-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1538

-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 143, 375
Couldn't classify 2063, 2106
Sorry, prediction snap_scaffold_1538-snap.1-T1 fails validation.
(GTA)	 AG	143-375	GT	AGG
(CTC)	 AG	477-527	GT	ATG
(TTG)	 AG	862-1056	GT	AAG
(GTT)	 AG	1307-1390	GT	AGG
(GGA)	 AG	2063-2106	GT	CCG
-recovered snap_scaffold_1538-snap.1-T1, internal, 143, 375
-recovered snap_scaffold_1538-snap.1-T1, internal, 477, 527
-recovered snap_scaffold_1538-snap.1-T1, internal, 862, 1056
-recovered snap_scaffold_1538-snap.1-T1, internal, 1307, 1390
-recovered snap_scaffold_1538-snap.1-T1, internal, 2063, 2106

-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 79, 251
Couldn't classify 1946, 2101
Sorry, prediction snap_scaffold_1538-snap.2-T1 fails validation.
(GAT)	 AG	79-251	GT	AGG
(GAT)	 AG	357-507	GT	AGG
(GCT)	 AG	841-956	GT	AGG
(ATG)	 AG	1270-1419	GT	AGG
(GAC)	 AG	1718-1895	GT	CCG
(GTG)	 AG	1946-2101	GT	AGG
add_exon() Sorry, snap_scaffold_1538-snap.2-T1 1270-1419-initial-1 is invalid.
-recovered snap_scaffold_1538-snap.2-T1, initial, 1270, 1419
-recovered snap_scaffold_1538-snap.2-T1, internal, 79, 251
-recovered snap_scaffold_1538-snap.2-T1, internal, 357, 507
-recovered snap_scaffold_1538-snap.2-T1, internal, 841, 956
-recovered snap_scaffold_1538-snap.2-T1, internal, 1270, 1419
-recovered snap_scaffold_1538-snap.2-T1, internal, 1718, 1895
-recovered snap_scaffold_1538-snap.2-T1, internal, 1946, 2101
Valid prediction for GlimmerHMM_glimmerT_62703-T1
Couldn't classify 79, 251
Couldn't classify 1946, 2101
Sorry, prediction pasa_asmbl_15975.p1 fails validation.
(GAT)	 AG	79-251	GT	AGG
(GAT)	 AG	357-507	GT	AGG
(GCT)	 AG	841-956	GT	AGG
(ATG)	 AG	1270-1419	GT	AGG
(GAC)	 AG	1718-1796	GT	AGG
(GTG)	 AG	1946-2101	GT	AGG
add_exon() Sorry, pasa_asmbl_15975.p1 1270-1419-initial-1 is invalid.
-recovered pasa_asmbl_15975.p1, initial, 1270, 1419
-recovered pasa_asmbl_15975.p1, internal, 79, 251
-recovered pasa_asmbl_15975.p1, internal, 357, 507
-recovered pasa_asmbl_15975.p1, internal, 841, 956
-recovered pasa_asmbl_15975.p1, internal, 1270, 1419
-recovered pasa_asmbl_15975.p1, internal, 1718, 1796
-recovered pasa_asmbl_15975.p1, internal, 1946, 2101
Couldn't classify 79, 251
Couldn't classify 2154, 2242
Sorry, prediction GeneMark_model.109454_t fails validation.
(GAT)	 AG	79-251	GT	AGG
(TTT)	 AG	384-507	GT	AGG
(GCT)	 AG	841-956	GT	AGG
(GGA)	 AG	983-1012	GT	AGG
(AAG)	 AG	1042-1050	GT	AGG
(GAG)	 AG	1078-1095	GT	AGG
(GAA)	 AG	1122-1145	GT	AAG
(GTA)	 AG	1169-1177	GT	CAG
(GGA)	 AG	1276-1419	GT	AGG
(GAC)	 AG	1718-1895	GT	CCG
(GTG)	 AG	1946-2101	GT	AGG
(GAG)	 AG	2154-2242	GT	GGG
-recovered GeneMark_model.109454_t, internal, 79, 251
-recovered GeneMark_model.109454_t, internal, 384, 507
-recovered GeneMark_model.109454_t, internal, 841, 956
-recovered GeneMark_model.109454_t, internal, 983, 1012
-recovered GeneMark_model.109454_t, internal, 1042, 1050
-recovered GeneMark_model.109454_t, internal, 1078, 1095
-recovered GeneMark_model.109454_t, internal, 1122, 1145
-recovered GeneMark_model.109454_t, internal, 1169, 1177
-recovered GeneMark_model.109454_t, internal, 1276, 1419
-recovered GeneMark_model.109454_t, internal, 1718, 1895
-recovered GeneMark_model.109454_t, internal, 1946, 2101
-recovered GeneMark_model.109454_t, internal, 2154, 2242
Couldn't classify 1946, 2101
Sorry, prediction Augustus_model.g41725.t1 fails validation.
(ATG)	 AG	88-251	GT	AGG
(GAT)	 AG	357-507	GT	AGG
(GCT)	 AG	841-956	GT	AGG
(ATG)	 AG	1270-1419	GT	AGG
(GAC)	 AG	1718-1796	GT	AGG
(GTG)	 AG	1946-2101	GT	AGG
-recovered Augustus_model.g41725.t1, initial, 88, 251
add_exon() Sorry, Augustus_model.g41725.t1 1270-1419-initial-1 is invalid.
-recovered Augustus_model.g41725.t1, initial, 1270, 1419
-recovered Augustus_model.g41725.t1, internal, 88, 251
-recovered Augustus_model.g41725.t1, internal, 357, 507
-recovered Augustus_model.g41725.t1, internal, 841, 956
-recovered Augustus_model.g41725.t1, internal, 1270, 1419
-recovered Augustus_model.g41725.t1, internal, 1718, 1796
-recovered Augustus_model.g41725.t1, internal, 1946, 2101

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2106, rend_intergenic: 151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 2251
-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: 2106, rend_intergenic: 151  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