-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_537

-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 GeneMark_model.107890_t
Couldn't classify 5896, 6004
Sorry, prediction GeneMark_model.107892_t fails validation.
(ATG)	 TG	5751-5796	GT	CGG
(GCG)	 AG	5896-6004	GC	CAG
-recovered GeneMark_model.107892_t, initial, 5751, 5796
-recovered GeneMark_model.107892_t, internal, 5896, 6004
Couldn't classify 5896, 5990
Sorry, prediction snap_scaffold_537-snap.2-T1 fails validation.
(ATG)	 GG	1373-1605	GT	AAG
(CAC)	 AG	2122-2590	GT	TGG
(GGA)	 AG	2613-2955	GT	AGG
(AAG)	 AG	2997-3061	GT	TCG
(GGT)	 AG	3131-3202	GT	AGG
(TAC)	 AG	3794-3904	GT	GGG
(AGT)	 AG	3916-3987	GT	GGG
(GGC)	 AG	4938-5205	GT	GGG
(TAG)	 AG	5537-5611	GT	AGG
(GCG)	 AG	5896-5990	GT	AGG
-recovered snap_scaffold_537-snap.2-T1, initial, 1373, 1605
add_exon() Sorry, snap_scaffold_537-snap.2-T1 2613-2955-terminal-3 is invalid.
-recovered snap_scaffold_537-snap.2-T1, terminal, 2613, 2955
-recovered snap_scaffold_537-snap.2-T1, internal, 2122, 2590
-recovered snap_scaffold_537-snap.2-T1, internal, 2613, 2955
-recovered snap_scaffold_537-snap.2-T1, internal, 2997, 3061
-recovered snap_scaffold_537-snap.2-T1, internal, 3131, 3202
-recovered snap_scaffold_537-snap.2-T1, internal, 3794, 3904
-recovered snap_scaffold_537-snap.2-T1, internal, 3916, 3987
-recovered snap_scaffold_537-snap.2-T1, internal, 4938, 5205
-recovered snap_scaffold_537-snap.2-T1, internal, 5537, 5611
-recovered snap_scaffold_537-snap.2-T1, internal, 5896, 5990

-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 87, 174
Sorry, prediction snap_scaffold_537-snap.3-T1 fails validation.
(CAG)	 AG	87-174	GT	TGG
(GGT)	 AG	393-491	GT	AGG
(TGT)	 AG	604-710	GT	AGG
(GGT)	 AG	951-1101	GT	GGG
(ACT)	 AG	1424-1507	GT	GGG
(TGC)	 AG	2075-2248	GT	AGG
(GTG)	 AG	2852-3015	GT	AGG
(GTA)	 AG	3316-3452	GT	GGG
(TGT)	 AG	3484-3610	TG	GAT
-recovered snap_scaffold_537-snap.3-T1, terminal, 3484, 3610
-recovered snap_scaffold_537-snap.3-T1, internal, 87, 174
-recovered snap_scaffold_537-snap.3-T1, internal, 393, 491
-recovered snap_scaffold_537-snap.3-T1, internal, 604, 710
-recovered snap_scaffold_537-snap.3-T1, internal, 951, 1101
-recovered snap_scaffold_537-snap.3-T1, internal, 1424, 1507
-recovered snap_scaffold_537-snap.3-T1, internal, 2075, 2248
-recovered snap_scaffold_537-snap.3-T1, internal, 2852, 3015
-recovered snap_scaffold_537-snap.3-T1, internal, 3316, 3452
Valid prediction for GeneMark_model.107891_t
Valid prediction for GlimmerHMM_glimmerT_61964-T1
Valid prediction for GlimmerHMM_glimmerT_61965-T1
Couldn't classify 1, 174
Couldn't classify 5829, 6019
Sorry, prediction HiQ_model.g41187.t1 fails validation.
(TGA)	 AG	1-174	GT	TGG
(GGT)	 AG	393-491	GT	AGG
(TGT)	 AG	604-710	GT	AGG
(GGT)	 AG	951-1101	GT	GGG
(ACT)	 AG	1424-1507	GT	GGG
(TGC)	 AG	2075-2248	GT	AGG
(GTG)	 AG	2852-3015	GT	AGG
(GTA)	 AG	3316-3452	GT	GGG
(GTT)	 AG	4372-4434	GT	AGG
(TGC)	 AG	5256-5368	GT	TGG
(ACT)	 AG	5829-6019		AG
-recovered HiQ_model.g41187.t1, internal, 393, 491
-recovered HiQ_model.g41187.t1, internal, 604, 710
-recovered HiQ_model.g41187.t1, internal, 951, 1101
-recovered HiQ_model.g41187.t1, internal, 1424, 1507
-recovered HiQ_model.g41187.t1, internal, 2075, 2248
-recovered HiQ_model.g41187.t1, internal, 2852, 3015
-recovered HiQ_model.g41187.t1, internal, 3316, 3452
-recovered HiQ_model.g41187.t1, internal, 4372, 4434
-recovered HiQ_model.g41187.t1, internal, 5256, 5368
Couldn't classify 393, 491
Sorry, prediction GlimmerHMM_glimmerT_61966-T1 fails validation.
(GGT)	 AG	393-491	GT	AGG
(TGT)	 AG	604-710	GT	AGG
(GGT)	 AG	951-1101	GT	GGG
(ACT)	 AG	1424-1507	GT	GGG
(GGC)	 AG	2096-2248	GT	AGG
(GTG)	 AG	2852-3015	GT	AGG
(GTA)	 AG	3316-3452	GT	GGG
(GAG)	 AG	3511-3610	TG	GAT
-recovered GlimmerHMM_glimmerT_61966-T1, terminal, 3511, 3610
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 393, 491
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 604, 710
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 951, 1101
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 1424, 1507
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 2096, 2248
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 2852, 3015
-recovered GlimmerHMM_glimmerT_61966-T1, internal, 3316, 3452
Valid prediction for GeneMark_model.107889_t
Couldn't classify 15, 174
Couldn't classify 5829, 5983
Sorry, prediction pasa_asmbl_46500.p1 fails validation.
(CTG)	 AG	15-174	GT	TGG
(GGT)	 AG	393-491	GT	AGG
(TGT)	 AG	604-710	GT	AGG
(GGT)	 AG	951-1101	GT	GGG
(ACT)	 AG	1424-1507	GT	GGG
(TGC)	 AG	2075-2248	GT	AGG
(GTG)	 AG	2852-3004	GT	CAG
(AAA)	 AG	3320-3452	GT	GGG
(GTT)	 AG	4372-4434	GT	AGG
(TGC)	 AG	5256-5368	GT	TGG
(ACT)	 AG	5829-5983	GG	TGG
-recovered pasa_asmbl_46500.p1, internal, 15, 174
-recovered pasa_asmbl_46500.p1, internal, 393, 491
-recovered pasa_asmbl_46500.p1, internal, 604, 710
-recovered pasa_asmbl_46500.p1, internal, 951, 1101
-recovered pasa_asmbl_46500.p1, internal, 1424, 1507
-recovered pasa_asmbl_46500.p1, internal, 2075, 2248
-recovered pasa_asmbl_46500.p1, internal, 2852, 3004
-recovered pasa_asmbl_46500.p1, internal, 3320, 3452
-recovered pasa_asmbl_46500.p1, internal, 4372, 4434
-recovered pasa_asmbl_46500.p1, internal, 5256, 5368
Valid prediction for CodingQuarry_transcript_52380-T1
Couldn't classify 5829, 5984
Sorry, prediction snap_scaffold_537-snap.1-T1 fails validation.
(ATG)	 TG	3644-3912	GT	TGG
(GTT)	 AG	4372-4434	GT	AGG
(TGC)	 AG	5256-5368	GT	TGG
(ACT)	 AG	5829-5984	GT	GGG
-recovered snap_scaffold_537-snap.1-T1, initial, 3644, 3912
-recovered snap_scaffold_537-snap.1-T1, internal, 4372, 4434
-recovered snap_scaffold_537-snap.1-T1, internal, 5256, 5368
-recovered snap_scaffold_537-snap.1-T1, internal, 5829, 5984

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2376, rend_intergenic: 1373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5990, rend_intergenic: 2410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 6019
-exon list size: 66


building trellis

1.5    
2.9    
4.4    
5.9    
7.4    
8.8    
10.3    
11.8    
13.2    
14.7    
16.2    
17.6    
19.1    
20.6    
22.1    
23.5    
25.0    
26.5    
27.9    
29.4    
30.9    
32.4    
33.8    
35.3    
36.8    
38.2    
39.7    
41.2    
42.6    
44.1    
45.6    
47.1    
48.5    
50.0    
51.5    
52.9    
54.4    
55.9    
57.4    
58.8    
60.3    
61.8    
63.2    
64.7    
66.2    
67.6    
69.1    
70.6    
72.1    
73.5    
75.0    
76.5    
77.9    
79.4    
80.9    
82.4    
83.8    
85.3    
86.8    
88.2    
89.7    
91.2    
92.6    
94.1    
95.6    
97.1    
98.5    
-found 1 predictions from path traversal
Error with prediction: snap lend_intergenic: 2376, rend_intergenic: 1373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5990, rend_intergenic: 2410  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