-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_179327-310601

-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 snap_scaffold_24-snap.53-T1
Valid prediction for GeneMark_model.92305_t
Valid prediction for GeneMark_model.92321_t
Valid prediction for GeneMark_model.92325_t
Valid prediction for GeneMark_model.92317_t
Valid prediction for GeneMark_model.92332_t
Valid prediction for GeneMark_model.92314_t
Valid prediction for GlimmerHMM_glimmerT_53114-T1
Valid prediction for GeneMark_model.92329_t
Valid prediction for GlimmerHMM_glimmerT_53116-T1
Valid prediction for GlimmerHMM_glimmerT_53119-T1
Valid prediction for GlimmerHMM_glimmerT_53125-T1
Valid prediction for snap_scaffold_24-snap.47-T1
Valid prediction for Augustus_model.g35608.t1
Valid prediction for GeneMark_model.92323_t
Valid prediction for GlimmerHMM_glimmerT_53121-T1
Valid prediction for snap_scaffold_24-snap.50-T1
Valid prediction for snap_scaffold_24-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_53109-T1
Valid prediction for GeneMark_model.92307_t
Valid prediction for GeneMark_model.92311_t
Valid prediction for GlimmerHMM_glimmerT_53108-T1
Valid prediction for GlimmerHMM_glimmerT_53113-T1
Valid prediction for GeneMark_model.92340_t
Valid prediction for GlimmerHMM_glimmerT_53123-T1
Valid prediction for snap_scaffold_24-snap.55-T1
Couldn't classify 123902, 123928
Couldn't classify 126580, 126702
Sorry, prediction pasa_asmbl_32009.p1 fails validation.
(GCT)	 TG	123902-123928	GT	AGG
(GGC)	 AG	124123-124218	GT	ATG
(GGT)	 AG	124944-125107	GT	AGG
(TGG)	 AG	125972-126040	GT	AGG
(GAG)	 AG	126263-126320	GT	AGG
(AGT)	 AG	126580-126702	AG	CCA
-recovered pasa_asmbl_32009.p1, internal, 124123, 124218
-recovered pasa_asmbl_32009.p1, internal, 124944, 125107
-recovered pasa_asmbl_32009.p1, internal, 125972, 126040
-recovered pasa_asmbl_32009.p1, internal, 126263, 126320
Valid prediction for snap_scaffold_24-snap.57-T1
Valid prediction for snap_scaffold_24-snap.63-T1
Valid prediction for GeneMark_model.92315_t
Valid prediction for GeneMark_model.92336_t
Valid prediction for GeneMark_model.92316_t
Valid prediction for GeneMark_model.92312_t
Valid prediction for snap_scaffold_24-snap.37-T1
Valid prediction for snap_scaffold_24-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_53120-T1
Valid prediction for Augustus_model.g35611.t1
Valid prediction for GeneMark_model.92338_t
Valid prediction for GeneMark_model.92330_t
Valid prediction for GeneMark_model.92309_t
Valid prediction for GeneMark_model.92327_t
Valid prediction for GeneMark_model.92319_t
Valid prediction for snap_scaffold_24-snap.38-T1
Valid prediction for Augustus_model.g35610.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 GeneMark_model.92326_t
Valid prediction for snap_scaffold_24-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_53118-T1
Valid prediction for snap_scaffold_24-snap.49-T1
Valid prediction for CodingQuarry_transcript_37143-T1
Valid prediction for GlimmerHMM_glimmerT_53117-T1
Valid prediction for snap_scaffold_24-snap.43-T1
Valid prediction for snap_scaffold_24-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_53115-T1
Valid prediction for snap_scaffold_24-snap.59-T1
Valid prediction for GeneMark_model.92337_t
Valid prediction for GlimmerHMM_glimmerT_53110-T1
Valid prediction for snap_scaffold_24-snap.51-T1
Valid prediction for GeneMark_model.92333_t
Valid prediction for snap_scaffold_24-snap.45-T1
Valid prediction for GeneMark_model.92313_t
Valid prediction for snap_scaffold_24-snap.36-T1
Valid prediction for snap_scaffold_24-snap.39-T1
Valid prediction for GeneMark_model.92308_t
Valid prediction for snap_scaffold_24-snap.48-T1
Valid prediction for GeneMark_model.92322_t
Valid prediction for snap_scaffold_24-snap.61-T1
Valid prediction for snap_scaffold_24-snap.44-T1
Valid prediction for GeneMark_model.92335_t
Valid prediction for GeneMark_model.92318_t
Valid prediction for snap_scaffold_24-snap.62-T1
Valid prediction for snap_scaffold_24-snap.42-T1
Valid prediction for GeneMark_model.92320_t
Valid prediction for snap_scaffold_24-snap.52-T1
Valid prediction for GeneMark_model.92331_t
Valid prediction for snap_scaffold_24-snap.54-T1
Valid prediction for GeneMark_model.92324_t
Valid prediction for snap_scaffold_24-snap.40-T1
Valid prediction for GlimmerHMM_glimmerT_53111-T1
Valid prediction for GeneMark_model.92339_t
Valid prediction for GeneMark_model.92328_t
Valid prediction for CodingQuarry_transcript_37142-T1
Valid prediction for GlimmerHMM_glimmerT_53112-T1
Valid prediction for GeneMark_model.92306_t
Valid prediction for snap_scaffold_24-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_53124-T1
Valid prediction for GlimmerHMM_glimmerT_53107-T1
Valid prediction for HiQ_model.g35609.t1
Valid prediction for pasa_asmbl_32695.p1
Valid prediction for GeneMark_model.92310_t
Valid prediction for GlimmerHMM_glimmerT_53122-T1
Valid prediction for snap_scaffold_24-snap.58-T1
Valid prediction for snap_scaffold_24-snap.65-T1
Valid prediction for snap_scaffold_24-snap.60-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 27444, rend_intergenic: 27441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24061, rend_intergenic: 19137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29254, rend_intergenic: 25453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49093, rend_intergenic: 46682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60508, rend_intergenic: 58595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115722, rend_intergenic: 112074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127713, rend_intergenic: 116550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 131275
-exon list size: 420


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.9    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 18 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 27444, rend_intergenic: 27441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24061, rend_intergenic: 19137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29254, rend_intergenic: 25453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49093, rend_intergenic: 46682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60508, rend_intergenic: 58595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115722, rend_intergenic: 112074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127713, rend_intergenic: 116550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19982
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-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 - 19929
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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 1 - 19872
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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 1 - 19813
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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 7822 - 19813
-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
GOT 5prime partial gene.

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