-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_4917695-5081929

-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.87545_t
Valid prediction for GeneMark_model.87526_t
Valid prediction for snap_scaffold_22-snap.953-T1
Valid prediction for snap_scaffold_22-snap.931-T1
Valid prediction for GeneMark_model.87524_t
Valid prediction for GeneMark_model.87552_t
Valid prediction for snap_scaffold_22-snap.948-T1
Valid prediction for snap_scaffold_22-snap.945-T1
Valid prediction for Augustus_model.g33939.t1
Valid prediction for snap_scaffold_22-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_50619-T1
Valid prediction for GlimmerHMM_glimmerT_50611-T1
Valid prediction for GeneMark_model.87554_t
Valid prediction for snap_scaffold_22-snap.927-T1
Valid prediction for Augustus_model.g33940.t1
Valid prediction for GeneMark_model.87543_t
Valid prediction for snap_scaffold_22-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_50604-T1
Valid prediction for GlimmerHMM_glimmerT_50600-T1
Valid prediction for GlimmerHMM_glimmerT_50612-T1
Valid prediction for snap_scaffold_22-snap.952-T1
Valid prediction for GeneMark_model.87541_t
Valid prediction for GeneMark_model.87521_t
Valid prediction for GlimmerHMM_glimmerT_50614-T1
Valid prediction for snap_scaffold_22-snap.933-T1
Valid prediction for CodingQuarry_transcript_34099-T1
Valid prediction for snap_scaffold_22-snap.929-T1
Valid prediction for snap_scaffold_22-snap.949-T1
Valid prediction for snap_scaffold_22-snap.950-T1
Valid prediction for snap_scaffold_22-snap.939-T1
Valid prediction for GeneMark_model.87539_t
Valid prediction for GlimmerHMM_glimmerT_50615-T1
Valid prediction for GeneMark_model.87538_t
Couldn't classify 79018, 79129
Couldn't classify 84401, 84591
Sorry, prediction pasa_asmbl_29346.p1 fails validation.
(TTC)	 AG	79018-79129	GT	AGG
(TCC)	 AG	79707-79818	GT	CGG
(AAT)	 AG	81011-81126	GT	ACG
(GTC)	 AG	81346-81523	GT	CGG
(GCT)	 AG	81703-81880	GT	AGG
(GTG)	 AG	82471-82632	GT	AGG
(GCA)	 AG	83125-83225	GT	AAG
(GAA)	 AG	83975-84213	GT	CTG
(CCT)	 AG	84401-84591	TG	GGT
-recovered pasa_asmbl_29346.p1, internal, 79018, 79129
-recovered pasa_asmbl_29346.p1, internal, 79707, 79818
-recovered pasa_asmbl_29346.p1, internal, 81011, 81126
-recovered pasa_asmbl_29346.p1, internal, 81346, 81523
-recovered pasa_asmbl_29346.p1, internal, 81703, 81880
-recovered pasa_asmbl_29346.p1, internal, 82471, 82632
-recovered pasa_asmbl_29346.p1, internal, 83125, 83225
-recovered pasa_asmbl_29346.p1, internal, 83975, 84213
Valid prediction for GlimmerHMM_glimmerT_50610-T1
Valid prediction for pasa_asmbl_29343.p2
Valid prediction for snap_scaffold_22-snap.947-T1
Valid prediction for snap_scaffold_22-snap.941-T1
Valid prediction for snap_scaffold_22-snap.935-T1
Valid prediction for GeneMark_model.87549_t
Couldn't classify 85550, 85876
Sorry, prediction pasa_asmbl_29348.p2 fails validation.
(CCC)	 CC	85550-85876	AC	AAA
Valid prediction for GlimmerHMM_glimmerT_50618-T1
Valid prediction for GeneMark_model.87536_t
Valid prediction for Augustus_model.g33944.t1
Valid prediction for GeneMark_model.87532_t
Valid prediction for GeneMark_model.87533_t
Valid prediction for GlimmerHMM_glimmerT_50608-T1
Valid prediction for snap_scaffold_22-snap.938-T1
Valid prediction for HiQ_model.g33937.t1
Couldn't classify 82471, 82632
Sorry, prediction GeneMark_model.87542_t fails validation.
(GTG)	 AG	82471-82632	GT	AGG
(GCA)	 AG	83125-83225	GT	AAG
(GAA)	 AG	83975-84213	GT	CTG
(CCT)	 AG	84401-84590	GT	GGG
(GCA)	 AG	85286-85390	GT	GGG
(CAC)	 AG	85534-85872	GT	AAG
(GGG)	 AG	85929-85937	GC	GAG
(CGA)	 AG	85959-86049	CC	AGC
-recovered GeneMark_model.87542_t, terminal, 85959, 86049
-recovered GeneMark_model.87542_t, internal, 82471, 82632
-recovered GeneMark_model.87542_t, internal, 83125, 83225
-recovered GeneMark_model.87542_t, internal, 83975, 84213
-recovered GeneMark_model.87542_t, internal, 84401, 84590
-recovered GeneMark_model.87542_t, internal, 85286, 85390
-recovered GeneMark_model.87542_t, internal, 85534, 85872
-recovered GeneMark_model.87542_t, internal, 85929, 85937
Valid prediction for GeneMark_model.87530_t
Valid prediction for GlimmerHMM_glimmerT_50606-T1
Valid prediction for CodingQuarry_transcript_34100-T1
Valid prediction for GeneMark_model.87546_t
Valid prediction for snap_scaffold_22-snap.928-T1
Valid prediction for GlimmerHMM_glimmerT_50601-T1
Couldn't classify 23193, 23290
Couldn't classify 27370, 27384
Sorry, prediction pasa_asmbl_29342.p1 fails validation.
(AGA)	 AC	23193-23290	GT	AGG
(GTT)	 AG	24440-24605	GT	AGG
(AAC)	 AG	24906-25080	GT	CCG
(TGT)	 AG	25761-25898	GT	GTG
(TGG)	 AG	26402-26514	GT	TGG
(ATC)	 AG	26740-26880	GT	AAG
(GCC)	 AG	27058-27213	GT	AGG
(CTT)	 AG	27370-27384	GA	GAG
-recovered pasa_asmbl_29342.p1, internal, 24440, 24605
-recovered pasa_asmbl_29342.p1, internal, 24906, 25080
-recovered pasa_asmbl_29342.p1, internal, 25761, 25898
-recovered pasa_asmbl_29342.p1, internal, 26402, 26514
-recovered pasa_asmbl_29342.p1, internal, 26740, 26880
-recovered pasa_asmbl_29342.p1, internal, 27058, 27213
Valid prediction for GlimmerHMM_glimmerT_50617-T1
Valid prediction for GlimmerHMM_glimmerT_50613-T1
Valid prediction for GeneMark_model.87528_t
Valid prediction for GlimmerHMM_glimmerT_50602-T1

-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_50603-T1
Valid prediction for snap_scaffold_22-snap.954-T1
Valid prediction for GeneMark_model.87535_t
Valid prediction for GeneMark_model.87550_t
Valid prediction for snap_scaffold_22-snap.942-T1
Valid prediction for GeneMark_model.87525_t
Valid prediction for GlimmerHMM_glimmerT_50599-T1
Valid prediction for GeneMark_model.87527_t
Valid prediction for snap_scaffold_22-snap.943-T1
Valid prediction for snap_scaffold_22-snap.925-T1
Valid prediction for snap_scaffold_22-snap.946-T1
Valid prediction for GeneMark_model.87548_t
Valid prediction for GlimmerHMM_glimmerT_50620-T1
Valid prediction for Augustus_model.g33936.t1
Valid prediction for snap_scaffold_22-snap.926-T1
Valid prediction for pasa_asmbl_29341.p1
Valid prediction for GeneMark_model.87544_t
Valid prediction for GeneMark_model.87529_t
Valid prediction for GlimmerHMM_glimmerT_50607-T1
Valid prediction for snap_scaffold_22-snap.951-T1
Valid prediction for snap_scaffold_22-snap.944-T1
Valid prediction for GlimmerHMM_glimmerT_50598-T1
Valid prediction for snap_scaffold_22-snap.936-T1
Valid prediction for GeneMark_model.87519_t
Valid prediction for snap_scaffold_22-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_50605-T1
Valid prediction for GeneMark_model.87547_t
Valid prediction for snap_scaffold_22-snap.930-T1
Valid prediction for GeneMark_model.87520_t
Valid prediction for GeneMark_model.87537_t
Valid prediction for GeneMark_model.87522_t
Valid prediction for GeneMark_model.87551_t
Valid prediction for GeneMark_model.87531_t
Valid prediction for GlimmerHMM_glimmerT_50609-T1
Valid prediction for GeneMark_model.87540_t
Valid prediction for Augustus_model.g33943.t1
Valid prediction for Augustus_model.g33942.t1
Valid prediction for GeneMark_model.87523_t
Valid prediction for GeneMark_model.87553_t
Valid prediction for Augustus_model.g33941.t1
Valid prediction for snap_scaffold_22-snap.932-T1
Valid prediction for GeneMark_model.87534_t
Valid prediction for GlimmerHMM_glimmerT_50616-T1
Valid prediction for Augustus_model.g33938.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 36010, rend_intergenic: 36007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18564, rend_intergenic: 6651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27564, rend_intergenic: 18756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85876, rend_intergenic: 78555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94095, rend_intergenic: 91046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130864, rend_intergenic: 130733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164235
-exon list size: 469


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 36010, rend_intergenic: 36007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18564, rend_intergenic: 6651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27564, rend_intergenic: 18756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85876, rend_intergenic: 78555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94095, rend_intergenic: 91046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130864, rend_intergenic: 130733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144536 - 164235
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144536 - 156669
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144536 - 156577
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144536 - 156377
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support