-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_17689923-17789119

-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.46317_t
Valid prediction for snap_scaffold_10-snap.3611-T1
Valid prediction for GeneMark_model.46294_t
Valid prediction for snap_scaffold_10-snap.3599-T1
Valid prediction for GeneMark_model.46302_t
Valid prediction for GeneMark_model.46316_t
Valid prediction for GeneMark_model.46313_t
Valid prediction for snap_scaffold_10-snap.3598-T1
Valid prediction for snap_scaffold_10-snap.3596-T1
Couldn't classify 10806, 11546
Sorry, prediction pasa_asmbl_4018.p1 fails validation.
(ATG)	 CC	10806-11546	AT	GTA
Valid prediction for GeneMark_model.46297_t
Valid prediction for GlimmerHMM_glimmerT_26801-T1
Valid prediction for GeneMark_model.46300_t
Valid prediction for snap_scaffold_10-snap.3594-T1
Valid prediction for GlimmerHMM_glimmerT_26806-T1
Valid prediction for GeneMark_model.46310_t
Valid prediction for snap_scaffold_10-snap.3606-T1
Valid prediction for GeneMark_model.46304_t
Valid prediction for GeneMark_model.46299_t
Valid prediction for snap_scaffold_10-snap.3607-T1
Valid prediction for GlimmerHMM_glimmerT_26803-T1
Valid prediction for GeneMark_model.46308_t
Valid prediction for snap_scaffold_10-snap.3602-T1
Valid prediction for GeneMark_model.46312_t
Valid prediction for snap_scaffold_10-snap.3601-T1
Valid prediction for GeneMark_model.46306_t
Valid prediction for snap_scaffold_10-snap.3595-T1
Valid prediction for snap_scaffold_10-snap.3604-T1
Valid prediction for CodingQuarry_transcript_5686-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_26807-T1
Valid prediction for snap_scaffold_10-snap.3612-T1
add_exon() Sorry, snap_scaffold_10-snap.3612-T1 921-1296-terminal-1 is invalid.
Valid prediction for GeneMark_model.46301_t
Couldn't classify 5075, 5148
Sorry, prediction GlimmerHMM_glimmerT_26809-T1 fails validation.
(AGC)	 AG	5075-5148	GT	CGG
(TTA)	 AG	8976-9003	GA	AAG
-recovered GlimmerHMM_glimmerT_26809-T1, terminal, 8976, 9003
-recovered GlimmerHMM_glimmerT_26809-T1, internal, 5075, 5148
Valid prediction for GeneMark_model.46296_t
Valid prediction for snap_scaffold_10-snap.3603-T1
Valid prediction for snap_scaffold_10-snap.3608-T1
Valid prediction for GlimmerHMM_glimmerT_26804-T1
Valid prediction for snap_scaffold_10-snap.3609-T1
Valid prediction for snap_scaffold_10-snap.3597-T1
Valid prediction for GlimmerHMM_glimmerT_26808-T1
Valid prediction for GeneMark_model.46319_t
Valid prediction for snap_scaffold_10-snap.3610-T1
Valid prediction for GeneMark_model.46318_t
Valid prediction for GeneMark_model.46295_t
Valid prediction for GeneMark_model.46307_t
Valid prediction for GeneMark_model.46315_t
Valid prediction for snap_scaffold_10-snap.3600-T1
Valid prediction for GeneMark_model.46298_t
Valid prediction for snap_scaffold_10-snap.3605-T1
Valid prediction for GeneMark_model.46305_t
Valid prediction for GeneMark_model.46311_t
Valid prediction for GeneMark_model.46314_t
Valid prediction for GlimmerHMM_glimmerT_26802-T1
Valid prediction for GeneMark_model.46309_t
Valid prediction for GeneMark_model.46303_t
Valid prediction for GlimmerHMM_glimmerT_26805-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12874, rend_intergenic: 10849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21859, rend_intergenic: 13887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32785, rend_intergenic: 25460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51202, rend_intergenic: 48474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64723, rend_intergenic: 54269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86522, rend_intergenic: 67218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89594, rend_intergenic: 86541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 99197
-exon list size: 266


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.4    
3.7    
4.1    
4.5    
4.9    
5.2    
5.6    
6.0    
6.3    
6.7    
7.1    
7.5    
7.8    
8.2    
8.6    
9.0    
9.3    
9.7    
10.1    
10.4    
10.8    
11.2    
11.6    
11.9    
12.3    
12.7    
13.1    
13.4    
13.8    
14.2    
14.6    
14.9    
15.3    
15.7    
16.0    
16.4    
16.8    
17.2    
17.5    
17.9    
18.3    
18.7    
19.0    
19.4    
19.8    
20.1    
20.5    
20.9    
21.3    
21.6    
22.0    
22.4    
22.8    
23.1    
23.5    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.5    
26.9    
27.2    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.9    
30.2    
30.6    
31.0    
31.3    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
34.0    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.6    
36.9    
37.3    
37.7    
38.1    
38.4    
38.8    
39.2    
39.6    
39.9    
40.3    
40.7    
41.0    
41.4    
41.8    
42.2    
42.5    
42.9    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.9    
46.3    
46.6    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.4    
53.7    
54.1    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.1    
57.5    
57.8    
58.2    
58.6    
59.0    
59.3    
59.7    
60.1    
60.4    
60.8    
61.2    
61.6    
61.9    
62.3    
62.7    
63.1    
63.4    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.0    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.7    
69.0    
69.4    
69.8    
70.1    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.8    
73.1    
73.5    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.5    
76.9    
77.2    
77.6    
78.0    
78.4    
78.7    
79.1    
79.5    
79.9    
80.2    
80.6    
81.0    
81.3    
81.7    
82.1    
82.5    
82.8    
83.2    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.2    
86.6    
86.9    
87.3    
87.7    
88.1    
88.4    
88.8    
89.2    
89.6    
89.9    
90.3    
90.7    
91.0    
91.4    
91.8    
92.2    
92.5    
92.9    
93.3    
93.7    
94.0    
94.4    
94.8    
95.1    
95.5    
95.9    
96.3    
96.6    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 12874, rend_intergenic: 10849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21859, rend_intergenic: 13887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32785, rend_intergenic: 25460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51202, rend_intergenic: 48474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64723, rend_intergenic: 54269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86522, rend_intergenic: 67218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89594, rend_intergenic: 86541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 83800 - 99197
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support