-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_652

-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 64, 154
Couldn't classify 4179, 4297
Sorry, prediction snap_scaffold_652-snap.2-T1 fails validation.
(CTG)	 AG	64-154	GT	ATG
(ACG)	 AG	3491-3835	GT	AGG
(GTT)	 AG	4179-4297	GT	TTG
-recovered snap_scaffold_652-snap.2-T1, internal, 64, 154
-recovered snap_scaffold_652-snap.2-T1, internal, 3491, 3835
-recovered snap_scaffold_652-snap.2-T1, internal, 4179, 4297
Couldn't classify 1132, 1225
Sorry, prediction GeneMark_model.108133_t fails validation.
(GGA)	 AG	1132-1225	GT	AGG
(GAG)	 AG	1269-1276	GT	AGG
(ATG)	 AG	1304-1553	GT	AGG
(GAG)	 AG	1589-1599	GT	TGG
(GTG)	 AG	1622-1765	GT	AGG
(GTG)	 AG	1812-1859	GT	AGG
(ATG)	 AG	1884-2012	GT	ATG
(GCC)	 AG	2186-2224	GT	GGG
(GGC)	 AG	2246-2278	GT	TGG
(TTC)	 AG	2299-2339	GT	TGG
(GGT)	 AG	2395-2503	GT	GAG
(GGG)	 AG	2555-2578	GT	GAG
(GAA)	 AG	3609-3614	GT	GGG
(AGG)	 AG	3656-3835	GT	AGG
(GAG)	 AG	3863-3917	GT	GAG
(GAC)	 AG	3952-3957	GA	GAG
add_exon() Sorry, GeneMark_model.108133_t 1304-1553-initial-1 is invalid.
-recovered GeneMark_model.108133_t, initial, 1304, 1553
add_exon() Sorry, GeneMark_model.108133_t 1884-2012-initial-1 is invalid.
-recovered GeneMark_model.108133_t, initial, 1884, 2012
-recovered GeneMark_model.108133_t, terminal, 2555, 2578
-recovered GeneMark_model.108133_t, terminal, 3952, 3957
-recovered GeneMark_model.108133_t, internal, 1132, 1225
-recovered GeneMark_model.108133_t, internal, 1269, 1276
-recovered GeneMark_model.108133_t, internal, 1304, 1553
-recovered GeneMark_model.108133_t, internal, 1589, 1599
-recovered GeneMark_model.108133_t, internal, 1622, 1765
-recovered GeneMark_model.108133_t, internal, 1812, 1859
-recovered GeneMark_model.108133_t, internal, 1884, 2012
-recovered GeneMark_model.108133_t, internal, 2186, 2224
-recovered GeneMark_model.108133_t, internal, 2246, 2278
-recovered GeneMark_model.108133_t, internal, 2299, 2339
-recovered GeneMark_model.108133_t, internal, 2395, 2503
-recovered GeneMark_model.108133_t, internal, 2555, 2578
-recovered GeneMark_model.108133_t, internal, 3609, 3614
-recovered GeneMark_model.108133_t, internal, 3656, 3835
-recovered GeneMark_model.108133_t, internal, 3863, 3917

-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 GlimmerHMM_glimmerT_62086-T1
Couldn't classify 106, 183
Sorry, prediction GeneMark_model.108134_t fails validation.
(GTC)	 AG	106-183	GT	AGG
(CAA)	 AG	873-955	GT	GGG
(GAG)	 AG	992-1073	GG	GAG
-recovered GeneMark_model.108134_t, terminal, 992, 1073
-recovered GeneMark_model.108134_t, internal, 106, 183
-recovered GeneMark_model.108134_t, internal, 873, 955
Couldn't classify 106, 183
Couldn't classify 4995, 5089
Sorry, prediction Augustus_model.g41272.t1 fails validation.
(GTC)	 AG	106-183	GT	AGG
(GAG)	 AG	507-572	GT	TGG
(GAC)	 AG	838-955	GT	GGG
(GTG)	 AG	1140-1218	GT	AGG
(GTA)	 AG	1576-1721	GT	AGG
(CTG)	 AG	2595-2824	GT	TGG
(GAG)	 AG	3004-3083	GT	AGG
(AGA)	 AG	4018-4093	GT	GAG
(ACA)	 AG	4593-4672	GT	AGG
(AGT)	 AG	4995-5089	GT	AGG
-recovered Augustus_model.g41272.t1, internal, 106, 183
-recovered Augustus_model.g41272.t1, internal, 507, 572
-recovered Augustus_model.g41272.t1, internal, 838, 955
-recovered Augustus_model.g41272.t1, internal, 1140, 1218
-recovered Augustus_model.g41272.t1, internal, 1576, 1721
-recovered Augustus_model.g41272.t1, internal, 2595, 2824
-recovered Augustus_model.g41272.t1, internal, 3004, 3083
-recovered Augustus_model.g41272.t1, internal, 4018, 4093
-recovered Augustus_model.g41272.t1, internal, 4593, 4672
-recovered Augustus_model.g41272.t1, internal, 4995, 5089
Couldn't classify 106, 183
Couldn't classify 4995, 5089
Sorry, prediction snap_scaffold_652-snap.1-T1 fails validation.
(GTC)	 AG	106-183	GT	AGG
(GAG)	 AG	507-572	GT	TGG
(GAC)	 AG	838-1108	GT	AAG
(GTG)	 AG	1140-1218	GT	AGG
(GTA)	 AG	1576-1721	GT	AGG
(CTG)	 AG	2595-2824	GT	TGG
(GAG)	 AG	3004-3083	GT	AGG
(AGA)	 AG	4018-4093	GT	GAG
(ACA)	 AG	4593-4672	GT	AGG
(AGT)	 AG	4995-5089	GT	AGG
-recovered snap_scaffold_652-snap.1-T1, internal, 106, 183
-recovered snap_scaffold_652-snap.1-T1, internal, 507, 572
-recovered snap_scaffold_652-snap.1-T1, internal, 838, 1108
-recovered snap_scaffold_652-snap.1-T1, internal, 1140, 1218
-recovered snap_scaffold_652-snap.1-T1, internal, 1576, 1721
-recovered snap_scaffold_652-snap.1-T1, internal, 2595, 2824
-recovered snap_scaffold_652-snap.1-T1, internal, 3004, 3083
-recovered snap_scaffold_652-snap.1-T1, internal, 4018, 4093
-recovered snap_scaffold_652-snap.1-T1, internal, 4593, 4672
-recovered snap_scaffold_652-snap.1-T1, internal, 4995, 5089
Couldn't classify 4995, 5097
Sorry, prediction pasa_asmbl_49437.p1 fails validation.
(ATG)	 CC	1160-1218	GT	AGG
(GTA)	 AG	1576-1721	GT	AGG
(CTG)	 AG	2595-2824	GT	TGG
(GAG)	 AG	3004-3083	GT	AGG
(AGA)	 AG	4018-4093	GT	GAG
(ACA)	 AG	4593-4672	GT	AGG
(AGT)	 AG	4995-5097	GG	GAG
-recovered pasa_asmbl_49437.p1, initial, 1160, 1218
-recovered pasa_asmbl_49437.p1, internal, 1576, 1721
-recovered pasa_asmbl_49437.p1, internal, 2595, 2824
-recovered pasa_asmbl_49437.p1, internal, 3004, 3083
-recovered pasa_asmbl_49437.p1, internal, 4018, 4093
-recovered pasa_asmbl_49437.p1, internal, 4593, 4672
Couldn't classify 106, 183
Sorry, prediction GlimmerHMM_glimmerT_62087-T1 fails validation.
(GTC)	 AG	106-183	GT	AGG
(GAG)	 AG	507-572	GT	TGG
(CAA)	 AG	873-959	GA	GAG
-recovered GlimmerHMM_glimmerT_62087-T1, terminal, 873, 959
-recovered GlimmerHMM_glimmerT_62087-T1, internal, 106, 183
-recovered GlimmerHMM_glimmerT_62087-T1, internal, 507, 572

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5024, rend_intergenic: 64  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 5129
-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 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5024, rend_intergenic: 64  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