
Sorry, prediction GlimmerHMM_glimmerT_61577-T1 fails validation.
(ATG)	 CT	2618-2695	GT	AAG
(GCG)	 AG	4212-4294	GT	CGG
(ACA)	 AG	4483-4627	GT	AAG
(AAC)	 AG	5007-5096	GT	AGG
(AGC)	 AG	5229-5348	GT	TGG
(GCG)	 AG	5692-5820	GT	GGG
-recovered GlimmerHMM_glimmerT_61577-T1, initial, 2618, 2695
-recovered GlimmerHMM_glimmerT_61577-T1, internal, 4212, 4294
-recovered GlimmerHMM_glimmerT_61577-T1, internal, 4483, 4627
-recovered GlimmerHMM_glimmerT_61577-T1, internal, 5007, 5096
-recovered GlimmerHMM_glimmerT_61577-T1, internal, 5229, 5348
-recovered GlimmerHMM_glimmerT_61577-T1, internal, 5692, 5820

-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 35, 185
Sorry, prediction snap_scaffold_249-snap.2-T1 fails validation.
(GAA)	 AG	35-185	GT	ATG
(CGC)	 AG	3354-3426	GT	GGG
(CCA)	 AG	3756-3855	GT	CTG
(AAC)	 AG	4516-4656	AC	AAA
-recovered snap_scaffold_249-snap.2-T1, terminal, 4516, 4656
-recovered snap_scaffold_249-snap.2-T1, internal, 35, 185
-recovered snap_scaffold_249-snap.2-T1, internal, 3354, 3426
-recovered snap_scaffold_249-snap.2-T1, internal, 3756, 3855
Couldn't classify 35, 185
Sorry, prediction GeneMark_model.107078_t fails validation.
(GAA)	 AG	35-185	GT	ATG
(TAT)	 AG	333-345	GT	AGG
(GGA)	 AG	3196-3320	GT	TGG
(CTT)	 AG	3346-3362	CC	AAC
-recovered GeneMark_model.107078_t, terminal, 333, 345
-recovered GeneMark_model.107078_t, terminal, 3346, 3362
-recovered GeneMark_model.107078_t, internal, 35, 185
-recovered GeneMark_model.107078_t, internal, 333, 345
-recovered GeneMark_model.107078_t, internal, 3196, 3320

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9054, rend_intergenic: 4445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9100
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 9054, rend_intergenic: 4445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support