-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_62

-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 GlimmerHMM_glimmerT_61139-T1
Valid prediction for GlimmerHMM_glimmerT_61137-T1
Couldn't classify 10683, 10700
Couldn't classify 13483, 13593
Sorry, prediction pasa_asmbl_49414.p1 fails validation.
(CTG)	 AC	10683-10700	GT	AGG
(GTG)	 AG	10811-10996	GT	AGG
(GCT)	 AG	11103-11316	GT	AGG
(GAA)	 AG	12149-12283	GT	TGG
(ACT)	 AG	12854-12972	GT	AAG
(ATA)	 AG	13240-13353	GT	AGG
(GTC)	 AG	13483-13593	GT	AGG
-recovered pasa_asmbl_49414.p1, internal, 10811, 10996
-recovered pasa_asmbl_49414.p1, internal, 11103, 11316
-recovered pasa_asmbl_49414.p1, internal, 12149, 12283
-recovered pasa_asmbl_49414.p1, internal, 12854, 12972
-recovered pasa_asmbl_49414.p1, internal, 13240, 13353
-recovered pasa_asmbl_49414.p1, internal, 13483, 13593
Couldn't classify 5479, 5516
Sorry, prediction pasa_asmbl_49413.p1 fails validation.
(CAA)	 GT	5479-5516	GT	CTG
(AGA)	 AG	5750-5842	GT	CGG
(CTG)	 AG	5933-6085	GT	AGG
(GAC)	 AG	6305-6454	GT	TGG
(GTA)	 AG	6609-6696	GT	GAG
-recovered pasa_asmbl_49413.p1, terminal, 6609, 6696
-recovered pasa_asmbl_49413.p1, internal, 5750, 5842
-recovered pasa_asmbl_49413.p1, internal, 5933, 6085
-recovered pasa_asmbl_49413.p1, internal, 6305, 6454
-recovered pasa_asmbl_49413.p1, internal, 6609, 6696
Valid prediction for snap_scaffold_62-snap.11-T1
Couldn't classify 3749, 3847
Couldn't classify 4976, 4987
Sorry, prediction pasa_asmbl_49412.p1 fails validation.
(CTG)	 AC	3749-3847	GT	AGG
(TCT)	 AG	3981-4123	GT	AGG
(TCA)	 AG	4397-4508	GT	GGG
(AGA)	 AG	4976-4987	GA	AGG
-recovered pasa_asmbl_49412.p1, internal, 3981, 4123
-recovered pasa_asmbl_49412.p1, internal, 4397, 4508
Valid prediction for pasa_asmbl_49415.p1
Valid prediction for GlimmerHMM_glimmerT_61133-T1
Valid prediction for Augustus_model.g40671.t1
Valid prediction for GlimmerHMM_glimmerT_61130-T1
Valid prediction for snap_scaffold_62-snap.12-T1
Valid prediction for Augustus_model.g40669.t1
Valid prediction for GlimmerHMM_glimmerT_61134-T1
Valid prediction for GlimmerHMM_glimmerT_61138-T1
Valid prediction for Augustus_model.g40672.t1
Valid prediction for GeneMark_model.106334_t
Valid prediction for snap_scaffold_62-snap.4-T1
Couldn't classify 3285, 3490
Sorry, prediction snap_scaffold_62-snap.2-T1 fails validation.
(GAG)	 AG	3285-3490	GT	AGG
(GGG)	 AG	3678-3847	GT	AGG
(TCT)	 AG	3981-4123	GT	AGG
(TCA)	 AG	4397-4508	GT	GGG
(ATG)	 AG	5458-5516	GT	CTG
(AGA)	 AG	5750-5842	GT	CGG
(CTG)	 AG	5933-6085	GT	AGG
(GAC)	 AG	6305-6454	GT	TGG
(GTA)	 AG	6609-6692	GT	TGG
(GCT)	 AG	7396-7477	GT	CAG
(ACT)	 AG	8183-8542	CC	GAC
-recovered snap_scaffold_62-snap.2-T1, initial, 5458, 5516
add_exon() Sorry, snap_scaffold_62-snap.2-T1 3285-3490-terminal-2 is invalid.
-recovered snap_scaffold_62-snap.2-T1, terminal, 3285, 3490
-recovered snap_scaffold_62-snap.2-T1, terminal, 8183, 8542
-recovered snap_scaffold_62-snap.2-T1, internal, 3285, 3490
-recovered snap_scaffold_62-snap.2-T1, internal, 3678, 3847
-recovered snap_scaffold_62-snap.2-T1, internal, 3981, 4123
-recovered snap_scaffold_62-snap.2-T1, internal, 4397, 4508
-recovered snap_scaffold_62-snap.2-T1, internal, 5458, 5516
-recovered snap_scaffold_62-snap.2-T1, internal, 5750, 5842
-recovered snap_scaffold_62-snap.2-T1, internal, 5933, 6085
-recovered snap_scaffold_62-snap.2-T1, internal, 6305, 6454
-recovered snap_scaffold_62-snap.2-T1, internal, 6609, 6692
-recovered snap_scaffold_62-snap.2-T1, internal, 7396, 7477
Valid prediction for GeneMark_model.106331_t
Valid prediction for GlimmerHMM_glimmerT_61136-T1
Valid prediction for Augustus_model.g40668.t1
Valid prediction for snap_scaffold_62-snap.10-T1
Valid prediction for GeneMark_model.106338_t
Valid prediction for Augustus_model.g40666.t1
Couldn't classify 24631, 24694
Sorry, prediction GeneMark_model.106339_t fails validation.
(ATG)	 AG	20253-20308	GT	AAG
(GGA)	 AG	20421-20534	GT	AGG
(AAC)	 AG	20714-20763	GT	GAG
(TGG)	 AG	20865-20999	GT	CGG
(GTT)	 AG	21751-21904	GT	AGG
(GAC)	 AG	22099-22216	GT	AGG
(GTG)	 AG	22569-22769	GT	TGG
(GAG)	 AG	22794-22853	GT	TGG
(CTG)	 AG	24541-24608	GT	AAG
(GGG)	 AG	24631-24694	GT	AGG
-recovered GeneMark_model.106339_t, initial, 20253, 20308
-recovered GeneMark_model.106339_t, internal, 20253, 20308
-recovered GeneMark_model.106339_t, internal, 20421, 20534
-recovered GeneMark_model.106339_t, internal, 20714, 20763
-recovered GeneMark_model.106339_t, internal, 20865, 20999
-recovered GeneMark_model.106339_t, internal, 21751, 21904
-recovered GeneMark_model.106339_t, internal, 22099, 22216
-recovered GeneMark_model.106339_t, internal, 22569, 22769
-recovered GeneMark_model.106339_t, internal, 22794, 22853
-recovered GeneMark_model.106339_t, internal, 24541, 24608
-recovered GeneMark_model.106339_t, internal, 24631, 24694

-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 GeneMark_model.106330_t
Valid prediction for snap_scaffold_62-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_61132-T1
Valid prediction for GeneMark_model.106335_t
Valid prediction for GlimmerHMM_glimmerT_61135-T1
Valid prediction for snap_scaffold_62-snap.5-T1
Valid prediction for snap_scaffold_62-snap.3-T1
Valid prediction for snap_scaffold_62-snap.9-T1
Valid prediction for GeneMark_model.106332_t
Valid prediction for GlimmerHMM_glimmerT_61131-T1
Valid prediction for snap_scaffold_62-snap.8-T1
Valid prediction for Augustus_model.g40670.t1
Valid prediction for snap_scaffold_62-snap.7-T1
Valid prediction for Augustus_model.g40667.t1
Couldn't classify 24958, 24987
Sorry, prediction GeneMark_model.106329_t fails validation.
(ATG)	 AT	21515-21532	GT	AAG
(GTC)	 AG	21557-21645	GT	AGG
(GAA)	 AG	21757-21870	GT	AAG
(AGT)	 AG	23600-23650	GT	AAG
(GCT)	 AG	23880-23894	GT	GGG
(GGC)	 AG	23922-23996	GT	GAG
(AGA)	 AG	24758-24766	GT	GAG
(AAA)	 AG	24857-24865	GC	GAG
(AGA)	 AG	24920-24934	GT	GAG
(GGA)	 AG	24958-24987	GT	GGG
-recovered GeneMark_model.106329_t, initial, 21515, 21532
-recovered GeneMark_model.106329_t, internal, 21557, 21645
-recovered GeneMark_model.106329_t, internal, 21757, 21870
-recovered GeneMark_model.106329_t, internal, 23600, 23650
-recovered GeneMark_model.106329_t, internal, 23880, 23894
-recovered GeneMark_model.106329_t, internal, 23922, 23996
-recovered GeneMark_model.106329_t, internal, 24758, 24766
-recovered GeneMark_model.106329_t, internal, 24857, 24865
-recovered GeneMark_model.106329_t, internal, 24920, 24934
-recovered GeneMark_model.106329_t, internal, 24958, 24987
Valid prediction for snap_scaffold_62-snap.1-T1
Valid prediction for GeneMark_model.106336_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8600, rend_intergenic: 3285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12899, rend_intergenic: 9324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23289, rend_intergenic: 20253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 25000
-exon list size: 165


building trellis

0.6    
1.2    
1.8    
2.4    
3.0    
3.6    
4.2    
4.8    
5.4    
6.0    
6.6    
7.2    
7.8    
8.4    
9.0    
9.6    
10.2    
10.8    
11.4    
12.0    
12.6    
13.2    
13.8    
14.4    
15.0    
15.6    
16.2    
16.8    
17.4    
18.0    
18.6    
19.2    
19.8    
20.4    
21.0    
21.6    
22.2    
22.8    
23.4    
24.0    
24.6    
25.1    
25.7    
26.3    
26.9    
27.5    
28.1    
28.7    
29.3    
29.9    
30.5    
31.1    
31.7    
32.3    
32.9    
33.5    
34.1    
34.7    
35.3    
35.9    
36.5    
37.1    
37.7    
38.3    
38.9    
39.5    
40.1    
40.7    
41.3    
41.9    
42.5    
43.1    
43.7    
44.3    
44.9    
45.5    
46.1    
46.7    
47.3    
47.9    
48.5    
49.1    
49.7    
50.3    
50.9    
51.5    
52.1    
52.7    
53.3    
53.9    
54.5    
55.1    
55.7    
56.3    
56.9    
57.5    
58.1    
58.7    
59.3    
59.9    
60.5    
61.1    
61.7    
62.3    
62.9    
63.5    
64.1    
64.7    
65.3    
65.9    
66.5    
67.1    
67.7    
68.3    
68.9    
69.5    
70.1    
70.7    
71.3    
71.9    
72.5    
73.1    
73.7    
74.3    
74.9    
75.4    
76.0    
76.6    
77.2    
77.8    
78.4    
79.0    
79.6    
80.2    
80.8    
81.4    
82.0    
82.6    
83.2    
83.8    
84.4    
85.0    
85.6    
86.2    
86.8    
87.4    
88.0    
88.6    
89.2    
89.8    
90.4    
91.0    
91.6    
92.2    
92.8    
93.4    
94.0    
94.6    
95.2    
95.8    
96.4    
97.0    
97.6    
98.2    
98.8    
99.4    
-found 10 predictions from path traversal
Error with prediction: snap lend_intergenic: 8600, rend_intergenic: 3285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12899, rend_intergenic: 9324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23289, rend_intergenic: 20253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support