-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_665

-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_665-snap.2-T1
Couldn't classify 694, 711
Couldn't classify 4987, 5021
Sorry, prediction GeneMark_model.108156_t fails validation.
(GGA)	 AG	694-711	GT	ACG
(GAG)	 AG	732-752	GT	AGG
(ACA)	 AG	776-814	GT	AGG
(ACA)	 AG	838-870	GT	AAG
(AGG)	 AG	901-924	GT	GGG
(AGA)	 AG	947-961	GT	GAG
(GGC)	 AG	1259-1345	GT	ACG
(GGT)	 AG	1488-1502	GT	CGG
(GGA)	 AG	1527-1535	GT	GGG
(GTT)	 AG	1561-1623	GT	GGG
(TGG)	 AG	1839-1853	GT	GAG
(GGA)	 AG	1896-1904	GT	GAG
(GAG)	 AG	1938-2096	GT	GAG
(AGG)	 AG	2123-2228	GT	TGG
(TTG)	 AG	2551-2696	GT	AGG
(GAC)	 AG	4987-5021	GT	AAG
add_exon() Sorry, GeneMark_model.108156_t 2551-2696-terminal-2 is invalid.
-recovered GeneMark_model.108156_t, terminal, 2551, 2696
-recovered GeneMark_model.108156_t, internal, 694, 711
-recovered GeneMark_model.108156_t, internal, 732, 752
-recovered GeneMark_model.108156_t, internal, 776, 814
-recovered GeneMark_model.108156_t, internal, 838, 870
-recovered GeneMark_model.108156_t, internal, 901, 924
-recovered GeneMark_model.108156_t, internal, 947, 961
-recovered GeneMark_model.108156_t, internal, 1259, 1345
-recovered GeneMark_model.108156_t, internal, 1488, 1502
-recovered GeneMark_model.108156_t, internal, 1527, 1535
-recovered GeneMark_model.108156_t, internal, 1561, 1623
-recovered GeneMark_model.108156_t, internal, 1839, 1853
-recovered GeneMark_model.108156_t, internal, 1896, 1904
-recovered GeneMark_model.108156_t, internal, 1938, 2096
-recovered GeneMark_model.108156_t, internal, 2123, 2228
-recovered GeneMark_model.108156_t, internal, 2551, 2696
-recovered GeneMark_model.108156_t, internal, 4987, 5021

-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 275, 336
Sorry, prediction GlimmerHMM_glimmerT_62103-T1 fails validation.
(GTC)	 AG	275-336	GT	TGG
(TCA)	 AG	824-870	TC	GAT
-recovered GlimmerHMM_glimmerT_62103-T1, terminal, 824, 870
-recovered GlimmerHMM_glimmerT_62103-T1, internal, 275, 336
Couldn't classify 275, 336
Sorry, prediction snap_scaffold_665-snap.1-T1 fails validation.
(GTC)	 AG	275-336	GT	TGG
(GTG)	 AG	844-866	GT	AGG
(ACC)	 AG	2211-2404	GT	AGG
(ACA)	 AG	4479-4513	CA	AAC
-recovered snap_scaffold_665-snap.1-T1, terminal, 4479, 4513
-recovered snap_scaffold_665-snap.1-T1, internal, 275, 336
-recovered snap_scaffold_665-snap.1-T1, internal, 844, 866
-recovered snap_scaffold_665-snap.1-T1, internal, 2211, 2404

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4790, rend_intergenic: 645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5064
-exon list size: 44


building trellis

2.2    
4.3    
6.5    
8.7    
10.9    
13.0    
15.2    
17.4    
19.6    
21.7    
23.9    
26.1    
28.3    
30.4    
32.6    
34.8    
37.0    
39.1    
41.3    
43.5    
45.7    
47.8    
50.0    
52.2    
54.3    
56.5    
58.7    
60.9    
63.0    
65.2    
67.4    
69.6    
71.7    
73.9    
76.1    
78.3    
80.4    
82.6    
84.8    
87.0    
89.1    
91.3    
93.5    
95.7    
97.8    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 4790, rend_intergenic: 645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support