-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_9867656-10002315

-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.106097_t
Valid prediction for snap_scaffold_28-snap.2221-T1
Valid prediction for GeneMark_model.106114_t
Valid prediction for GeneMark_model.106095_t
Valid prediction for GeneMark_model.106098_t
Valid prediction for snap_scaffold_28-snap.2237-T1
Valid prediction for snap_scaffold_28-snap.2239-T1
Valid prediction for snap_scaffold_28-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_60904-T1
Valid prediction for GeneMark_model.106105_t
Valid prediction for snap_scaffold_28-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_60905-T1
Valid prediction for Augustus_model.g40520.t1
Valid prediction for GeneMark_model.106093_t
Valid prediction for GlimmerHMM_glimmerT_60899-T1
Valid prediction for GlimmerHMM_glimmerT_60900-T1
Valid prediction for GeneMark_model.106112_t
Valid prediction for GlimmerHMM_glimmerT_60896-T1
Valid prediction for Augustus_model.g40524.t1
Valid prediction for snap_scaffold_28-snap.2233-T1
Valid prediction for snap_scaffold_28-snap.2229-T1
Valid prediction for snap_scaffold_28-snap.2226-T1
Valid prediction for GeneMark_model.106103_t
Valid prediction for GeneMark_model.106107_t
Valid prediction for snap_scaffold_28-snap.2223-T1
Valid prediction for Augustus_model.g40525.t1
Valid prediction for snap_scaffold_28-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_60903-T1
Valid prediction for GeneMark_model.106096_t
Valid prediction for GlimmerHMM_glimmerT_60901-T1
Valid prediction for snap_scaffold_28-snap.2225-T1
Valid prediction for GeneMark_model.106102_t
Valid prediction for GlimmerHMM_glimmerT_60907-T1
Valid prediction for GeneMark_model.106108_t
Valid prediction for GlimmerHMM_glimmerT_60897-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_28-snap.2218-T1
Valid prediction for GeneMark_model.106099_t
Valid prediction for snap_scaffold_28-snap.2224-T1
Valid prediction for Augustus_model.g40521.t1
Valid prediction for GeneMark_model.106115_t
Valid prediction for GeneMark_model.106116_t
Valid prediction for snap_scaffold_28-snap.2234-T1
Valid prediction for GeneMark_model.106110_t
Valid prediction for Augustus_model.g40522.t1
Valid prediction for GlimmerHMM_glimmerT_60906-T1
Valid prediction for snap_scaffold_28-snap.2236-T1
Valid prediction for GeneMark_model.106117_t
Valid prediction for snap_scaffold_28-snap.2222-T1
Valid prediction for snap_scaffold_28-snap.2227-T1
Valid prediction for GeneMark_model.106104_t
Valid prediction for GeneMark_model.106100_t
Valid prediction for GlimmerHMM_glimmerT_60902-T1
Couldn't classify 48249, 48322
Couldn't classify 52339, 52374
Sorry, prediction pasa_asmbl_37860.p1 fails validation.
(AGC)	 CC	48249-48322	GT	AGG
(TTA)	 AG	48559-48640	GT	AGG
(GCC)	 AG	50183-50287	GT	AGG
(GCA)	 AG	50401-50469	GT	AGG
(CTT)	 AG	50689-50769	GT	CAG
(ATC)	 AG	52339-52374	GA	TGG
-recovered pasa_asmbl_37860.p1, internal, 48559, 48640
-recovered pasa_asmbl_37860.p1, internal, 50183, 50287
-recovered pasa_asmbl_37860.p1, internal, 50401, 50469
-recovered pasa_asmbl_37860.p1, internal, 50689, 50769
Valid prediction for GeneMark_model.106106_t
Valid prediction for GeneMark_model.106111_t
Valid prediction for GeneMark_model.106109_t
Valid prediction for GeneMark_model.106094_t
Valid prediction for snap_scaffold_28-snap.2230-T1
Valid prediction for snap_scaffold_28-snap.2238-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.106113_t
Valid prediction for snap_scaffold_28-snap.2231-T1
Valid prediction for Augustus_model.g40523.t1
Valid prediction for snap_scaffold_28-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_60898-T1
Valid prediction for snap_scaffold_28-snap.2220-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28342, rend_intergenic: 26048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52866, rend_intergenic: 44476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78527, rend_intergenic: 63982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103850, rend_intergenic: 102397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125960, rend_intergenic: 124139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134660
-exon list size: 334


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 28342, rend_intergenic: 26048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52866, rend_intergenic: 44476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78527, rend_intergenic: 63982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103850, rend_intergenic: 102397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125960, rend_intergenic: 124139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support