-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_120

-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 12822, 12960
Sorry, prediction snap_scaffold_120-snap.4-T1 fails validation.
(ATG)	 AG	6553-6571	GT	CCG
(ACC)	 AG	11876-12099	GT	AGG
(CGT)	 AG	12519-12653	GT	AGG
(GAG)	 AG	12822-12960	GT	AGG
-recovered snap_scaffold_120-snap.4-T1, initial, 6553, 6571
-recovered snap_scaffold_120-snap.4-T1, internal, 6553, 6571
-recovered snap_scaffold_120-snap.4-T1, internal, 11876, 12099
-recovered snap_scaffold_120-snap.4-T1, internal, 12519, 12653
-recovered snap_scaffold_120-snap.4-T1, internal, 12822, 12960
Couldn't classify 12822, 12960
Sorry, prediction GlimmerHMM_glimmerT_59833-T1 fails validation.
(ATG)	 TC	11460-11596	GT	AGG
(TTT)	 AG	11898-12099	GT	AGG
(CGT)	 AG	12519-12653	GT	AGG
(GAG)	 AG	12822-12960	GT	AGG
-recovered GlimmerHMM_glimmerT_59833-T1, initial, 11460, 11596
-recovered GlimmerHMM_glimmerT_59833-T1, internal, 11898, 12099
-recovered GlimmerHMM_glimmerT_59833-T1, internal, 12519, 12653
-recovered GlimmerHMM_glimmerT_59833-T1, internal, 12822, 12960
Valid prediction for Augustus_model.g39641.t1
Valid prediction for snap_scaffold_120-snap.2-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 snap_scaffold_120-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_59831-T1
Valid prediction for snap_scaffold_120-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_59832-T1
Couldn't classify 1797, 1964
Sorry, prediction snap_scaffold_120-snap.5-T1 fails validation.
(GTC)	 AG	1797-1964	GT	GGG
(AAG)	 AG	6833-6879	GA	AGG
-recovered snap_scaffold_120-snap.5-T1, terminal, 6833, 6879
-recovered snap_scaffold_120-snap.5-T1, internal, 1797, 1964
Couldn't classify 12976, 13164
Sorry, prediction Augustus_model.g39640.t1 fails validation.
(ATG)	 TC	8670-8730	GT	AGG
(GCC)	 AG	9307-9408	GT	TGG
(ACC)	 AG	9630-10069	GT	AGG
(CTT)	 AG	10711-10845	GT	AGG
(GCG)	 AG	11548-11578	GT	TGG
(ATG)	 AG	12976-13164	GT	TGG
-recovered Augustus_model.g39640.t1, initial, 8670, 8730
add_exon() Sorry, Augustus_model.g39640.t1 12976-13164-initial-1 is invalid.
-recovered Augustus_model.g39640.t1, initial, 12976, 13164
-recovered Augustus_model.g39640.t1, internal, 9307, 9408
-recovered Augustus_model.g39640.t1, internal, 9630, 10069
-recovered Augustus_model.g39640.t1, internal, 10711, 10845
-recovered Augustus_model.g39640.t1, internal, 11548, 11578
-recovered Augustus_model.g39640.t1, internal, 12976, 13164

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 1928, rend_intergenic: 1365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 2520, rend_intergenic: 2031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12960, rend_intergenic: 7579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 14457
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 1928, rend_intergenic: 1365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 2520, rend_intergenic: 2031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12960, rend_intergenic: 7579  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