-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_16954981-17091757

-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 Augustus_model.g11270.t1
Valid prediction for GlimmerHMM_glimmerT_16764-T1
Valid prediction for GeneMark_model.28051_t
Valid prediction for snap_scaffold_6-snap.3594-T1
Valid prediction for GlimmerHMM_glimmerT_16753-T1
Valid prediction for GlimmerHMM_glimmerT_16760-T1
Valid prediction for GlimmerHMM_glimmerT_16758-T1
Valid prediction for GeneMark_model.28058_t
Valid prediction for GlimmerHMM_glimmerT_16765-T1
Valid prediction for GeneMark_model.28037_t
Valid prediction for GeneMark_model.28062_t
Valid prediction for GeneMark_model.28064_t
Valid prediction for HiQ_model.g11273.t1
Valid prediction for GeneMark_model.28052_t
Valid prediction for GlimmerHMM_glimmerT_16747-T1
Valid prediction for GeneMark_model.28045_t
Couldn't classify 88628, 88958
Couldn't classify 90467, 90499
Sorry, prediction pasa_asmbl_47665.p1 fails validation.
(GGA)	 CG	88628-88958	GT	GGG
(GTA)	 AG	89211-89381	GT	CAG
(TGT)	 AG	89755-89871	GT	AGG
(GTC)	 AG	90005-90201	GT	AGG
(TCC)	 AG	90467-90499	AC	ACA
-recovered pasa_asmbl_47665.p1, internal, 89211, 89381
-recovered pasa_asmbl_47665.p1, internal, 89755, 89871
-recovered pasa_asmbl_47665.p1, internal, 90005, 90201
Valid prediction for CodingQuarry_transcript_55245-T1
Valid prediction for GeneMark_model.28043_t
Valid prediction for GeneMark_model.28029_t
Valid prediction for Augustus_model.g11268.t1
Valid prediction for snap_scaffold_6-snap.3590-T1
Valid prediction for Augustus_model.g11275.t1
Valid prediction for GlimmerHMM_glimmerT_16766-T1
Valid prediction for CodingQuarry_transcript_55246-T1
Valid prediction for GeneMark_model.28049_t
Valid prediction for GlimmerHMM_glimmerT_16762-T1
Valid prediction for GeneMark_model.28027_t
Valid prediction for snap_scaffold_6-snap.3602-T1
Valid prediction for snap_scaffold_6-snap.3603-T1
Valid prediction for snap_scaffold_6-snap.3597-T1
Valid prediction for HiQ_model.g11272.t1
Valid prediction for GlimmerHMM_glimmerT_16761-T1
Valid prediction for Augustus_model.g11269.t1
Valid prediction for GeneMark_model.28056_t
Valid prediction for GeneMark_model.28035_t
Valid prediction for snap_scaffold_6-snap.3606-T1
Valid prediction for snap_scaffold_6-snap.3600-T1
Valid prediction for snap_scaffold_6-snap.3584-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.28060_t
Valid prediction for snap_scaffold_6-snap.3598-T1
Valid prediction for GeneMark_model.28031_t
Couldn't classify 88021, 88150
Sorry, prediction pasa_asmbl_47663.p1 fails validation.
(ATG)	 AG	84482-84667	GT	GTG
(GAA)	 AG	85430-85454	GT	AGG
(CTG)	 AG	85915-85970	GT	AGG
(GGA)	 AG	86365-86589	GT	AGG
(GAA)	 AG	86716-86864	GT	AGG
(GCC)	 AG	86990-87163	GT	AGG
(ACA)	 AG	88021-88150	TC	CCT
-recovered pasa_asmbl_47663.p1, initial, 84482, 84667
-recovered pasa_asmbl_47663.p1, internal, 84482, 84667
-recovered pasa_asmbl_47663.p1, internal, 85430, 85454
-recovered pasa_asmbl_47663.p1, internal, 85915, 85970
-recovered pasa_asmbl_47663.p1, internal, 86365, 86589
-recovered pasa_asmbl_47663.p1, internal, 86716, 86864
-recovered pasa_asmbl_47663.p1, internal, 86990, 87163
Valid prediction for GeneMark_model.28055_t
Valid prediction for GlimmerHMM_glimmerT_16756-T1
Valid prediction for GlimmerHMM_glimmerT_16759-T1
Valid prediction for GlimmerHMM_glimmerT_16754-T1
Valid prediction for Augustus_model.g11274.t1
Valid prediction for snap_scaffold_6-snap.3604-T1
Valid prediction for GeneMark_model.28033_t
Valid prediction for GeneMark_model.28040_t
Valid prediction for snap_scaffold_6-snap.3587-T1
Valid prediction for GeneMark_model.28050_t
Valid prediction for snap_scaffold_6-snap.3586-T1
Valid prediction for pasa_asmbl_47662.p1

-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_16763-T1
Valid prediction for GeneMark_model.28036_t
Valid prediction for GlimmerHMM_glimmerT_16755-T1
Valid prediction for GeneMark_model.28059_t
Valid prediction for snap_scaffold_6-snap.3591-T1
Valid prediction for snap_scaffold_6-snap.3599-T1
Valid prediction for GeneMark_model.28063_t
Valid prediction for snap_scaffold_6-snap.3596-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.28025_t
Valid prediction for GeneMark_model.28026_t
Valid prediction for GeneMark_model.28048_t
Valid prediction for GeneMark_model.28053_t
Valid prediction for snap_scaffold_6-snap.3605-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.28039_t
Valid prediction for GeneMark_model.28065_t
Valid prediction for snap_scaffold_6-snap.3607-T1
Valid prediction for GlimmerHMM_glimmerT_16751-T1
Valid prediction for snap_scaffold_6-snap.3585-T1
Valid prediction for GlimmerHMM_glimmerT_16757-T1
Valid prediction for GeneMark_model.28032_t
Valid prediction for GlimmerHMM_glimmerT_16750-T1
Valid prediction for GeneMark_model.28028_t
Valid prediction for snap_scaffold_6-snap.3595-T1
Valid prediction for GeneMark_model.28047_t
Valid prediction for GeneMark_model.28066_t
Valid prediction for snap_scaffold_6-snap.3593-T1
Valid prediction for GeneMark_model.28057_t
Valid prediction for snap_scaffold_6-snap.3592-T1
Valid prediction for Augustus_model.g11271.t1
Valid prediction for GeneMark_model.28038_t
Valid prediction for GeneMark_model.28041_t
Valid prediction for GeneMark_model.28034_t
Valid prediction for snap_scaffold_6-snap.3601-T1
Valid prediction for GeneMark_model.28030_t
Valid prediction for GlimmerHMM_glimmerT_16749-T1
Valid prediction for GeneMark_model.28054_t
Valid prediction for GeneMark_model.28046_t
Valid prediction for GlimmerHMM_glimmerT_16748-T1
Valid prediction for GlimmerHMM_glimmerT_16752-T1
Valid prediction for GeneMark_model.28061_t
Valid prediction for snap_scaffold_6-snap.3589-T1
Valid prediction for GeneMark_model.28044_t
Valid prediction for GeneMark_model.28042_t
Valid prediction for snap_scaffold_6-snap.3588-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19411, rend_intergenic: 17270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43784, rend_intergenic: 39268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47156, rend_intergenic: 44556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52665, rend_intergenic: 47503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65736, rend_intergenic: 60665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92304, rend_intergenic: 89207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95663, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103256, rend_intergenic: 96864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120918, rend_intergenic: 116622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128082, rend_intergenic: 123492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134900, rend_intergenic: 128316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136777
-exon list size: 527


building trellis

0.2    
0.4    
0.6    
0.8    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 19411, rend_intergenic: 17270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43784, rend_intergenic: 39268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47156, rend_intergenic: 44556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52665, rend_intergenic: 47503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65736, rend_intergenic: 60665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92304, rend_intergenic: 89207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95663, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103256, rend_intergenic: 96864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120918, rend_intergenic: 116622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128082, rend_intergenic: 123492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134900, rend_intergenic: 128316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17723
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-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 1 - 17269
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 15411
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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