-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_540

-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 GlimmerHMM_glimmerT_61969-T1
Couldn't classify 73, 665
Sorry, prediction GeneMark_model.107895_t fails validation.
(CAA)	 AG	73-665	GT	AGG
(GTC)	 AG	718-744	GT	AGG
(GGT)	 AG	882-903	GG	AGG
-recovered GeneMark_model.107895_t, terminal, 882, 903
-recovered GeneMark_model.107895_t, internal, 73, 665
-recovered GeneMark_model.107895_t, internal, 718, 744
Valid prediction for Augustus_model.g41190.t1
add_exon() Sorry, Augustus_model.g41190.t1 48-634-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g41190.t1 1093-1172-terminal-3 is invalid.
Valid prediction for snap_scaffold_540-snap.1-T1
add_exon() Sorry, snap_scaffold_540-snap.1-T1 48-690-initial-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: -)Valid prediction for snap_scaffold_540-snap.2-T1
Valid prediction for Augustus_model.g41191.t1
Couldn't classify 893, 1051
Sorry, prediction GlimmerHMM_glimmerT_61970-T1 fails validation.
(GAA)	 AG	893-1051	GT	AGG
(GAG)	 AG	1185-1301	GT	CTG
(GTG)	 AG	1391-1535	GT	AGG
(TGG)	 AG	1743-1849	GT	AGG
(ATG)	 AG	2653-2763	GG	AAG
-recovered GlimmerHMM_glimmerT_61970-T1, terminal, 2653, 2763
-recovered GlimmerHMM_glimmerT_61970-T1, internal, 893, 1051
-recovered GlimmerHMM_glimmerT_61970-T1, internal, 1185, 1301
-recovered GlimmerHMM_glimmerT_61970-T1, internal, 1391, 1535
-recovered GlimmerHMM_glimmerT_61970-T1, internal, 1743, 1849
Valid prediction for GeneMark_model.107896_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3399, rend_intergenic: 301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6000
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 3399, rend_intergenic: 301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support