-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_13485530-13793623

-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_16-snap.2577-T1
Couldn't classify 2303, 2740
Sorry, prediction pasa_asmbl_16736.p1 fails validation.
(TAC)	 TC	2303-2740	AC	AAA
Valid prediction for snap_scaffold_16-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_39362-T1
Valid prediction for GlimmerHMM_glimmerT_39360-T1
Valid prediction for snap_scaffold_16-snap.2609-T1
Valid prediction for snap_scaffold_16-snap.2572-T1
Valid prediction for GlimmerHMM_glimmerT_39357-T1
Valid prediction for snap_scaffold_16-snap.2612-T1
Valid prediction for snap_scaffold_16-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_39347-T1
Valid prediction for snap_scaffold_16-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_39355-T1
Valid prediction for snap_scaffold_16-snap.2610-T1
Valid prediction for snap_scaffold_16-snap.2599-T1
Valid prediction for snap_scaffold_16-snap.2598-T1
Valid prediction for snap_scaffold_16-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_39361-T1
Valid prediction for GlimmerHMM_glimmerT_39354-T1
Valid prediction for GlimmerHMM_glimmerT_39343-T1
Valid prediction for snap_scaffold_16-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_39352-T1
Valid prediction for GlimmerHMM_glimmerT_39356-T1
Valid prediction for HiQ_model.g26252.t1
Valid prediction for snap_scaffold_16-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_39344-T1
Valid prediction for snap_scaffold_16-snap.2589-T1
Valid prediction for GlimmerHMM_glimmerT_39353-T1
Valid prediction for GlimmerHMM_glimmerT_39365-T1
Valid prediction for snap_scaffold_16-snap.2623-T1
Valid prediction for snap_scaffold_16-snap.2586-T1
Valid prediction for GlimmerHMM_glimmerT_39366-T1
Valid prediction for snap_scaffold_16-snap.2582-T1
Valid prediction for snap_scaffold_16-snap.2574-T1
Valid prediction for snap_scaffold_16-snap.2579-T1
Valid prediction for snap_scaffold_16-snap.2617-T1
Valid prediction for snap_scaffold_16-snap.2604-T1
Valid prediction for snap_scaffold_16-snap.2611-T1
Valid prediction for snap_scaffold_16-snap.2619-T1
Couldn't classify 31044, 31258
Sorry, prediction pasa_asmbl_16660.p1 fails validation.
(CCT)	 GC	31044-31258	GT	AGG
(GTT)	 AG	31684-31931	GT	AGG
(GAC)	 AG	32184-32668	AG	GAA
-recovered pasa_asmbl_16660.p1, terminal, 32184, 32668
-recovered pasa_asmbl_16660.p1, internal, 31684, 31931
Valid prediction for snap_scaffold_16-snap.2597-T1
Valid prediction for snap_scaffold_16-snap.2588-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_16-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_39359-T1
Valid prediction for snap_scaffold_16-snap.2591-T1
Valid prediction for Augustus_model.g26256.t1
Valid prediction for GlimmerHMM_glimmerT_39351-T1
Valid prediction for snap_scaffold_16-snap.2606-T1
Valid prediction for Augustus_model.g26255.t1
Valid prediction for snap_scaffold_16-snap.2600-T1
Valid prediction for snap_scaffold_16-snap.2585-T1
Valid prediction for snap_scaffold_16-snap.2583-T1
Valid prediction for Augustus_model.g26257.t1
Couldn't classify 235930, 236040
Sorry, prediction Augustus_model.g26254.t1 fails validation.
(ATG)	 TG	235312-235351	GT	CTG
(AGG)	 AG	235930-236040	GT	CAG
-recovered Augustus_model.g26254.t1, initial, 235312, 235351
-recovered Augustus_model.g26254.t1, internal, 235930, 236040
Valid prediction for snap_scaffold_16-snap.2580-T1
Valid prediction for snap_scaffold_16-snap.2571-T1
Valid prediction for Augustus_model.g26253.t1
Valid prediction for snap_scaffold_16-snap.2614-T1
Valid prediction for snap_scaffold_16-snap.2573-T1
Valid prediction for Augustus_model.g26251.t1
Valid prediction for GlimmerHMM_glimmerT_39363-T1
Valid prediction for snap_scaffold_16-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_39348-T1
Valid prediction for snap_scaffold_16-snap.2608-T1
Valid prediction for GlimmerHMM_glimmerT_39364-T1
Valid prediction for GlimmerHMM_glimmerT_39358-T1
Valid prediction for GlimmerHMM_glimmerT_39345-T1
Valid prediction for snap_scaffold_16-snap.2594-T1
Valid prediction for snap_scaffold_16-snap.2593-T1
Valid prediction for GlimmerHMM_glimmerT_39349-T1
Valid prediction for snap_scaffold_16-snap.2590-T1
Valid prediction for snap_scaffold_16-snap.2576-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.2616-T1
Valid prediction for snap_scaffold_16-snap.2596-T1
Valid prediction for snap_scaffold_16-snap.2587-T1
Valid prediction for snap_scaffold_16-snap.2620-T1
Valid prediction for GlimmerHMM_glimmerT_39350-T1
Valid prediction for snap_scaffold_16-snap.2575-T1
Valid prediction for GlimmerHMM_glimmerT_39346-T1
Valid prediction for snap_scaffold_16-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_39342-T1
Valid prediction for snap_scaffold_16-snap.2621-T1
Valid prediction for snap_scaffold_16-snap.2607-T1
Valid prediction for snap_scaffold_16-snap.2578-T1
Valid prediction for snap_scaffold_16-snap.2595-T1
Valid prediction for snap_scaffold_16-snap.2618-T1
Valid prediction for Augustus_model.g26258.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21420, rend_intergenic: 14776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22507, rend_intergenic: 22089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34164, rend_intergenic: 28762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38063, rend_intergenic: 35196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46235, rend_intergenic: 38281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80876, rend_intergenic: 64201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85031, rend_intergenic: 82751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88575, rend_intergenic: 85225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100542, rend_intergenic: 91401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104393, rend_intergenic: 100602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121888, rend_intergenic: 117310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137381, rend_intergenic: 124499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158689, rend_intergenic: 141190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209024, rend_intergenic: 178633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211201, rend_intergenic: 209669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217246, rend_intergenic: 213683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228626, rend_intergenic: 218530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230752, rend_intergenic: 229195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260597, rend_intergenic: 239196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273419, rend_intergenic: 266872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 277815, rend_intergenic: 273788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286315, rend_intergenic: 282969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304156, rend_intergenic: 292061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 308094
-exon list size: 340


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
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    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
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    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
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    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
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    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
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    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 21420, rend_intergenic: 14776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22507, rend_intergenic: 22089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34164, rend_intergenic: 28762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38063, rend_intergenic: 35196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46235, rend_intergenic: 38281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80876, rend_intergenic: 64201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85031, rend_intergenic: 82751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88575, rend_intergenic: 85225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100542, rend_intergenic: 91401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104393, rend_intergenic: 100602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121888, rend_intergenic: 117310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137381, rend_intergenic: 124499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158689, rend_intergenic: 141190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209024, rend_intergenic: 178633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211201, rend_intergenic: 209669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217246, rend_intergenic: 213683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228626, rend_intergenic: 218530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230752, rend_intergenic: 229195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260597, rend_intergenic: 239196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273419, rend_intergenic: 266872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 277815, rend_intergenic: 273788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286315, rend_intergenic: 282969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 304156, rend_intergenic: 292061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10284
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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

-building DP trellis

-building trellis in range 257030 - 308094
-exon list size: 48


building trellis

2.0    
4.0    
6.0    
8.0    
10.0    
12.0    
14.0    
16.0    
18.0    
20.0    
22.0    
24.0    
26.0    
28.0    
30.0    
32.0    
34.0    
36.0    
38.0    
40.0    
42.0    
44.0    
46.0    
48.0    
50.0    
52.0    
54.0    
56.0    
58.0    
60.0    
62.0    
64.0    
66.0    
68.0    
70.0    
72.0    
74.0    
76.0    
78.0    
80.0    
82.0    
84.0    
86.0    
88.0    
90.0    
92.0    
94.0    
96.0    
98.0    
-found 6 predictions from path traversal
GOT 5prime partial gene.
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 294072 - 308094
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 295109 - 308094
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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