-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_3571911-3780202

-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_5-snap.719-T1
Valid prediction for snap_scaffold_5-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_11718-T1
Valid prediction for CodingQuarry_transcript_52005-T1
Valid prediction for Augustus_model.g7655.t1
Valid prediction for snap_scaffold_5-snap.717-T1
Valid prediction for Augustus_model.g7643.t1
Couldn't classify 47682, 48129
Sorry, prediction pasa_asmbl_45225.p1 fails validation.
(ACC)	 GT	47682-48129	GT	GGG
(CTG)	 AG	48407-48518	GT	TCG
(CCC)	 AG	50616-50622	GG	GAG
-recovered pasa_asmbl_45225.p1, terminal, 50616, 50622
-recovered pasa_asmbl_45225.p1, internal, 48407, 48518
Valid prediction for snap_scaffold_5-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_11703-T1
Couldn't classify 62528, 63091
Sorry, prediction pasa_asmbl_45231.p1 fails validation.
(CAT)	 GA	62528-63091	CC	CGC
Valid prediction for Augustus_model.g7648.t1
Valid prediction for Augustus_model.g7650.t1
Valid prediction for GlimmerHMM_glimmerT_11716-T1
Valid prediction for snap_scaffold_5-snap.700-T1
Valid prediction for Augustus_model.g7652.t1
Valid prediction for snap_scaffold_5-snap.696-T1
Valid prediction for snap_scaffold_5-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_11714-T1
Valid prediction for snap_scaffold_5-snap.724-T1
Valid prediction for snap_scaffold_5-snap.715-T1
Valid prediction for snap_scaffold_5-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_11717-T1
Valid prediction for snap_scaffold_5-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_11706-T1
Valid prediction for snap_scaffold_5-snap.706-T1
Couldn't classify 64916, 66244
Sorry, prediction pasa_asmbl_45233.p1 fails validation.
(AAG)	 CC	64916-66244	AG	GAA
Valid prediction for Augustus_model.g7644.t1
Valid prediction for GlimmerHMM_glimmerT_11707-T1
Valid prediction for snap_scaffold_5-snap.692-T1
Valid prediction for snap_scaffold_5-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_11711-T1
Valid prediction for Augustus_model.g7646.t1
Valid prediction for GlimmerHMM_glimmerT_11715-T1
Valid prediction for snap_scaffold_5-snap.718-T1
Valid prediction for snap_scaffold_5-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_11709-T1
Valid prediction for Augustus_model.g7651.t1
Valid prediction for snap_scaffold_5-snap.722-T1
Valid prediction for snap_scaffold_5-snap.732-T1
Valid prediction for GlimmerHMM_glimmerT_11722-T1
Valid prediction for snap_scaffold_5-snap.705-T1
Valid prediction for snap_scaffold_5-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_11713-T1
Valid prediction for GlimmerHMM_glimmerT_11705-T1
Valid prediction for GlimmerHMM_glimmerT_11719-T1
Valid prediction for snap_scaffold_5-snap.690-T1
Valid prediction for snap_scaffold_5-snap.720-T1
Valid prediction for snap_scaffold_5-snap.708-T1
Valid prediction for snap_scaffold_5-snap.711-T1
Valid prediction for Augustus_model.g7639.t1
Valid prediction for GlimmerHMM_glimmerT_11712-T1
Valid prediction for snap_scaffold_5-snap.701-T1
Valid prediction for Augustus_model.g7649.t1
Valid prediction for snap_scaffold_5-snap.729-T1
Valid prediction for Augustus_model.g7642.t1
Valid prediction for Augustus_model.g7654.t1
Valid prediction for snap_scaffold_5-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_11702-T1
Valid prediction for HiQ_model.g7656.t1
Couldn't classify 199539, 199676
Sorry, prediction pasa_asmbl_45237.p1 fails validation.
(GCG)	 TA	199539-199676	GT	AAG
(GAG)	 AG	200121-200291	GT	TGG
(ATA)	 AG	200945-201028	GT	CGG
(GCC)	 AG	202223-202415	GT	GGG
(TGG)	 AG	202914-203050	GT	ATG
(TCT)	 AG	203578-203748	AG	AGA
-recovered pasa_asmbl_45237.p1, terminal, 203578, 203748
-recovered pasa_asmbl_45237.p1, internal, 200121, 200291
-recovered pasa_asmbl_45237.p1, internal, 200945, 201028
-recovered pasa_asmbl_45237.p1, internal, 202223, 202415
-recovered pasa_asmbl_45237.p1, internal, 202914, 203050

-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_11704-T1
Valid prediction for snap_scaffold_5-snap.723-T1
Valid prediction for snap_scaffold_5-snap.698-T1
Valid prediction for snap_scaffold_5-snap.704-T1
Valid prediction for Augustus_model.g7647.t1
Valid prediction for snap_scaffold_5-snap.693-T1
Valid prediction for snap_scaffold_5-snap.728-T1
Valid prediction for Augustus_model.g7641.t1
Valid prediction for snap_scaffold_5-snap.731-T1
Valid prediction for Augustus_model.g7638.t1
Valid prediction for GlimmerHMM_glimmerT_11721-T1
Valid prediction for GlimmerHMM_glimmerT_11701-T1
Valid prediction for Augustus_model.g7653.t1
Valid prediction for snap_scaffold_5-snap.702-T1
Valid prediction for snap_scaffold_5-snap.697-T1
Couldn't classify 92649, 92960
Sorry, prediction pasa_asmbl_45235.p3 fails validation.
(TGT)	 GT	92649-92960	AA	GAA
Valid prediction for snap_scaffold_5-snap.716-T1
Valid prediction for Augustus_model.g7645.t1
Valid prediction for snap_scaffold_5-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_11710-T1
Valid prediction for snap_scaffold_5-snap.721-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.712-T1
Valid prediction for snap_scaffold_5-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_11708-T1
Valid prediction for snap_scaffold_5-snap.733-T1
Valid prediction for Augustus_model.g7640.t1
Valid prediction for GlimmerHMM_glimmerT_11720-T1
Valid prediction for snap_scaffold_5-snap.727-T1
Valid prediction for snap_scaffold_5-snap.694-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.703-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15905, rend_intergenic: 9092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19919, rend_intergenic: 16016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36136, rend_intergenic: 24574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45752, rend_intergenic: 41909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49463, rend_intergenic: 46981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58652, rend_intergenic: 52755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109048, rend_intergenic: 108406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119186, rend_intergenic: 110101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159297, rend_intergenic: 155857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173929, rend_intergenic: 166711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199092, rend_intergenic: 196949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203748, rend_intergenic: 200090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208292
-exon list size: 309


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.5    
3.9    
4.2    
4.5    
4.8    
5.1    
5.5    
5.8    
6.1    
6.4    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.4    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.6    
37.9    
38.3    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
94.2    
94.5    
94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 15905, rend_intergenic: 9092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19919, rend_intergenic: 16016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36136, rend_intergenic: 24574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45752, rend_intergenic: 41909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49463, rend_intergenic: 46981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58652, rend_intergenic: 52755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109048, rend_intergenic: 108406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119186, rend_intergenic: 110101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159297, rend_intergenic: 155857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173929, rend_intergenic: 166711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199092, rend_intergenic: 196949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203748, rend_intergenic: 200090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support