-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_118

-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_118-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_61326-T1
Valid prediction for GeneMark_model.106631_t
Valid prediction for snap_scaffold_118-snap.1-T1
Valid prediction for GeneMark_model.106632_t
Valid prediction for snap_scaffold_118-snap.5-T1
Valid prediction for snap_scaffold_118-snap.6-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 12032, 12081
Sorry, prediction GeneMark_model.106630_t fails validation.
(ATG)	 TC	9207-9220	GT	GGG
(AGA)	 AG	9271-9394	GT	AGG
(AAG)	 AG	10181-10327	GT	AGG
(GCT)	 AG	10655-10843	GT	TGG
(GCC)	 AG	11378-11636	GT	AGG
(ATG)	 AG	12032-12081	GT	GAG
-recovered GeneMark_model.106630_t, initial, 9207, 9220
add_exon() Sorry, GeneMark_model.106630_t 12032-12081-initial-1 is invalid.
-recovered GeneMark_model.106630_t, initial, 12032, 12081
-recovered GeneMark_model.106630_t, internal, 9271, 9394
-recovered GeneMark_model.106630_t, internal, 10181, 10327
-recovered GeneMark_model.106630_t, internal, 10655, 10843
-recovered GeneMark_model.106630_t, internal, 11378, 11636
-recovered GeneMark_model.106630_t, internal, 12032, 12081
Valid prediction for GlimmerHMM_glimmerT_61325-T1
Valid prediction for Augustus_model.g40794.t1
Valid prediction for GlimmerHMM_glimmerT_61327-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61327-T1 2543-2696-terminal-1 is invalid.
Couldn't classify 2543, 2662
Sorry, prediction snap_scaffold_118-snap.4-T1 fails validation.
(GTT)	 AG	2543-2662	GT	GTG
(GAA)	 AG	3054-3146	GT	TGG
(GAC)	 AG	5737-5752	CC	AAC
-recovered snap_scaffold_118-snap.4-T1, terminal, 5737, 5752
-recovered snap_scaffold_118-snap.4-T1, internal, 2543, 2662
-recovered snap_scaffold_118-snap.4-T1, internal, 3054, 3146
Couldn't classify 2088, 2150
Sorry, prediction GeneMark_model.106633_t fails validation.
(CGG)	 AG	2088-2150	GT	CAG
(CGC)	 AG	2211-2223	GT	AAG
(CCC)	 AG	2481-2653	GT	AAG
(AAG)	 AG	2871-2898	CG	GAC
-recovered GeneMark_model.106633_t, terminal, 2871, 2898
-recovered GeneMark_model.106633_t, internal, 2088, 2150
-recovered GeneMark_model.106633_t, internal, 2211, 2223
-recovered GeneMark_model.106633_t, internal, 2481, 2653
Valid prediction for snap_scaffold_118-snap.2-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3163, rend_intergenic: 1444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7677, rend_intergenic: 3716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11994, rend_intergenic: 8888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 14536
-exon list size: 45


building trellis

2.1    
4.3    
6.4    
8.5    
10.6    
12.8    
14.9    
17.0    
19.1    
21.3    
23.4    
25.5    
27.7    
29.8    
31.9    
34.0    
36.2    
38.3    
40.4    
42.6    
44.7    
46.8    
48.9    
51.1    
53.2    
55.3    
57.4    
59.6    
61.7    
63.8    
66.0    
68.1    
70.2    
72.3    
74.5    
76.6    
78.7    
80.9    
83.0    
85.1    
87.2    
89.4    
91.5    
93.6    
95.7    
97.9    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 3163, rend_intergenic: 1444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7677, rend_intergenic: 3716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11994, rend_intergenic: 8888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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