-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_126

-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 246, 354
Sorry, prediction pasa_asmbl_9243.p1 fails validation.
(AGG)	 GC	246-354	GT	TGG
(GAG)	 AG	1414-1431	GT	TGG
(AGG)	 AG	2188-2214	GT	AGG
(GGA)	 AG	2305-2484	GT	AGG
(AGT)	 AG	3318-3452	GT	AGG
(ACG)	 AG	5590-5741	GA	AAG
add_exon() Sorry, pasa_asmbl_9243.p1 2305-2484-terminal-1 is invalid.
-recovered pasa_asmbl_9243.p1, terminal, 2305, 2484
-recovered pasa_asmbl_9243.p1, terminal, 5590, 5741
-recovered pasa_asmbl_9243.p1, internal, 1414, 1431
-recovered pasa_asmbl_9243.p1, internal, 2188, 2214
-recovered pasa_asmbl_9243.p1, internal, 2305, 2484
-recovered pasa_asmbl_9243.p1, internal, 3318, 3452
Couldn't classify 277, 354
Sorry, prediction snap_scaffold_126-snap.1-T1 fails validation.
(TCT)	 AG	277-354	GT	TGG
(GAT)	 AG	1505-1942	GT	CAG
(GAG)	 AG	2128-2214	GT	AGG
(GGA)	 AG	2305-2484	GT	AGG
(AGT)	 AG	3318-3463	CC	GAC
add_exon() Sorry, snap_scaffold_126-snap.1-T1 2305-2484-terminal-1 is invalid.
-recovered snap_scaffold_126-snap.1-T1, terminal, 2305, 2484
-recovered snap_scaffold_126-snap.1-T1, terminal, 3318, 3463
-recovered snap_scaffold_126-snap.1-T1, internal, 277, 354
-recovered snap_scaffold_126-snap.1-T1, internal, 1505, 1942
-recovered snap_scaffold_126-snap.1-T1, internal, 2128, 2214
-recovered snap_scaffold_126-snap.1-T1, internal, 2305, 2484
Valid prediction for GlimmerHMM_glimmerT_61340-T1
Couldn't classify 13459, 13467
Sorry, prediction GeneMark_model.106662_t fails validation.
(ATG)	 TG	10249-10320	GT	ACG
(AGA)	 AG	10423-10433	GT	GAG
(AGT)	 AG	10628-10669	GT	GAG
(AGA)	 AG	10779-10785	GT	GAG
(AGA)	 AG	10811-10821	GT	GAG
(AGA)	 AG	10849-10857	GT	GAG
(AGG)	 AG	10892-10897	GT	GAG
(TGC)	 AG	11082-11114	GT	GAG
(TGC)	 AG	11707-11713	GT	CTG
(AGG)	 AG	12116-12162	GT	AGG
(CTC)	 AG	12187-12321	GT	CTG
(CTA)	 AG	12467-12490	GT	CAG
(TAG)	 AG	12511-12591	GT	CAG
(CAG)	 AG	12614-12667	GT	CAG
(CAG)	 AG	12827-12853	GT	CAG
(TAG)	 AG	12877-12927	GT	CAG
(GAT)	 AG	13018-13062	GT	GCG
(GGG)	 AG	13459-13467	GT	AGG
-recovered GeneMark_model.106662_t, initial, 10249, 10320
add_exon() Sorry, GeneMark_model.106662_t 11082-11114-terminal-1 is invalid.
-recovered GeneMark_model.106662_t, terminal, 11082, 11114
-recovered GeneMark_model.106662_t, internal, 10423, 10433
-recovered GeneMark_model.106662_t, internal, 10628, 10669
-recovered GeneMark_model.106662_t, internal, 10779, 10785
-recovered GeneMark_model.106662_t, internal, 10811, 10821
-recovered GeneMark_model.106662_t, internal, 10849, 10857
-recovered GeneMark_model.106662_t, internal, 10892, 10897
-recovered GeneMark_model.106662_t, internal, 11082, 11114
-recovered GeneMark_model.106662_t, internal, 11707, 11713
-recovered GeneMark_model.106662_t, internal, 12116, 12162
-recovered GeneMark_model.106662_t, internal, 12187, 12321
-recovered GeneMark_model.106662_t, internal, 12467, 12490
-recovered GeneMark_model.106662_t, internal, 12511, 12591
-recovered GeneMark_model.106662_t, internal, 12614, 12667
-recovered GeneMark_model.106662_t, internal, 12827, 12853
-recovered GeneMark_model.106662_t, internal, 12877, 12927
-recovered GeneMark_model.106662_t, internal, 13018, 13062
-recovered GeneMark_model.106662_t, internal, 13459, 13467
Valid prediction for GlimmerHMM_glimmerT_61341-T1
Couldn't classify 248, 354
Sorry, prediction Augustus_model.g40801.t1 fails validation.
(GTA)	 AG	248-354	GT	TGG
(GAG)	 AG	1414-1431	GT	TGG
(AGG)	 AG	2188-2214	GT	AGG
(GGA)	 AG	2305-2484	GT	AGG
(AGT)	 AG	3318-3452	GT	AGG
(ACG)	 AG	5590-5741	GA	AAG
add_exon() Sorry, Augustus_model.g40801.t1 2305-2484-terminal-1 is invalid.
-recovered Augustus_model.g40801.t1, terminal, 2305, 2484
-recovered Augustus_model.g40801.t1, terminal, 5590, 5741
-recovered Augustus_model.g40801.t1, internal, 248, 354
-recovered Augustus_model.g40801.t1, internal, 1414, 1431
-recovered Augustus_model.g40801.t1, internal, 2188, 2214
-recovered Augustus_model.g40801.t1, internal, 2305, 2484
-recovered Augustus_model.g40801.t1, internal, 3318, 3452
Couldn't classify 12155, 12328
Sorry, prediction snap_scaffold_126-snap.2-T1 fails validation.
(ATG)	 AA	6615-6623	GT	TCG
(AAC)	 AG	7105-7514	GT	AGG
(ACG)	 AG	7525-7804	GT	GGG
(GGA)	 AG	7897-8034	GT	CGG
(AGG)	 AG	8119-8203	GT	GGG
(CGA)	 AG	12155-12328	GT	CAG
-recovered snap_scaffold_126-snap.2-T1, initial, 6615, 6623
-recovered snap_scaffold_126-snap.2-T1, internal, 7105, 7514
-recovered snap_scaffold_126-snap.2-T1, internal, 7525, 7804
-recovered snap_scaffold_126-snap.2-T1, internal, 7897, 8034
-recovered snap_scaffold_126-snap.2-T1, internal, 8119, 8203
-recovered snap_scaffold_126-snap.2-T1, internal, 12155, 12328
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 277, 354
Sorry, prediction GeneMark_model.106660_t fails validation.
(TCT)	 AG	277-354	GT	TGG
(GAG)	 AG	1414-1431	GT	TGG
(AGG)	 AG	1478-1942	GT	CAG
(GGA)	 AG	2305-2484	GT	AGG
(AGT)	 AG	3318-3452	GT	AGG
(ACG)	 AG	5590-5741	GA	AAG
add_exon() Sorry, GeneMark_model.106660_t 2305-2484-terminal-1 is invalid.
-recovered GeneMark_model.106660_t, terminal, 2305, 2484
-recovered GeneMark_model.106660_t, terminal, 5590, 5741
-recovered GeneMark_model.106660_t, internal, 277, 354
-recovered GeneMark_model.106660_t, internal, 1414, 1431
-recovered GeneMark_model.106660_t, internal, 1478, 1942
-recovered GeneMark_model.106660_t, internal, 2305, 2484
-recovered GeneMark_model.106660_t, internal, 3318, 3452

-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 1113, 1204
Sorry, prediction GlimmerHMM_glimmerT_61342-T1 fails validation.
(GTC)	 AG	1113-1204	GT	AGG
(AAG)	 AG	1898-2044	GT	ACG
(GAC)	 AG	5365-5465	GT	AGG
(GAA)	 AG	5833-7063	GC	GAG
-recovered GlimmerHMM_glimmerT_61342-T1, terminal, 5833, 7063
-recovered GlimmerHMM_glimmerT_61342-T1, internal, 1113, 1204
-recovered GlimmerHMM_glimmerT_61342-T1, internal, 1898, 2044
-recovered GlimmerHMM_glimmerT_61342-T1, internal, 5365, 5465
-recovered GlimmerHMM_glimmerT_61342-T1, internal, 5833, 7063
Couldn't classify 1113, 1204
Sorry, prediction snap_scaffold_126-snap.3-T1 fails validation.
(GTC)	 AG	1113-1204	GT	AGG
(AAG)	 AG	1898-2044	GT	ACG
(GTG)	 AG	3828-3869	GT	AGG
(GAC)	 AG	5365-5465	GT	AGG
(GAA)	 AG	5833-7063	GC	GAG
-recovered snap_scaffold_126-snap.3-T1, terminal, 5833, 7063
-recovered snap_scaffold_126-snap.3-T1, internal, 1113, 1204
-recovered snap_scaffold_126-snap.3-T1, internal, 1898, 2044
-recovered snap_scaffold_126-snap.3-T1, internal, 3828, 3869
-recovered snap_scaffold_126-snap.3-T1, internal, 5365, 5465
-recovered snap_scaffold_126-snap.3-T1, internal, 5833, 7063
Valid prediction for GeneMark_model.106661_t
Couldn't classify 789, 818
Sorry, prediction Augustus_model.g40802.t1 fails validation.
(GCT)	 AG	789-818	GT	AGG
(GTC)	 AG	1113-1204	GT	AGG
(AAG)	 AG	1898-2044	GT	ACG
(GAC)	 AG	5365-5465	GT	AGG
(GAA)	 AG	5833-7063	GC	GAG
-recovered Augustus_model.g40802.t1, terminal, 5833, 7063
-recovered Augustus_model.g40802.t1, internal, 789, 818
-recovered Augustus_model.g40802.t1, internal, 1113, 1204
-recovered Augustus_model.g40802.t1, internal, 1898, 2044
-recovered Augustus_model.g40802.t1, internal, 5365, 5465
-recovered Augustus_model.g40802.t1, internal, 5833, 7063

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12328, rend_intergenic: 7117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 14179
-exon list size: 89


building trellis

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6.6    
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8.8    
9.9    
11.0    
12.1    
13.2    
14.3    
15.4    
16.5    
17.6    
18.7    
19.8    
20.9    
22.0    
23.1    
24.2    
25.3    
26.4    
27.5    
28.6    
29.7    
30.8    
31.9    
33.0    
34.1    
35.2    
36.3    
37.4    
38.5    
39.6    
40.7    
41.8    
42.9    
44.0    
45.1    
46.2    
47.3    
48.4    
49.5    
50.5    
51.6    
52.7    
53.8    
54.9    
56.0    
57.1    
58.2    
59.3    
60.4    
61.5    
62.6    
63.7    
64.8    
65.9    
67.0    
68.1    
69.2    
70.3    
71.4    
72.5    
73.6    
74.7    
75.8    
76.9    
78.0    
79.1    
80.2    
81.3    
82.4    
83.5    
84.6    
85.7    
86.8    
87.9    
89.0    
90.1    
91.2    
92.3    
93.4    
94.5    
95.6    
96.7    
97.8    
98.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 12328, rend_intergenic: 7117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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