-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_3561616-3718005

-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 GlimmerHMM_glimmerT_9102-T1
Valid prediction for GlimmerHMM_glimmerT_9122-T1
Valid prediction for GlimmerHMM_glimmerT_9101-T1
Valid prediction for snap_scaffold_4-snap.832-T1
Valid prediction for snap_scaffold_4-snap.819-T1
Valid prediction for Augustus_model.g5851.t1
Valid prediction for snap_scaffold_4-snap.830-T1
Valid prediction for Augustus_model.g5842.t1
Valid prediction for snap_scaffold_4-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_9127-T1
Valid prediction for GlimmerHMM_glimmerT_9119-T1
Valid prediction for Augustus_model.g5844.t1
Valid prediction for snap_scaffold_4-snap.835-T1
Valid prediction for snap_scaffold_4-snap.844-T1
Valid prediction for snap_scaffold_4-snap.820-T1
Valid prediction for snap_scaffold_4-snap.833-T1
Valid prediction for GlimmerHMM_glimmerT_9116-T1
Valid prediction for snap_scaffold_4-snap.831-T1
Valid prediction for snap_scaffold_4-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_9104-T1
Valid prediction for GlimmerHMM_glimmerT_9110-T1
Valid prediction for GlimmerHMM_glimmerT_9128-T1
Valid prediction for snap_scaffold_4-snap.845-T1
Valid prediction for snap_scaffold_4-snap.823-T1
Valid prediction for snap_scaffold_4-snap.840-T1
Valid prediction for snap_scaffold_4-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_9114-T1
Valid prediction for Augustus_model.g5841.t1
Valid prediction for GlimmerHMM_glimmerT_9125-T1
Valid prediction for snap_scaffold_4-snap.818-T1
Valid prediction for Augustus_model.g5857.t1
Valid prediction for GlimmerHMM_glimmerT_9107-T1
Valid prediction for snap_scaffold_4-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_9105-T1
Valid prediction for Augustus_model.g5847.t1
Valid prediction for GlimmerHMM_glimmerT_9103-T1
Valid prediction for GlimmerHMM_glimmerT_9121-T1
Valid prediction for GlimmerHMM_glimmerT_9111-T1
Valid prediction for snap_scaffold_4-snap.849-T1
Valid prediction for Augustus_model.g5850.t1
Valid prediction for snap_scaffold_4-snap.825-T1
Valid prediction for Augustus_model.g5852.t1
Valid prediction for Augustus_model.g5855.t1
Valid prediction for snap_scaffold_4-snap.839-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_4-snap.838-T1
Valid prediction for snap_scaffold_4-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_9130-T1
Valid prediction for snap_scaffold_4-snap.852-T1
Valid prediction for snap_scaffold_4-snap.848-T1
Valid prediction for GlimmerHMM_glimmerT_9115-T1
Valid prediction for GlimmerHMM_glimmerT_9131-T1
Valid prediction for snap_scaffold_4-snap.826-T1
Valid prediction for Augustus_model.g5854.t1
Valid prediction for Augustus_model.g5853.t1
Valid prediction for Augustus_model.g5849.t1
Valid prediction for snap_scaffold_4-snap.834-T1
Valid prediction for GlimmerHMM_glimmerT_9106-T1
Valid prediction for GlimmerHMM_glimmerT_9132-T1
Valid prediction for snap_scaffold_4-snap.837-T1
Valid prediction for snap_scaffold_4-snap.816-T1
Valid prediction for snap_scaffold_4-snap.827-T1
Valid prediction for GlimmerHMM_glimmerT_9117-T1
Valid prediction for snap_scaffold_4-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_9120-T1
Valid prediction for snap_scaffold_4-snap.828-T1
Valid prediction for snap_scaffold_4-snap.842-T1
Valid prediction for Augustus_model.g5848.t1
Valid prediction for GlimmerHMM_glimmerT_9108-T1
Valid prediction for Augustus_model.g5856.t1
Valid prediction for snap_scaffold_4-snap.841-T1
Couldn't classify 6448, 6469
Couldn't classify 9558, 9834
Sorry, prediction pasa_asmbl_43605.p2 fails validation.
(GAA)	 CT	6448-6469	GT	CGG
(CCC)	 AG	9177-9279	GT	AGG
(TAC)	 AG	9558-9834	GT	GGG
-recovered pasa_asmbl_43605.p2, internal, 9177, 9279
-recovered pasa_asmbl_43605.p2, internal, 9558, 9834
Valid prediction for GlimmerHMM_glimmerT_9129-T1
Valid prediction for GlimmerHMM_glimmerT_9112-T1
Valid prediction for snap_scaffold_4-snap.855-T1
Valid prediction for snap_scaffold_4-snap.821-T1
Valid prediction for snap_scaffold_4-snap.836-T1
Valid prediction for Augustus_model.g5845.t1
Valid prediction for GlimmerHMM_glimmerT_9123-T1
Valid prediction for snap_scaffold_4-snap.851-T1
Couldn't classify 31900, 31930
Couldn't classify 36886, 36997
Sorry, prediction pasa_asmbl_42453.p1 fails validation.
(CAT)	 AC	31900-31930	GT	GGG
(GTC)	 AG	33549-33646	GT	GGG
(GTC)	 AG	34911-35027	GT	GGG
(AGA)	 AG	35926-36080	GT	AGG
(CGT)	 AG	36886-36997	CG	GAC
-recovered pasa_asmbl_42453.p1, internal, 33549, 33646
-recovered pasa_asmbl_42453.p1, internal, 34911, 35027
-recovered pasa_asmbl_42453.p1, internal, 35926, 36080
Valid prediction for Augustus_model.g5858.t1
Valid prediction for snap_scaffold_4-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_9118-T1
Valid prediction for snap_scaffold_4-snap.824-T1
Valid prediction for snap_scaffold_4-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_9126-T1
Valid prediction for snap_scaffold_4-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_9124-T1
Valid prediction for Augustus_model.g5846.t1
Valid prediction for GlimmerHMM_glimmerT_9113-T1
Valid prediction for Augustus_model.g5843.t1
Valid prediction for GlimmerHMM_glimmerT_9109-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48970, rend_intergenic: 47046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76540, rend_intergenic: 72874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88602, rend_intergenic: 87603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100248, rend_intergenic: 96272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104016, rend_intergenic: 100876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124860, rend_intergenic: 107625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132883, rend_intergenic: 129642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147861, rend_intergenic: 145872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156390
-exon list size: 314


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 48970, rend_intergenic: 47046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76540, rend_intergenic: 72874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88602, rend_intergenic: 87603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100248, rend_intergenic: 96272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104016, rend_intergenic: 100876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124860, rend_intergenic: 107625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132883, rend_intergenic: 129642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147861, rend_intergenic: 145872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support