-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_101

-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 snap_scaffold_101-snap.2-T1
Couldn't classify 274, 324
Sorry, prediction snap_scaffold_101-snap.1-T1 fails validation.
(ATC)	 AG	274-324	GT	AGG
(TGG)	 AG	697-878	GT	GGG
(CTA)	 AG	1721-1744	TT	AAT
-recovered snap_scaffold_101-snap.1-T1, terminal, 1721, 1744
-recovered snap_scaffold_101-snap.1-T1, internal, 274, 324
-recovered snap_scaffold_101-snap.1-T1, internal, 697, 878
Couldn't classify 8685, 8728
Sorry, prediction GeneMark_model.106555_t fails validation.
(ATG)	 GG	7765-7767	GT	TGG
(TCC)	 AG	8158-8213	GT	CAG
(GTC)	 AG	8265-8492	GT	CCG
(GGG)	 AG	8685-8728	GT	CGG
-recovered GeneMark_model.106555_t, initial, 7765, 7767
-recovered GeneMark_model.106555_t, internal, 8158, 8213
-recovered GeneMark_model.106555_t, internal, 8265, 8492
-recovered GeneMark_model.106555_t, internal, 8685, 8728
Valid prediction for GeneMark_model.106553_t

-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 15524, 15652
Sorry, prediction Augustus_model.g40767.t1 fails validation.
(ATG)	 CC	14947-15133	GT	AGG
(GAA)	 AG	15524-15652	GT	AGG
-recovered Augustus_model.g40767.t1, initial, 14947, 15133
-recovered Augustus_model.g40767.t1, internal, 15524, 15652
Valid prediction for GlimmerHMM_glimmerT_61285-T1
Valid prediction for Augustus_model.g40768.t1
Valid prediction for CodingQuarry_transcript_5690-T1
Valid prediction for GlimmerHMM_glimmerT_61286-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61286-T1 7613-7772-terminal-1 is invalid.
Valid prediction for snap_scaffold_101-snap.3-T1
Couldn't classify 15, 309
Couldn't classify 404, 559
Sorry, prediction GeneMark_model.106556_t fails validation.
(TGT)	 AG	15-309	GT	CTG
(CAC)	 AG	404-559	GT	CTG
-recovered GeneMark_model.106556_t, internal, 15, 309
-recovered GeneMark_model.106556_t, internal, 404, 559
Valid prediction for GlimmerHMM_glimmerT_61283-T1
Couldn't classify 60, 309
Sorry, prediction snap_scaffold_101-snap.4-T1 fails validation.
(CAC)	 AG	60-309	GT	CTG
(CAC)	 AG	404-559	GT	CTG
(GAG)	 AG	7613-7772	TA	GAT
-recovered snap_scaffold_101-snap.4-T1, terminal, 7613, 7772
-recovered snap_scaffold_101-snap.4-T1, internal, 60, 309
-recovered snap_scaffold_101-snap.4-T1, internal, 404, 559
Valid prediction for GlimmerHMM_glimmerT_61284-T1
Couldn't classify 15524, 15652
Sorry, prediction GeneMark_model.106552_t fails validation.
(ATG)	 AG	10316-10318	GT	TGG
(TGG)	 AG	10546-10571	GT	ATG
(AAC)	 AG	10605-10641	GT	AGG
(AAC)	 AG	10718-10898	GT	AGG
(GAG)	 AG	11025-11124	GT	AGG
(GGA)	 AG	11434-11526	GT	AGG
(GGG)	 AG	11556-11573	GT	GAG
(GGC)	 AG	12214-12293	GT	TGG
(CCC)	 AG	14842-14937	GT	TGG
(AGA)	 AG	14987-15133	GT	AGG
(GAA)	 AG	15524-15652	GT	AGG
-recovered GeneMark_model.106552_t, initial, 10316, 10318
-recovered GeneMark_model.106552_t, internal, 10316, 10318
-recovered GeneMark_model.106552_t, internal, 10546, 10571
-recovered GeneMark_model.106552_t, internal, 10605, 10641
-recovered GeneMark_model.106552_t, internal, 10718, 10898
-recovered GeneMark_model.106552_t, internal, 11025, 11124
-recovered GeneMark_model.106552_t, internal, 11434, 11526
-recovered GeneMark_model.106552_t, internal, 11556, 11573
-recovered GeneMark_model.106552_t, internal, 12214, 12293
-recovered GeneMark_model.106552_t, internal, 14842, 14937
-recovered GeneMark_model.106552_t, internal, 14987, 15133
-recovered GeneMark_model.106552_t, internal, 15524, 15652

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5804, rend_intergenic: 4718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 15854
-exon list size: 61


building trellis

1.6    
3.2    
4.8    
6.3    
7.9    
9.5    
11.1    
12.7    
14.3    
15.9    
17.5    
19.0    
20.6    
22.2    
23.8    
25.4    
27.0    
28.6    
30.2    
31.7    
33.3    
34.9    
36.5    
38.1    
39.7    
41.3    
42.9    
44.4    
46.0    
47.6    
49.2    
50.8    
52.4    
54.0    
55.6    
57.1    
58.7    
60.3    
61.9    
63.5    
65.1    
66.7    
68.3    
69.8    
71.4    
73.0    
74.6    
76.2    
77.8    
79.4    
81.0    
82.5    
84.1    
85.7    
87.3    
88.9    
90.5    
92.1    
93.7    
95.2    
96.8    
98.4    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 5804, rend_intergenic: 4718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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