-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_12756699-13002580

-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 Augustus_model.g21761.t1
Valid prediction for GlimmerHMM_glimmerT_32573-T1
Valid prediction for Augustus_model.g21760.t1
Valid prediction for snap_scaffold_13-snap.2420-T1
Valid prediction for pasa_asmbl_11361.p1
Valid prediction for snap_scaffold_13-snap.2425-T1
Valid prediction for snap_scaffold_13-snap.2429-T1
Valid prediction for snap_scaffold_13-snap.2407-T1
Valid prediction for snap_scaffold_13-snap.2417-T1
Valid prediction for snap_scaffold_13-snap.2414-T1
Valid prediction for snap_scaffold_13-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_32583-T1
Valid prediction for GlimmerHMM_glimmerT_32568-T1
Valid prediction for snap_scaffold_13-snap.2436-T1
Valid prediction for snap_scaffold_13-snap.2427-T1
Valid prediction for Augustus_model.g21764.t1
Valid prediction for GlimmerHMM_glimmerT_32572-T1
Valid prediction for snap_scaffold_13-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_32576-T1
Valid prediction for snap_scaffold_13-snap.2431-T1
Valid prediction for snap_scaffold_13-snap.2411-T1
Valid prediction for GlimmerHMM_glimmerT_32586-T1
Valid prediction for snap_scaffold_13-snap.2438-T1
Valid prediction for snap_scaffold_13-snap.2451-T1
Valid prediction for snap_scaffold_13-snap.2453-T1
Valid prediction for GlimmerHMM_glimmerT_32570-T1
Valid prediction for snap_scaffold_13-snap.2409-T1
Couldn't classify 50337, 50765
Sorry, prediction pasa_asmbl_11359.p1 fails validation.
(AGG)	 CA	50337-50765	GG	GTG
Valid prediction for GlimmerHMM_glimmerT_32578-T1
Valid prediction for Augustus_model.g21759.t1
Valid prediction for snap_scaffold_13-snap.2419-T1
Valid prediction for snap_scaffold_13-snap.2450-T1
Valid prediction for snap_scaffold_13-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_32567-T1
Valid prediction for GlimmerHMM_glimmerT_32575-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_13-snap.2445-T1
Valid prediction for snap_scaffold_13-snap.2437-T1
Valid prediction for GlimmerHMM_glimmerT_32584-T1
Couldn't classify 131498, 131707
Couldn't classify 134281, 134406
Sorry, prediction pasa_asmbl_10143.p1 fails validation.
(ACC)	 AG	131498-131707	GT	AGG
(TGG)	 AG	133914-133994	GT	AGG
(TAT)	 AG	134281-134406	AA	ACA
-recovered pasa_asmbl_10143.p1, internal, 131498, 131707
-recovered pasa_asmbl_10143.p1, internal, 133914, 133994
Valid prediction for GlimmerHMM_glimmerT_32580-T1
Valid prediction for snap_scaffold_13-snap.2447-T1
Valid prediction for GlimmerHMM_glimmerT_32574-T1
Valid prediction for snap_scaffold_13-snap.2442-T1
Valid prediction for snap_scaffold_13-snap.2430-T1
Valid prediction for GlimmerHMM_glimmerT_32577-T1
Valid prediction for snap_scaffold_13-snap.2444-T1
Valid prediction for snap_scaffold_13-snap.2424-T1
Valid prediction for GlimmerHMM_glimmerT_32581-T1
Valid prediction for snap_scaffold_13-snap.2406-T1
Valid prediction for snap_scaffold_13-snap.2455-T1
Valid prediction for Augustus_model.g21758.t1
Valid prediction for snap_scaffold_13-snap.2426-T1
Valid prediction for snap_scaffold_13-snap.2416-T1
Valid prediction for snap_scaffold_13-snap.2418-T1
Valid prediction for Augustus_model.g21757.t1
Valid prediction for snap_scaffold_13-snap.2423-T1
Valid prediction for snap_scaffold_13-snap.2452-T1
Valid prediction for snap_scaffold_13-snap.2439-T1
Valid prediction for snap_scaffold_13-snap.2408-T1
Valid prediction for snap_scaffold_13-snap.2413-T1
Valid prediction for snap_scaffold_13-snap.2415-T1
Valid prediction for snap_scaffold_13-snap.2434-T1
Valid prediction for GlimmerHMM_glimmerT_32571-T1
Valid prediction for snap_scaffold_13-snap.2448-T1
Valid prediction for snap_scaffold_13-snap.2412-T1
Valid prediction for snap_scaffold_13-snap.2432-T1
Valid prediction for GlimmerHMM_glimmerT_32587-T1
Couldn't classify 156458, 156850
Sorry, prediction pasa_asmbl_11360.p1 fails validation.
(CTG)	 AC	156458-156850	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_32582-T1
Valid prediction for HiQ_model.g21762.t1
Valid prediction for GlimmerHMM_glimmerT_32585-T1
Valid prediction for snap_scaffold_13-snap.2446-T1
Valid prediction for snap_scaffold_13-snap.2433-T1
Valid prediction for Augustus_model.g21763.t1
Valid prediction for GlimmerHMM_glimmerT_32579-T1
Valid prediction for snap_scaffold_13-snap.2422-T1
Valid prediction for snap_scaffold_13-snap.2454-T1
Valid prediction for GlimmerHMM_glimmerT_32569-T1
Valid prediction for snap_scaffold_13-snap.2449-T1
Valid prediction for snap_scaffold_13-snap.2441-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2428-T1
Valid prediction for snap_scaffold_13-snap.2440-T1
Valid prediction for snap_scaffold_13-snap.2421-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15983, rend_intergenic: 6411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21306, rend_intergenic: 17662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30643, rend_intergenic: 23280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33608, rend_intergenic: 31710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36115, rend_intergenic: 35455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70546, rend_intergenic: 48518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91857, rend_intergenic: 70588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95266, rend_intergenic: 94672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100313, rend_intergenic: 96444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120977, rend_intergenic: 104435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122885, rend_intergenic: 121121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127019, rend_intergenic: 126530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135337, rend_intergenic: 127736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152620, rend_intergenic: 137837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174877, rend_intergenic: 164843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197447, rend_intergenic: 178717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198504, rend_intergenic: 198390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215182, rend_intergenic: 200022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221389, rend_intergenic: 216191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236866, rend_intergenic: 224043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242106, rend_intergenic: 239938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245882
-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 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 15983, rend_intergenic: 6411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21306, rend_intergenic: 17662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30643, rend_intergenic: 23280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33608, rend_intergenic: 31710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36115, rend_intergenic: 35455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70546, rend_intergenic: 48518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91857, rend_intergenic: 70588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95266, rend_intergenic: 94672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100313, rend_intergenic: 96444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120977, rend_intergenic: 104435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122885, rend_intergenic: 121121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127019, rend_intergenic: 126530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135337, rend_intergenic: 127736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152620, rend_intergenic: 137837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174877, rend_intergenic: 164843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197447, rend_intergenic: 178717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198504, rend_intergenic: 198390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215182, rend_intergenic: 200022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221389, rend_intergenic: 216191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236866, rend_intergenic: 224043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242106, rend_intergenic: 239938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19264
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-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

-building DP trellis

-building trellis in range 6266 - 19264
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 231202 - 245882
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support