-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_127

-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_127-snap.7-T1
Couldn't classify 8130, 8489
Sorry, prediction pasa_asmbl_9282.p1 fails validation.
(AGC)	 GC	8130-8489	CG	GAC
Valid prediction for GlimmerHMM_glimmerT_59850-T1
Valid prediction for Augustus_model.g39648.t1
Valid prediction for snap_scaffold_127-snap.5-T1
Valid prediction for Augustus_model.g39650.t1
Valid prediction for GlimmerHMM_glimmerT_59848-T1
Valid prediction for snap_scaffold_127-snap.2-T1
add_exon() Sorry, snap_scaffold_127-snap.2-T1 1718-1950-initial-1 is invalid.
add_exon() Sorry, snap_scaffold_127-snap.2-T1 2361-2460-internal-3 is invalid.
add_exon() Sorry, snap_scaffold_127-snap.2-T1 5011-5209-terminal-1 is invalid.
Couldn't classify 10745, 11266
Sorry, prediction pasa_asmbl_9283.p1 fails validation.
(CCG)	 CG	10745-11266	CG	AGC

-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 Augustus_model.g39649.t1
Valid prediction for GlimmerHMM_glimmerT_59847-T1
Valid prediction for GlimmerHMM_glimmerT_59849-T1
Couldn't classify 12627, 12881
Sorry, prediction snap_scaffold_127-snap.1-T1 fails validation.
(ATG)	 AG	5985-6088	GT	CGG
(GCG)	 AG	8939-8956	GT	GGG
(CTC)	 AG	12034-12192	GT	AGG
(AGG)	 AG	12627-12881	GT	AGG
-recovered snap_scaffold_127-snap.1-T1, initial, 5985, 6088
-recovered snap_scaffold_127-snap.1-T1, internal, 5985, 6088
-recovered snap_scaffold_127-snap.1-T1, internal, 8939, 8956
-recovered snap_scaffold_127-snap.1-T1, internal, 12034, 12192
-recovered snap_scaffold_127-snap.1-T1, internal, 12627, 12881
Valid prediction for Augustus_model.g39647.t1
Valid prediction for snap_scaffold_127-snap.4-T1
Couldn't classify 182, 448
Sorry, prediction snap_scaffold_127-snap.6-T1 fails validation.
(GCG)	 AG	182-448	GT	AGG
(AGG)	 AG	1234-1274	GT	CAG
(TGG)	 AG	1399-1667	GT	TTG
(TCA)	 AG	1740-1972	GT	CAG
(GGG)	 AG	2219-2364	TC	GAT
-recovered snap_scaffold_127-snap.6-T1, terminal, 2219, 2364
-recovered snap_scaffold_127-snap.6-T1, internal, 182, 448
-recovered snap_scaffold_127-snap.6-T1, internal, 1234, 1274
-recovered snap_scaffold_127-snap.6-T1, internal, 1399, 1667
-recovered snap_scaffold_127-snap.6-T1, internal, 1740, 1972
Valid prediction for snap_scaffold_127-snap.3-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7971, rend_intergenic: 1718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13774, rend_intergenic: 12673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 13955
-exon list size: 41


building trellis

2.3    
4.7    
7.0    
9.3    
11.6    
14.0    
16.3    
18.6    
20.9    
23.3    
25.6    
27.9    
30.2    
32.6    
34.9    
37.2    
39.5    
41.9    
44.2    
46.5    
48.8    
51.2    
53.5    
55.8    
58.1    
60.5    
62.8    
65.1    
67.4    
69.8    
72.1    
74.4    
76.7    
79.1    
81.4    
83.7    
86.0    
88.4    
90.7    
93.0    
95.3    
97.7    
-found 5 predictions from path traversal
Error with prediction: snap lend_intergenic: 7971, rend_intergenic: 1718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13774, rend_intergenic: 12673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support