-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_321

-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: +)Couldn't classify 6493, 6576
Sorry, prediction snap_scaffold_321-snap.3-T1 fails validation.
(ATG)	 GA	3774-3786	GT	AGG
(TTC)	 AG	3871-4134	GT	GGG
(GGG)	 AG	6493-6576	GT	GGG
-recovered snap_scaffold_321-snap.3-T1, initial, 3774, 3786
-recovered snap_scaffold_321-snap.3-T1, internal, 3871, 4134
-recovered snap_scaffold_321-snap.3-T1, internal, 6493, 6576
Couldn't classify 1291, 1427
Sorry, prediction snap_scaffold_321-snap.1-T1 fails validation.
(TAC)	 AG	1291-1427	GT	AGG
(CCT)	 AG	3336-3508	GA	AGG
-recovered snap_scaffold_321-snap.1-T1, terminal, 3336, 3508
-recovered snap_scaffold_321-snap.1-T1, internal, 1291, 1427

-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 CodingQuarry_transcript_46520-T1
Couldn't classify 94, 180
Couldn't classify 6657, 6851
Sorry, prediction snap_scaffold_321-snap.2-T1 fails validation.
(GGG)	 AG	94-180	GT	AGG
(CCT)	 AG	1135-1227	GT	CGG
(CCT)	 AG	3419-3475	GT	CGG
(GGG)	 AG	3859-3921	GT	AGG
(GGT)	 AG	4745-4869	GT	AGG
(GCT)	 AG	5004-5054	GT	AGG
(GTG)	 AG	5943-5990	GT	AGG
(GTT)	 AG	6657-6851	GT	TGG
add_exon() Sorry, snap_scaffold_321-snap.2-T1 94-180-terminal-1 is invalid.
-recovered snap_scaffold_321-snap.2-T1, terminal, 94, 180
-recovered snap_scaffold_321-snap.2-T1, internal, 94, 180
-recovered snap_scaffold_321-snap.2-T1, internal, 1135, 1227
-recovered snap_scaffold_321-snap.2-T1, internal, 3419, 3475
-recovered snap_scaffold_321-snap.2-T1, internal, 3859, 3921
-recovered snap_scaffold_321-snap.2-T1, internal, 4745, 4869
-recovered snap_scaffold_321-snap.2-T1, internal, 5004, 5054
-recovered snap_scaffold_321-snap.2-T1, internal, 5943, 5990
-recovered snap_scaffold_321-snap.2-T1, internal, 6657, 6851
Valid prediction for GlimmerHMM_glimmerT_60195-T1
Valid prediction for CodingQuarry_transcript_46521-T1
Couldn't classify 3, 180
Sorry, prediction pasa_asmbl_40958.p1 fails validation.
(TGT)	 TG	3-180	GT	AGG
(CCT)	 AG	1135-1227	GT	CGG
(CCT)	 AG	3419-3475	GT	CGG
(GGG)	 AG	3859-3921	GT	AGG
(GGT)	 AG	4745-4869	GT	AGG
(GCT)	 AG	5004-5054	GT	AGG
(GTG)	 AG	5943-5990	GT	AGG
(GTC)	 AG	6066-6143	CA	AAC
-recovered pasa_asmbl_40958.p1, terminal, 6066, 6143
-recovered pasa_asmbl_40958.p1, internal, 1135, 1227
-recovered pasa_asmbl_40958.p1, internal, 3419, 3475
-recovered pasa_asmbl_40958.p1, internal, 3859, 3921
-recovered pasa_asmbl_40958.p1, internal, 4745, 4869
-recovered pasa_asmbl_40958.p1, internal, 5004, 5054
-recovered pasa_asmbl_40958.p1, internal, 5943, 5990
Valid prediction for HiQ_model.g39849.t1
Couldn't classify 94, 180
Sorry, prediction GlimmerHMM_glimmerT_60196-T1 fails validation.
(GGG)	 AG	94-180	GT	AGG
(CCT)	 AG	1135-1227	GT	CGG
(CCT)	 AG	3419-3475	GT	CGG
(GGG)	 AG	3859-3983	TC	AAT
add_exon() Sorry, GlimmerHMM_glimmerT_60196-T1 94-180-terminal-1 is invalid.
-recovered GlimmerHMM_glimmerT_60196-T1, terminal, 94, 180
-recovered GlimmerHMM_glimmerT_60196-T1, terminal, 3859, 3983
-recovered GlimmerHMM_glimmerT_60196-T1, internal, 94, 180
-recovered GlimmerHMM_glimmerT_60196-T1, internal, 1135, 1227
-recovered GlimmerHMM_glimmerT_60196-T1, internal, 3419, 3475
Valid prediction for GlimmerHMM_glimmerT_60194-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3508, rend_intergenic: 1298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8055, rend_intergenic: 3774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8148
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 3508, rend_intergenic: 1298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8055, rend_intergenic: 3774  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