-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1084

-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 GeneMark_model.108865_t
Couldn't classify 715, 835
Couldn't classify 2890, 3029
Sorry, prediction Augustus_model.g41514.t1 fails validation.
(TAT)	 AG	715-835	GT	TGG
(CCA)	 AG	1379-1532	GT	GAG
(GGT)	 AG	1764-1998	GT	GGG
(GGA)	 AG	2890-3029	GT	AGG
-recovered Augustus_model.g41514.t1, internal, 715, 835
-recovered Augustus_model.g41514.t1, internal, 1379, 1532
-recovered Augustus_model.g41514.t1, internal, 1764, 1998
-recovered Augustus_model.g41514.t1, internal, 2890, 3029
Valid prediction for GeneMark_model.108867_t
Couldn't classify 2890, 3029
Sorry, prediction GlimmerHMM_glimmerT_62452-T1 fails validation.
(ATG)	 CT	1401-1649	GT	CCG
(GGT)	 AG	1764-1998	GT	GGG
(GGA)	 AG	2890-3029	GT	AGG
-recovered GlimmerHMM_glimmerT_62452-T1, initial, 1401, 1649
-recovered GlimmerHMM_glimmerT_62452-T1, internal, 1764, 1998
-recovered GlimmerHMM_glimmerT_62452-T1, internal, 2890, 3029
Valid prediction for GlimmerHMM_glimmerT_62451-T1
add_exon() Sorry, GlimmerHMM_glimmerT_62451-T1 257-426-terminal-1 is invalid.
Couldn't classify 257, 422
Couldn't classify 2890, 3029
Sorry, prediction snap_scaffold_1084-snap.2-T1 fails validation.
(AGC)	 AG	257-422	GT	ATG
(TTC)	 AG	728-830	GT	ACG
(TCG)	 AG	1386-1649	GT	CCG
(GGT)	 AG	1764-1998	GT	GGG
(GGA)	 AG	2890-3029	GT	AGG
-recovered snap_scaffold_1084-snap.2-T1, internal, 257, 422
-recovered snap_scaffold_1084-snap.2-T1, internal, 728, 830
-recovered snap_scaffold_1084-snap.2-T1, internal, 1386, 1649
-recovered snap_scaffold_1084-snap.2-T1, internal, 1764, 1998
-recovered snap_scaffold_1084-snap.2-T1, internal, 2890, 3029

-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.108866_t
Couldn't classify 313, 630
Couldn't classify 2943, 3087
Sorry, prediction snap_scaffold_1084-snap.1-T1 fails validation.
(AGC)	 AG	313-630	GT	AAG
(TTC)	 AG	807-873	GT	AAG
(GCG)	 AG	1343-1512	GT	AGG
(GGC)	 AG	2943-3087	GT	ATG
-recovered snap_scaffold_1084-snap.1-T1, internal, 313, 630
-recovered snap_scaffold_1084-snap.1-T1, internal, 807, 873
-recovered snap_scaffold_1084-snap.1-T1, internal, 1343, 1512
-recovered snap_scaffold_1084-snap.1-T1, internal, 2943, 3087
Couldn't classify 10, 85
Sorry, prediction GeneMark_model.108868_t fails validation.
(GGA)	 AG	10-85	GT	AAG
(GAT)	 AG	327-336	GT	AGG
(GTT)	 AG	381-635	GA	AAG
-recovered GeneMark_model.108868_t, terminal, 381, 635
-recovered GeneMark_model.108868_t, internal, 10, 85
-recovered GeneMark_model.108868_t, internal, 327, 336

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3022, rend_intergenic: 257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 3334
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 3022, rend_intergenic: 257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support