-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_53

-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 3463, 3786
Sorry, prediction snap_scaffold_53-snap.1-T1 fails validation.
(AGG)	 AG	3463-3786	GT	GGG
(ATA)	 AG	4947-5101	GT	AGG
(GGT)	 AG	5651-6016	CC	GAC
-recovered snap_scaffold_53-snap.1-T1, terminal, 5651, 6016
-recovered snap_scaffold_53-snap.1-T1, internal, 3463, 3786
-recovered snap_scaffold_53-snap.1-T1, internal, 4947, 5101
Valid prediction for Augustus_model.g39476.t1
Valid prediction for GlimmerHMM_glimmerT_59591-T1
Valid prediction for Augustus_model.g39478.t1
Couldn't classify 7905, 8179
Sorry, prediction pasa_asmbl_46539.p1 fails validation.
(ATG)	 GG	7398-7437	GT	TGG
(CTC)	 AG	7905-8179	AC	TGA
-recovered pasa_asmbl_46539.p1, initial, 7398, 7437
Couldn't classify 15309, 15481
Couldn't classify 15997, 16144
Sorry, prediction pasa_asmbl_46540.p1 fails validation.
(AGA)	 AC	15309-15481	GT	AGG
(AAT)	 AG	15667-15837	GT	AGG
(GCT)	 AG	15997-16144	AA	TCA
-recovered pasa_asmbl_46540.p1, internal, 15667, 15837
Valid prediction for snap_scaffold_53-snap.3-T1
Valid prediction for Augustus_model.g39477.t1

-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 31, 550
Sorry, prediction snap_scaffold_53-snap.5-T1 fails validation.
(CTT)	 AG	31-550	GT	CAG
(TCA)	 AG	1834-1974	GT	GGG
(TTA)	 AG	2046-2151	GT	CAG
(AAG)	 AG	2441-2634	GT	CGG
(GCC)	 AG	2739-2887	GT	GAG
(TCT)	 AG	2987-3260	GT	AAG
(GCT)	 AG	3367-3471	GT	CTG
(GTG)	 AG	3731-3829	TG	GAT
-recovered snap_scaffold_53-snap.5-T1, terminal, 3731, 3829
-recovered snap_scaffold_53-snap.5-T1, internal, 31, 550
-recovered snap_scaffold_53-snap.5-T1, internal, 1834, 1974
-recovered snap_scaffold_53-snap.5-T1, internal, 2046, 2151
-recovered snap_scaffold_53-snap.5-T1, internal, 2441, 2634
-recovered snap_scaffold_53-snap.5-T1, internal, 2739, 2887
-recovered snap_scaffold_53-snap.5-T1, internal, 2987, 3260
-recovered snap_scaffold_53-snap.5-T1, internal, 3367, 3471
Couldn't classify 1, 550
Sorry, prediction GlimmerHMM_glimmerT_59592-T1 fails validation.
(CAA)	 AA	1-550	GT	CAG
(TGC)	 AG	1869-1974	GT	GGG
(AAG)	 AG	2441-2634	GT	CGG
(GCC)	 AG	2739-2887	GT	GAG
(TCT)	 AG	2987-3260	GT	AAG
(GCT)	 AG	3367-3471	GT	CTG
(GTG)	 AG	3731-3829	TG	GAT
-recovered GlimmerHMM_glimmerT_59592-T1, terminal, 3731, 3829
-recovered GlimmerHMM_glimmerT_59592-T1, internal, 1869, 1974
-recovered GlimmerHMM_glimmerT_59592-T1, internal, 2441, 2634
-recovered GlimmerHMM_glimmerT_59592-T1, internal, 2739, 2887
-recovered GlimmerHMM_glimmerT_59592-T1, internal, 2987, 3260
-recovered GlimmerHMM_glimmerT_59592-T1, internal, 3367, 3471
Valid prediction for snap_scaffold_53-snap.4-T1
Valid prediction for snap_scaffold_53-snap.2-T1
Valid prediction for Augustus_model.g39479.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6016, rend_intergenic: 5937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7819, rend_intergenic: 6024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19798, rend_intergenic: 8961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 27609
-exon list size: 56


building trellis

1.7    
3.4    
5.2    
6.9    
8.6    
10.3    
12.1    
13.8    
15.5    
17.2    
19.0    
20.7    
22.4    
24.1    
25.9    
27.6    
29.3    
31.0    
32.8    
34.5    
36.2    
37.9    
39.7    
41.4    
43.1    
44.8    
46.6    
48.3    
50.0    
51.7    
53.4    
55.2    
56.9    
58.6    
60.3    
62.1    
63.8    
65.5    
67.2    
69.0    
70.7    
72.4    
74.1    
75.9    
77.6    
79.3    
81.0    
82.8    
84.5    
86.2    
87.9    
89.7    
91.4    
93.1    
94.8    
96.6    
98.3    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 6016, rend_intergenic: 5937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7819, rend_intergenic: 6024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19798, rend_intergenic: 8961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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