-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_111

-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_111-snap.1-T1
Valid prediction for GeneMark_model.106597_t
Valid prediction for CodingQuarry_transcript_8344-T1
Valid prediction for snap_scaffold_111-snap.2-T1
Valid prediction for Augustus_model.g40783.t1
Valid prediction for HiQ_model.g40784.t1
Valid prediction for pasa_asmbl_7365.p1
Valid prediction for GeneMark_model.106598_t
Valid prediction for GlimmerHMM_glimmerT_61310-T1
Valid prediction for GlimmerHMM_glimmerT_61309-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: -)Valid prediction for GlimmerHMM_glimmerT_61311-T1
Valid prediction for snap_scaffold_111-snap.3-T1
Valid prediction for CodingQuarry_transcript_8345-T1
Couldn't classify 16, 90
Sorry, prediction GeneMark_model.106599_t fails validation.
(ACC)	 AG	16-90	GT	AGG
(CGT)	 AG	133-149	GT	GGG
(GGC)	 AG	177-260	GC	GCG
(AGC)	 AG	2339-2350	GT	GCG
(CGT)	 AG	2396-2561	GT	AGG
(GGA)	 AG	2594-2601	GT	CAG
(GGG)	 AG	2655-2744	GT	AGG
(GAG)	 AG	2767-2908	GG	AAG
-recovered GeneMark_model.106599_t, terminal, 2767, 2908
-recovered GeneMark_model.106599_t, internal, 16, 90
-recovered GeneMark_model.106599_t, internal, 133, 149
-recovered GeneMark_model.106599_t, internal, 177, 260
-recovered GeneMark_model.106599_t, internal, 2339, 2350
-recovered GeneMark_model.106599_t, internal, 2396, 2561
-recovered GeneMark_model.106599_t, internal, 2594, 2601
-recovered GeneMark_model.106599_t, internal, 2655, 2744

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12562, rend_intergenic: 8457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 15000
-exon list size: 50


building trellis

1.9    
3.8    
5.8    
7.7    
9.6    
11.5    
13.5    
15.4    
17.3    
19.2    
21.2    
23.1    
25.0    
26.9    
28.8    
30.8    
32.7    
34.6    
36.5    
38.5    
40.4    
42.3    
44.2    
46.2    
48.1    
50.0    
51.9    
53.8    
55.8    
57.7    
59.6    
61.5    
63.5    
65.4    
67.3    
69.2    
71.2    
73.1    
75.0    
76.9    
78.8    
80.8    
82.7    
84.6    
86.5    
88.5    
90.4    
92.3    
94.2    
96.2    
98.1    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 12562, rend_intergenic: 8457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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