-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_661

-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: +)Couldn't classify 23, 106
Sorry, prediction GeneMark_model.108148_t fails validation.
(GCT)	 AG	23-106	GT	AGG
(AGG)	 AG	201-461	GT	GAG
(TGG)	 AG	487-579	GT	AAG
(GGG)	 AG	602-634	GT	TGG
(GAG)	 AG	659-667	GT	GAG
(GGA)	 AG	693-737	GT	AGG
(AAA)	 AG	766-859	GT	GTG
(GAC)	 AG	885-949	GT	AAG
(AAT)	 AG	991-1048	GT	AGG
(GTT)	 AG	2082-2192	AC	AGA
-recovered GeneMark_model.108148_t, terminal, 2082, 2192
-recovered GeneMark_model.108148_t, internal, 23, 106
-recovered GeneMark_model.108148_t, internal, 201, 461
-recovered GeneMark_model.108148_t, internal, 487, 579
-recovered GeneMark_model.108148_t, internal, 602, 634
-recovered GeneMark_model.108148_t, internal, 659, 667
-recovered GeneMark_model.108148_t, internal, 693, 737
-recovered GeneMark_model.108148_t, internal, 766, 859
-recovered GeneMark_model.108148_t, internal, 885, 949
-recovered GeneMark_model.108148_t, internal, 991, 1048
Couldn't classify 4476, 4685
Sorry, prediction Augustus_model.g41281.t1 fails validation.
(ATG)	 TC	1037-1048	GT	AGG
(GTT)	 AG	2082-2174	GT	CAG
(ATT)	 AG	3299-3466	GT	AGG
(GTG)	 AG	4476-4685	GT	GGG
-recovered Augustus_model.g41281.t1, initial, 1037, 1048
-recovered Augustus_model.g41281.t1, internal, 2082, 2174
-recovered Augustus_model.g41281.t1, internal, 3299, 3466
-recovered Augustus_model.g41281.t1, internal, 4476, 4685
Couldn't classify 47, 426
Sorry, prediction snap_scaffold_661-snap.2-T1 fails validation.
(GCT)	 AG	47-426	GT	AGG
(GAC)	 AG	885-995	AG	GAA
-recovered snap_scaffold_661-snap.2-T1, terminal, 885, 995
-recovered snap_scaffold_661-snap.2-T1, internal, 47, 426
Couldn't classify 2082, 2174
Couldn't classify 4476, 4643
Sorry, prediction pasa_asmbl_49446.p1 fails validation.
(GTT)	 AG	2082-2174	GT	CAG
(ATT)	 AG	3299-3466	GT	AGG
(GTG)	 AG	4476-4643	GT	AGG
-recovered pasa_asmbl_49446.p1, internal, 2082, 2174
-recovered pasa_asmbl_49446.p1, internal, 3299, 3466
-recovered pasa_asmbl_49446.p1, internal, 4476, 4643
Valid prediction for GlimmerHMM_glimmerT_62098-T1
Couldn't classify 4789, 4885
Sorry, prediction GeneMark_model.108150_t fails validation.
(ATG)	 CT	3371-3466	GT	AGG
(GTG)	 AG	4476-4643	GT	AGG
(TGG)	 AG	4669-4685	GT	GGG
(AGG)	 AG	4789-4885	GT	CAG
-recovered GeneMark_model.108150_t, initial, 3371, 3466
-recovered GeneMark_model.108150_t, internal, 4476, 4643
-recovered GeneMark_model.108150_t, internal, 4669, 4685
-recovered GeneMark_model.108150_t, internal, 4789, 4885
Valid prediction for Augustus_model.g41280.t1
Couldn't classify 4476, 4643
Sorry, prediction GlimmerHMM_glimmerT_62099-T1 fails validation.
(ATG)	 TC	1037-1048	GT	AGG
(GTT)	 AG	2082-2174	GT	CAG
(ATT)	 AG	3299-3466	GT	AGG
(GTG)	 AG	4476-4643	GT	AGG
-recovered GlimmerHMM_glimmerT_62099-T1, initial, 1037, 1048
-recovered GlimmerHMM_glimmerT_62099-T1, internal, 2082, 2174
-recovered GlimmerHMM_glimmerT_62099-T1, internal, 3299, 3466
-recovered GlimmerHMM_glimmerT_62099-T1, internal, 4476, 4643
Couldn't classify 4476, 4753
Sorry, prediction snap_scaffold_661-snap.3-T1 fails validation.
(ATG)	 TC	1037-1048	GT	AGG
(GTT)	 AG	2082-2174	GT	CAG
(ATT)	 AG	3299-3466	GT	AGG
(GTG)	 AG	4476-4753	GT	ATG
-recovered snap_scaffold_661-snap.3-T1, initial, 1037, 1048
-recovered snap_scaffold_661-snap.3-T1, internal, 2082, 2174
-recovered snap_scaffold_661-snap.3-T1, internal, 3299, 3466
-recovered snap_scaffold_661-snap.3-T1, internal, 4476, 4753

-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.108149_t
Couldn't classify 354, 553
Couldn't classify 4788, 5067
Sorry, prediction snap_scaffold_661-snap.1-T1 fails validation.
(AGC)	 AG	354-553	GT	TGG
(ACA)	 AG	2916-3112	GT	GAG
(AGC)	 AG	4123-4197	GT	GAG
(CTG)	 AG	4788-5067	GT	GGG
-recovered snap_scaffold_661-snap.1-T1, internal, 354, 553
-recovered snap_scaffold_661-snap.1-T1, internal, 2916, 3112
-recovered snap_scaffold_661-snap.1-T1, internal, 4123, 4197
-recovered snap_scaffold_661-snap.1-T1, internal, 4788, 5067

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4731, rend_intergenic: 47  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5084
-exon list size: 51


building trellis

1.9    
3.8    
5.7    
7.5    
9.4    
11.3    
13.2    
15.1    
17.0    
18.9    
20.8    
22.6    
24.5    
26.4    
28.3    
30.2    
32.1    
34.0    
35.8    
37.7    
39.6    
41.5    
43.4    
45.3    
47.2    
49.1    
50.9    
52.8    
54.7    
56.6    
58.5    
60.4    
62.3    
64.2    
66.0    
67.9    
69.8    
71.7    
73.6    
75.5    
77.4    
79.2    
81.1    
83.0    
84.9    
86.8    
88.7    
90.6    
92.5    
94.3    
96.2    
98.1    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 4731, rend_intergenic: 47  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