-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1999

-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 220, 398
Couldn't classify 1439, 1597
Sorry, prediction snap_scaffold_1999-snap.2-T1 fails validation.
(GCC)	 AG	220-398	GT	AGG
(ACC)	 AG	1110-1239	GT	GCG
(GAT)	 AG	1439-1597	GT	TGG
-recovered snap_scaffold_1999-snap.2-T1, internal, 220, 398
-recovered snap_scaffold_1999-snap.2-T1, internal, 1110, 1239
-recovered snap_scaffold_1999-snap.2-T1, internal, 1439, 1597
Couldn't classify 29, 143
Couldn't classify 1439, 1597
Sorry, prediction GeneMark_model.109934_t fails validation.
(GGA)	 AG	29-143	GT	AGG
(GCC)	 AG	220-398	GT	AGG
(AAA)	 AG	421-435	GC	GAG
(GGA)	 AG	459-614	GT	AGG
(AGA)	 AG	637-648	GT	AGG
(AGA)	 AG	669-674	GT	AGG
(AGA)	 AG	695-706	GT	AGG
(AGA)	 AG	727-732	GT	AGG
(AGA)	 AG	771-782	GT	AGG
(AGA)	 AG	803-808	GT	AGG
(AGA)	 AG	833-1024	GT	AGG
(AGA)	 AG	1051-1056	GT	AGG
(GTT)	 AG	1080-1239	GT	GCG
(GAT)	 AG	1439-1597	GT	TGG
-recovered GeneMark_model.109934_t, internal, 29, 143
-recovered GeneMark_model.109934_t, internal, 220, 398
-recovered GeneMark_model.109934_t, internal, 421, 435
-recovered GeneMark_model.109934_t, internal, 459, 614
-recovered GeneMark_model.109934_t, internal, 637, 648
-recovered GeneMark_model.109934_t, internal, 669, 674
-recovered GeneMark_model.109934_t, internal, 695, 706
-recovered GeneMark_model.109934_t, internal, 727, 732
-recovered GeneMark_model.109934_t, internal, 771, 782
-recovered GeneMark_model.109934_t, internal, 803, 808
-recovered GeneMark_model.109934_t, internal, 833, 1024
-recovered GeneMark_model.109934_t, internal, 1051, 1056
-recovered GeneMark_model.109934_t, internal, 1080, 1239
-recovered GeneMark_model.109934_t, internal, 1439, 1597
Couldn't classify 1439, 1597
Sorry, prediction GlimmerHMM_glimmerT_62929-T1 fails validation.
(ATG)	 AG	346-398	GT	AGG
(ACC)	 AG	1110-1239	GT	GCG
(GAT)	 AG	1439-1597	GT	TGG
-recovered GlimmerHMM_glimmerT_62929-T1, initial, 346, 398
-recovered GlimmerHMM_glimmerT_62929-T1, internal, 346, 398
-recovered GlimmerHMM_glimmerT_62929-T1, internal, 1110, 1239
-recovered GlimmerHMM_glimmerT_62929-T1, internal, 1439, 1597
Couldn't classify 220, 398
Couldn't classify 1439, 1597
Sorry, prediction Augustus_model.g41907.t1 fails validation.
(GCC)	 AG	220-398	GT	AGG
(ACC)	 AG	1110-1239	GT	GCG
(GAT)	 AG	1439-1597	GT	TGG
-recovered Augustus_model.g41907.t1, internal, 220, 398
-recovered Augustus_model.g41907.t1, internal, 1110, 1239
-recovered Augustus_model.g41907.t1, internal, 1439, 1597
Couldn't classify 220, 398
Couldn't classify 1439, 1678
Sorry, prediction pasa_asmbl_22803.p1 fails validation.
(GCC)	 AG	220-398	GT	AGG
(ACC)	 AG	1110-1239	GT	GCG
(GAT)	 AG	1439-1678	A	TTA
-recovered pasa_asmbl_22803.p1, internal, 220, 398
-recovered pasa_asmbl_22803.p1, internal, 1110, 1239

-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 133, 223
Couldn't classify 1344, 1479
Sorry, prediction snap_scaffold_1999-snap.1-T1 fails validation.
(CCT)	 AG	133-223	GT	AGG
(GAT)	 AG	1344-1479	GT	AGG
-recovered snap_scaffold_1999-snap.1-T1, internal, 133, 223
-recovered snap_scaffold_1999-snap.1-T1, internal, 1344, 1479

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 1547, rend_intergenic: 220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 1679
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 1547, rend_intergenic: 220  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