-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_252

-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 6093, 6218
Sorry, prediction snap_scaffold_252-snap.2-T1 fails validation.
(ATG)	 AT	3386-3493	GT	TAG
(TTG)	 AG	5459-5504	GT	CAG
(ACT)	 AG	6093-6218	GT	CAG
-recovered snap_scaffold_252-snap.2-T1, initial, 3386, 3493
-recovered snap_scaffold_252-snap.2-T1, internal, 5459, 5504
-recovered snap_scaffold_252-snap.2-T1, internal, 6093, 6218
Valid prediction for GeneMark_model.107085_t
Valid prediction for GlimmerHMM_glimmerT_61581-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61581-T1 155-332-terminal-1 is invalid.
Valid prediction for Augustus_model.g40949.t1
add_exon() Sorry, Augustus_model.g40949.t1 140-332-terminal-1 is invalid.
Valid prediction for snap_scaffold_252-snap.1-T1
add_exon() Sorry, snap_scaffold_252-snap.1-T1 140-332-terminal-1 is invalid.

-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 815, 841
Sorry, prediction GeneMark_model.107086_t fails validation.
(AGA)	 AG	815-841	GT	GAG
(AGA)	 AG	867-893	GT	GAG
(TCA)	 AG	917-979	GT	GAG
(ACA)	 AG	1003-1050	GT	GCG
(ACA)	 AG	1137-1304	GT	GAG
(AGG)	 AG	1328-1471	GT	GGG
(GGT)	 AG	1654-1693	GT	TAG
(GTG)	 AG	2541-2629	GT	GAG
(AGG)	 AG	2662-2775	GT	AGG
(GAA)	 AG	2799-2813	GT	AGG
(GTG)	 AG	3508-3657	GT	GAG
(GCG)	 AG	3687-3704	GT	GTG
(GAG)	 AG	3738-3897	GG	GAG
-recovered GeneMark_model.107086_t, terminal, 3738, 3897
-recovered GeneMark_model.107086_t, internal, 815, 841
-recovered GeneMark_model.107086_t, internal, 867, 893
-recovered GeneMark_model.107086_t, internal, 917, 979
-recovered GeneMark_model.107086_t, internal, 1003, 1050
-recovered GeneMark_model.107086_t, internal, 1137, 1304
-recovered GeneMark_model.107086_t, internal, 1328, 1471
-recovered GeneMark_model.107086_t, internal, 1654, 1693
-recovered GeneMark_model.107086_t, internal, 2541, 2629
-recovered GeneMark_model.107086_t, internal, 2662, 2775
-recovered GeneMark_model.107086_t, internal, 2799, 2813
-recovered GeneMark_model.107086_t, internal, 3508, 3657
-recovered GeneMark_model.107086_t, internal, 3687, 3704
Valid prediction for snap_scaffold_252-snap.3-T1
Couldn't classify 8755, 8855
Sorry, prediction GeneMark_model.107084_t fails validation.
(ATG)	 AT	8392-8546	GT	GCG
(GAG)	 AG	8755-8855	GT	AGG
-recovered GeneMark_model.107084_t, initial, 8392, 8546
-recovered GeneMark_model.107084_t, internal, 8755, 8855
Couldn't classify 1096, 1471
Sorry, prediction snap_scaffold_252-snap.4-T1 fails validation.
(GCA)	 AG	1096-1471	GT	GGG
(GAC)	 AG	2582-2779	GA	GAG
-recovered snap_scaffold_252-snap.4-T1, terminal, 2582, 2779
-recovered snap_scaffold_252-snap.4-T1, internal, 1096, 1471
Valid prediction for GlimmerHMM_glimmerT_61582-T1
Valid prediction for GlimmerHMM_glimmerT_61583-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6218, rend_intergenic: 3449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 9020
-exon list size: 58


building trellis

1.7    
3.3    
5.0    
6.7    
8.3    
10.0    
11.7    
13.3    
15.0    
16.7    
18.3    
20.0    
21.7    
23.3    
25.0    
26.7    
28.3    
30.0    
31.7    
33.3    
35.0    
36.7    
38.3    
40.0    
41.7    
43.3    
45.0    
46.7    
48.3    
50.0    
51.7    
53.3    
55.0    
56.7    
58.3    
60.0    
61.7    
63.3    
65.0    
66.7    
68.3    
70.0    
71.7    
73.3    
75.0    
76.7    
78.3    
80.0    
81.7    
83.3    
85.0    
86.7    
88.3    
90.0    
91.7    
93.3    
95.0    
96.7    
98.3    
-found 3 predictions from path traversal
Error with prediction: snap lend_intergenic: 6218, rend_intergenic: 3449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support