-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_116

-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 13062, 13214
Sorry, prediction GeneMark_model.106619_t fails validation.
(AGA)	 AG	13062-13214	GC	GAG
(AGA)	 AG	13240-13316	GT	GGG
(ACA)	 AG	13741-13762	GT	ATG
(GTG)	 AG	13881-13937	GT	GGG
(GGC)	 AG	13978-14092	GT	GGG
(GGC)	 AG	14422-14529	AC	AAA
-recovered GeneMark_model.106619_t, terminal, 14422, 14529
-recovered GeneMark_model.106619_t, internal, 13062, 13214
-recovered GeneMark_model.106619_t, internal, 13240, 13316
-recovered GeneMark_model.106619_t, internal, 13741, 13762
-recovered GeneMark_model.106619_t, internal, 13881, 13937
-recovered GeneMark_model.106619_t, internal, 13978, 14092
Couldn't classify 6331, 6486
Sorry, prediction snap_scaffold_116-snap.2-T1 fails validation.
(ATG)	 GG	1373-1555	GT	AGG
(ATC)	 AG	2775-3026	GT	AGG
(CGC)	 AG	4854-5054	GT	AGG
(AAT)	 AG	5148-5273	GT	AGG
(ACG)	 AG	6331-6486	GT	GAG
-recovered snap_scaffold_116-snap.2-T1, initial, 1373, 1555
-recovered snap_scaffold_116-snap.2-T1, internal, 2775, 3026
-recovered snap_scaffold_116-snap.2-T1, internal, 4854, 5054
-recovered snap_scaffold_116-snap.2-T1, internal, 5148, 5273
-recovered snap_scaffold_116-snap.2-T1, internal, 6331, 6486
Valid prediction for GeneMark_model.106615_t
Valid prediction for GeneMark_model.106617_t
Valid prediction for snap_scaffold_116-snap.1-T1
add_exon() Sorry, snap_scaffold_116-snap.1-T1 914-1361-terminal-1 is invalid.
Couldn't classify 232, 266
Sorry, prediction GeneMark_model.106613_t fails validation.
(TGT)	 AG	232-266	GT	GAG
(GGG)	 AG	287-298	GT	GAG
(GAA)	 AG	580-588	GT	GAG
(TGA)	 AG	625-651	GT	GAG
(TGA)	 AG	678-722	GT	GAG
(GAG)	 AG	744-812	GT	GAG
(GGG)	 AG	955-1188	GT	GAG
(GAG)	 AG	1264-1350	GC	AGG
(ATT)	 AG	1394-1559	AT	AAA
-recovered GeneMark_model.106613_t, terminal, 1394, 1559
-recovered GeneMark_model.106613_t, internal, 232, 266
-recovered GeneMark_model.106613_t, internal, 287, 298
-recovered GeneMark_model.106613_t, internal, 580, 588
-recovered GeneMark_model.106613_t, internal, 625, 651
-recovered GeneMark_model.106613_t, internal, 678, 722
-recovered GeneMark_model.106613_t, internal, 744, 812
-recovered GeneMark_model.106613_t, internal, 955, 1188
-recovered GeneMark_model.106613_t, internal, 1264, 1350

-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 7836, 7942
Sorry, prediction GeneMark_model.106618_t fails validation.
(GTC)	 AG	7836-7942	GT	AGG
(CGG)	 AG	8225-8273	GT	AGG
(CGA)	 AG	8300-8432	GT	AGG
(TGG)	 AG	8539-8561	GT	AGG
(CTG)	 AG	8588-8637	GG	AAG
-recovered GeneMark_model.106618_t, terminal, 8588, 8637
-recovered GeneMark_model.106618_t, internal, 7836, 7942
-recovered GeneMark_model.106618_t, internal, 8225, 8273
-recovered GeneMark_model.106618_t, internal, 8300, 8432
-recovered GeneMark_model.106618_t, internal, 8539, 8561
Valid prediction for GeneMark_model.106620_t
add_exon() Sorry, GeneMark_model.106620_t 59-185-terminal-1 is invalid.
Valid prediction for Augustus_model.g40791.t1
Valid prediction for GeneMark_model.106616_t
Valid prediction for GlimmerHMM_glimmerT_61320-T1
Couldn't classify 7836, 7942
Couldn't classify 9735, 10007
Sorry, prediction snap_scaffold_116-snap.3-T1 fails validation.
(GTC)	 AG	7836-7942	GT	AGG
(CTG)	 AG	8588-8740	GT	CTG
(GGC)	 AG	9550-9692	GT	AAG
(CCG)	 AG	9735-10007	GT	CTG
-recovered snap_scaffold_116-snap.3-T1, internal, 7836, 7942
-recovered snap_scaffold_116-snap.3-T1, internal, 8588, 8740
-recovered snap_scaffold_116-snap.3-T1, internal, 9550, 9692
-recovered snap_scaffold_116-snap.3-T1, internal, 9735, 10007
Valid prediction for GlimmerHMM_glimmerT_61321-T1
Valid prediction for GeneMark_model.106614_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6486, rend_intergenic: 4822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 14828
-exon list size: 80


building trellis

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14.6    
15.9    
17.1    
18.3    
19.5    
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22.0    
23.2    
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25.6    
26.8    
28.0    
29.3    
30.5    
31.7    
32.9    
34.1    
35.4    
36.6    
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41.5    
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45.1    
46.3    
47.6    
48.8    
50.0    
51.2    
52.4    
53.7    
54.9    
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57.3    
58.5    
59.8    
61.0    
62.2    
63.4    
64.6    
65.9    
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68.3    
69.5    
70.7    
72.0    
73.2    
74.4    
75.6    
76.8    
78.0    
79.3    
80.5    
81.7    
82.9    
84.1    
85.4    
86.6    
87.8    
89.0    
90.2    
91.5    
92.7    
93.9    
95.1    
96.3    
97.6    
98.8    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 6486, rend_intergenic: 4822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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