-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_4378162-4603158

-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_17-snap.915-T1
Valid prediction for snap_scaffold_17-snap.921-T1
Valid prediction for snap_scaffold_17-snap.940-T1
Valid prediction for snap_scaffold_17-snap.942-T1
Valid prediction for snap_scaffold_17-snap.931-T1
Valid prediction for GlimmerHMM_glimmerT_40171-T1
Valid prediction for GlimmerHMM_glimmerT_40190-T1
Valid prediction for GlimmerHMM_glimmerT_40177-T1
Valid prediction for snap_scaffold_17-snap.934-T1
Sorry, intron length (8) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_40182-T1
Valid prediction for GlimmerHMM_glimmerT_40179-T1
Valid prediction for GlimmerHMM_glimmerT_40195-T1
Valid prediction for Augustus_model.g26762.t1
Valid prediction for snap_scaffold_17-snap.951-T1
Valid prediction for snap_scaffold_17-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_40186-T1
Valid prediction for snap_scaffold_17-snap.959-T1
Valid prediction for snap_scaffold_17-snap.925-T1
Valid prediction for snap_scaffold_17-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_40188-T1
Valid prediction for snap_scaffold_17-snap.936-T1
Valid prediction for snap_scaffold_17-snap.948-T1
Valid prediction for snap_scaffold_17-snap.937-T1
Valid prediction for snap_scaffold_17-snap.952-T1
Valid prediction for GlimmerHMM_glimmerT_40173-T1
Valid prediction for GlimmerHMM_glimmerT_40191-T1
Valid prediction for snap_scaffold_17-snap.920-T1
Valid prediction for snap_scaffold_17-snap.956-T1
Valid prediction for snap_scaffold_17-snap.918-T1
Valid prediction for snap_scaffold_17-snap.927-T1
Valid prediction for snap_scaffold_17-snap.933-T1
Valid prediction for snap_scaffold_17-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_40181-T1
Valid prediction for GlimmerHMM_glimmerT_40184-T1
Valid prediction for snap_scaffold_17-snap.958-T1
Valid prediction for snap_scaffold_17-snap.943-T1
Valid prediction for snap_scaffold_17-snap.957-T1
Valid prediction for snap_scaffold_17-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_40170-T1
Valid prediction for snap_scaffold_17-snap.950-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 GlimmerHMM_glimmerT_40192-T1
Valid prediction for snap_scaffold_17-snap.947-T1
Valid prediction for snap_scaffold_17-snap.916-T1
Valid prediction for Augustus_model.g26757.t1
Valid prediction for GlimmerHMM_glimmerT_40187-T1
Valid prediction for Augustus_model.g26760.t1
Valid prediction for snap_scaffold_17-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_40189-T1
Valid prediction for GlimmerHMM_glimmerT_40178-T1
Couldn't classify 157109, 157309
Couldn't classify 157495, 157884
Sorry, prediction pasa_asmbl_17864.p1 fails validation.
(TCG)	 AT	157109-157309	GT	AGG
(GTG)	 AG	157495-157884	GA	CGG
Valid prediction for snap_scaffold_17-snap.944-T1
Valid prediction for snap_scaffold_17-snap.930-T1
Valid prediction for snap_scaffold_17-snap.946-T1
Valid prediction for CodingQuarry_transcript_21948-T1
Valid prediction for snap_scaffold_17-snap.939-T1
Valid prediction for Augustus_model.g26765.t1
Valid prediction for snap_scaffold_17-snap.922-T1
Valid prediction for snap_scaffold_17-snap.919-T1
Valid prediction for Augustus_model.g26764.t1
Valid prediction for Augustus_model.g26759.t1
Valid prediction for GlimmerHMM_glimmerT_40172-T1
Valid prediction for GlimmerHMM_glimmerT_40174-T1
Valid prediction for snap_scaffold_17-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_40194-T1
Valid prediction for snap_scaffold_17-snap.924-T1
Valid prediction for snap_scaffold_17-snap.923-T1
Valid prediction for GlimmerHMM_glimmerT_40185-T1
Valid prediction for snap_scaffold_17-snap.941-T1
Valid prediction for snap_scaffold_17-snap.926-T1
Valid prediction for snap_scaffold_17-snap.935-T1
Valid prediction for snap_scaffold_17-snap.932-T1
Valid prediction for snap_scaffold_17-snap.928-T1
Valid prediction for Augustus_model.g26758.t1
Valid prediction for GlimmerHMM_glimmerT_40176-T1
Valid prediction for snap_scaffold_17-snap.917-T1
Valid prediction for Augustus_model.g26763.t1
Valid prediction for GlimmerHMM_glimmerT_40180-T1
Couldn't classify 158234, 158587
Sorry, prediction pasa_asmbl_17863.p1 fails validation.
(ATG)	 AG	158234-158587	CT	CCC
Valid prediction for snap_scaffold_17-snap.954-T1
Couldn't classify 173959, 174120
Couldn't classify 174968, 175327
Sorry, prediction pasa_asmbl_17858.p1 fails validation.
(CAG)	 CC	173959-174120	GT	AGG
(TTA)	 AG	174349-174487	GT	GGG
(AGG)	 AG	174659-174726	GT	AGG
(GGT)	 AG	174968-175327	CC	GAC
-recovered pasa_asmbl_17858.p1, internal, 174349, 174487
-recovered pasa_asmbl_17858.p1, internal, 174659, 174726
Valid prediction for GlimmerHMM_glimmerT_40175-T1
Valid prediction for GlimmerHMM_glimmerT_40183-T1
Valid prediction for Augustus_model.g26761.t1
Valid prediction for GlimmerHMM_glimmerT_40193-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24195, rend_intergenic: 22730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36657, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51033, rend_intergenic: 44680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72766, rend_intergenic: 67657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76989, rend_intergenic: 72806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83250, rend_intergenic: 79405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90055, rend_intergenic: 89788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97479, rend_intergenic: 90231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118993, rend_intergenic: 100680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134951, rend_intergenic: 131941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136861, rend_intergenic: 134955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142056, rend_intergenic: 137210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150162, rend_intergenic: 142905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155617, rend_intergenic: 152257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156820, rend_intergenic: 156224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169233, rend_intergenic: 164202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195193, rend_intergenic: 170293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208923, rend_intergenic: 196121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224997
-exon list size: 367


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.5    
9.8    
10.0    
10.3    
10.6    
10.8    
11.1    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 24195, rend_intergenic: 22730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36657, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51033, rend_intergenic: 44680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72766, rend_intergenic: 67657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76989, rend_intergenic: 72806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83250, rend_intergenic: 79405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90055, rend_intergenic: 89788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97479, rend_intergenic: 90231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118993, rend_intergenic: 100680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134951, rend_intergenic: 131941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136861, rend_intergenic: 134955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142056, rend_intergenic: 137210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150162, rend_intergenic: 142905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155617, rend_intergenic: 152257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156820, rend_intergenic: 156224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169233, rend_intergenic: 164202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195193, rend_intergenic: 170293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208923, rend_intergenic: 196121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support