-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_3496195-3629252

-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.58659_t
Valid prediction for GlimmerHMM_glimmerT_34302-T1
Valid prediction for snap_scaffold_14-snap.615-T1
Valid prediction for snap_scaffold_14-snap.621-T1
Valid prediction for GeneMark_model.58663_t
Valid prediction for GlimmerHMM_glimmerT_34301-T1
Valid prediction for GeneMark_model.58674_t
Valid prediction for snap_scaffold_14-snap.626-T1
Valid prediction for Augustus_model.g23069.t1
Valid prediction for snap_scaffold_14-snap.610-T1
Valid prediction for GeneMark_model.58665_t
Valid prediction for GeneMark_model.58654_t
Valid prediction for GeneMark_model.58650_t
Valid prediction for snap_scaffold_14-snap.614-T1
Valid prediction for snap_scaffold_14-snap.618-T1
Valid prediction for GeneMark_model.58667_t
Valid prediction for snap_scaffold_14-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_34292-T1
Valid prediction for GlimmerHMM_glimmerT_34289-T1
Valid prediction for GeneMark_model.58676_t
Valid prediction for Augustus_model.g23066.t1
Valid prediction for snap_scaffold_14-snap.630-T1
Valid prediction for CodingQuarry_transcript_15573-T1
Valid prediction for GeneMark_model.58658_t
Valid prediction for snap_scaffold_14-snap.624-T1
Valid prediction for GeneMark_model.58689_t
Valid prediction for GeneMark_model.58682_t
Couldn't classify 9088, 9166
Couldn't classify 10245, 10364
Sorry, prediction pasa_asmbl_11923.p1 fails validation.
(GGC)	 CG	9088-9166	GT	CGG
(GTC)	 AG	9631-9811	GT	AGG
(CTG)	 AG	9924-10050	GT	CGG
(AGT)	 AG	10245-10364	GT	AGG
-recovered pasa_asmbl_11923.p1, internal, 9631, 9811
-recovered pasa_asmbl_11923.p1, internal, 9924, 10050
-recovered pasa_asmbl_11923.p1, internal, 10245, 10364
Valid prediction for GeneMark_model.58691_t
Valid prediction for GeneMark_model.58699_t
Valid prediction for CodingQuarry_transcript_15579-T1
Valid prediction for GeneMark_model.58678_t
Valid prediction for GeneMark_model.58646_t
Valid prediction for CodingQuarry_transcript_15578-T1
Valid prediction for snap_scaffold_14-snap.625-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.58684_t
Valid prediction for snap_scaffold_14-snap.620-T1
Valid prediction for CodingQuarry_transcript_15576-T1
Valid prediction for GeneMark_model.58661_t
Valid prediction for snap_scaffold_14-snap.619-T1
Valid prediction for GeneMark_model.58695_t
Valid prediction for snap_scaffold_14-snap.617-T1
Valid prediction for GeneMark_model.58686_t
Valid prediction for GeneMark_model.58688_t
Valid prediction for GeneMark_model.58697_t
Valid prediction for GeneMark_model.58670_t
Valid prediction for HiQ_model.g23072.t1
Valid prediction for snap_scaffold_14-snap.604-T1
Valid prediction for CodingQuarry_transcript_15577-T1
Valid prediction for GeneMark_model.58700_t
Valid prediction for GeneMark_model.58680_t
Valid prediction for snap_scaffold_14-snap.601-T1
Valid prediction for GlimmerHMM_glimmerT_34299-T1
Valid prediction for GlimmerHMM_glimmerT_34295-T1
Couldn't classify 94282, 94375
Sorry, prediction pasa_asmbl_11932.p1 fails validation.
(GGT)	 AA	94282-94375	GT	CTG
(ACG)	 AG	94830-94994	GT	ATG
(TCA)	 AG	95219-95424	AG	AGA
-recovered pasa_asmbl_11932.p1, terminal, 95219, 95424
-recovered pasa_asmbl_11932.p1, internal, 94830, 94994
Couldn't classify 24210, 24276
Sorry, prediction pasa_asmbl_11925.p1 fails validation.
(AGA)	 TC	24210-24276	GT	AGG
(CGT)	 AG	25940-26074	GT	AGG
(AGT)	 AG	26231-26452	GT	AGG
(GTG)	 AG	26594-26792	GT	GAG
(TTC)	 AG	27097-27268	GT	CCG
(GTG)	 AG	27501-27923	GG	AGG
add_exon() Sorry, pasa_asmbl_11925.p1 26231-26452-terminal-1 is invalid.
-recovered pasa_asmbl_11925.p1, terminal, 26231, 26452
-recovered pasa_asmbl_11925.p1, terminal, 27501, 27923
-recovered pasa_asmbl_11925.p1, internal, 25940, 26074
-recovered pasa_asmbl_11925.p1, internal, 26231, 26452
-recovered pasa_asmbl_11925.p1, internal, 26594, 26792
-recovered pasa_asmbl_11925.p1, internal, 27097, 27268
Valid prediction for Augustus_model.g23076.t1
Couldn't classify 16029, 16200
Couldn't classify 19956, 20127
Sorry, prediction pasa_asmbl_11924.p1 fails validation.
(GTG)	 TG	16029-16200	GT	AGG
(GGT)	 AG	17046-17188	GT	TGG
(GCC)	 AG	18225-18415	GT	GGG
(TGA)	 AG	19956-20127	TA	TCT
-recovered pasa_asmbl_11924.p1, internal, 17046, 17188
-recovered pasa_asmbl_11924.p1, internal, 18225, 18415
Valid prediction for snap_scaffold_14-snap.607-T1
Valid prediction for GeneMark_model.58648_t
Valid prediction for GeneMark_model.58652_t
Valid prediction for GeneMark_model.58656_t
Valid prediction for GeneMark_model.58672_t
Valid prediction for GlimmerHMM_glimmerT_34291-T1
Valid prediction for Augustus_model.g23071.t1
Valid prediction for GeneMark_model.58694_t
Valid prediction for GeneMark_model.58692_t
Valid prediction for pasa_asmbl_11929.p1
Valid prediction for GlimmerHMM_glimmerT_34290-T1
Valid prediction for snap_scaffold_14-snap.605-T1
Valid prediction for Augustus_model.g23075.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 snap_scaffold_14-snap.628-T1
Valid prediction for GeneMark_model.58668_t
Valid prediction for Augustus_model.g23068.t1
Valid prediction for snap_scaffold_14-snap.632-T1
Valid prediction for GeneMark_model.58653_t
Valid prediction for GlimmerHMM_glimmerT_34298-T1
Valid prediction for snap_scaffold_14-snap.616-T1
Valid prediction for GeneMark_model.58677_t
Valid prediction for snap_scaffold_14-snap.631-T1
Valid prediction for CodingQuarry_transcript_15574-T1
Valid prediction for snap_scaffold_14-snap.612-T1
Valid prediction for Augustus_model.g23067.t1
Valid prediction for GeneMark_model.58649_t
Valid prediction for GeneMark_model.58662_t
Valid prediction for GeneMark_model.58664_t
Valid prediction for snap_scaffold_14-snap.613-T1
Couldn't classify 82449, 82823
Sorry, prediction pasa_asmbl_13000.p1 fails validation.
(GAC)	 GA	82449-82823	AA	AGA
Valid prediction for snap_scaffold_14-snap.609-T1
Valid prediction for GeneMark_model.58675_t
Valid prediction for snap_scaffold_14-snap.606-T1
Valid prediction for GeneMark_model.58651_t
Valid prediction for snap_scaffold_14-snap.608-T1
Valid prediction for Augustus_model.g23074.t1
Valid prediction for GeneMark_model.58647_t
Valid prediction for GeneMark_model.58683_t
Valid prediction for snap_scaffold_14-snap.603-T1
Valid prediction for snap_scaffold_14-snap.602-T1
Valid prediction for GeneMark_model.58690_t
Valid prediction for GeneMark_model.58681_t
Valid prediction for GeneMark_model.58693_t
Valid prediction for GeneMark_model.58666_t
Valid prediction for snap_scaffold_14-snap.623-T1
Valid prediction for GeneMark_model.58669_t
Valid prediction for GeneMark_model.58655_t
Valid prediction for snap_scaffold_14-snap.633-T1
Valid prediction for GeneMark_model.58660_t
Valid prediction for GlimmerHMM_glimmerT_34303-T1
Valid prediction for snap_scaffold_14-snap.622-T1
Valid prediction for GlimmerHMM_glimmerT_34300-T1
Valid prediction for Augustus_model.g23070.t1
Valid prediction for snap_scaffold_14-snap.611-T1
Valid prediction for Augustus_model.g23073.t1
Valid prediction for GlimmerHMM_glimmerT_34294-T1
Valid prediction for GeneMark_model.58679_t
Valid prediction for pasa_asmbl_13004.p1
Valid prediction for GeneMark_model.58696_t
Valid prediction for snap_scaffold_14-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_34296-T1
Valid prediction for GeneMark_model.58673_t
Valid prediction for GlimmerHMM_glimmerT_34293-T1
Valid prediction for GeneMark_model.58698_t
Valid prediction for GeneMark_model.58671_t
Valid prediction for GeneMark_model.58645_t
Valid prediction for GeneMark_model.58687_t
Valid prediction for GeneMark_model.58685_t
Valid prediction for GeneMark_model.58657_t
Valid prediction for GlimmerHMM_glimmerT_34297-T1
Valid prediction for Augustus_model.g23077.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27923, rend_intergenic: 8161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39434, rend_intergenic: 33827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57746, rend_intergenic: 54473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72877, rend_intergenic: 66666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77171, rend_intergenic: 73406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79056, rend_intergenic: 77292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105090, rend_intergenic: 101955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114495, rend_intergenic: 110077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117690, rend_intergenic: 115261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126793, rend_intergenic: 123199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133058
-exon list size: 617


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
1.0    
1.1    
1.3    
1.5    
1.6    
1.8    
1.9    
2.1    
2.3    
2.4    
2.6    
2.7    
2.9    
3.1    
3.2    
3.4    
3.6    
3.7    
3.9    
4.0    
4.2    
4.4    
4.5    
4.7    
4.8    
5.0    
5.2    
5.3    
5.5    
5.7    
5.8    
6.0    
6.1    
6.3    
6.5    
6.6    
6.8    
6.9    
7.1    
7.3    
7.4    
7.6    
7.8    
7.9    
8.1    
8.2    
8.4    
8.6    
8.7    
8.9    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.0    
10.2    
10.3    
10.5    
10.7    
10.8    
11.0    
11.1    
11.3    
11.5    
11.6    
11.8    
12.0    
12.1    
12.3    
12.4    
12.6    
12.8    
12.9    
13.1    
13.2    
13.4    
13.6    
13.7    
13.9    
14.1    
14.2    
14.4    
14.5    
14.7    
14.9    
15.0    
15.2    
15.3    
15.5    
15.7    
15.8    
16.0    
16.2    
16.3    
16.5    
16.6    
16.8    
17.0    
17.1    
17.3    
17.4    
17.6    
17.8    
17.9    
18.1    
18.3    
18.4    
18.6    
18.7    
18.9    
19.1    
19.2    
19.4    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.5    
20.7    
20.8    
21.0    
21.2    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.6    
22.8    
22.9    
23.1    
23.3    
23.4    
23.6    
23.7    
23.9    
24.1    
24.2    
24.4    
24.6    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.8    
26.0    
26.2    
26.3    
26.5    
26.7    
26.8    
27.0    
27.1    
27.3    
27.5    
27.6    
27.8    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
28.9    
29.1    
29.2    
29.4    
29.6    
29.7    
29.9    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.0    
31.2    
31.3    
31.5    
31.7    
31.8    
32.0    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.8    
33.9    
34.1    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.2    
35.4    
35.5    
35.7    
35.9    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.3    
37.5    
37.6    
37.8    
38.0    
38.1    
38.3    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.4    
39.6    
39.7    
39.9    
40.1    
40.2    
40.4    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.6    
43.8    
43.9    
44.1    
44.3    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.0    
46.2    
46.4    
46.5    
46.7    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.3    
53.5    
53.6    
53.8    
54.0    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 27923, rend_intergenic: 8161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39434, rend_intergenic: 33827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57746, rend_intergenic: 54473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72877, rend_intergenic: 66666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77171, rend_intergenic: 73406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79056, rend_intergenic: 77292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105090, rend_intergenic: 101955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114495, rend_intergenic: 110077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117690, rend_intergenic: 115261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126793, rend_intergenic: 123199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support