-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_1-171736

-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_7-snap.15-T1
Valid prediction for snap_scaffold_7-snap.44-T1
Valid prediction for GlimmerHMM_glimmerT_16685-T1
Valid prediction for snap_scaffold_7-snap.27-T1
Valid prediction for snap_scaffold_7-snap.24-T1
Valid prediction for Augustus_model.g11158.t1
Valid prediction for snap_scaffold_7-snap.33-T1
Valid prediction for CodingQuarry_transcript_57413-T1
Valid prediction for snap_scaffold_7-snap.11-T1
Valid prediction for snap_scaffold_7-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_16676-T1
Valid prediction for snap_scaffold_7-snap.1-T1
Valid prediction for snap_scaffold_7-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_16679-T1
Valid prediction for snap_scaffold_7-snap.21-T1
Valid prediction for pasa_asmbl_49533.p1
Valid prediction for snap_scaffold_7-snap.19-T1
Valid prediction for Augustus_model.g11168.t1
Valid prediction for snap_scaffold_7-snap.41-T1
Valid prediction for snap_scaffold_7-snap.7-T1
Valid prediction for snap_scaffold_7-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_16683-T1
Valid prediction for snap_scaffold_7-snap.8-T1
Valid prediction for snap_scaffold_7-snap.36-T1
Valid prediction for GlimmerHMM_glimmerT_16677-T1
Valid prediction for snap_scaffold_7-snap.16-T1
Valid prediction for Augustus_model.g11152.t1
Valid prediction for snap_scaffold_7-snap.45-T1
Valid prediction for snap_scaffold_7-snap.22-T1
Valid prediction for snap_scaffold_7-snap.31-T1
Valid prediction for snap_scaffold_7-snap.3-T1
Valid prediction for snap_scaffold_7-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_16695-T1
Valid prediction for GlimmerHMM_glimmerT_16692-T1
Valid prediction for snap_scaffold_7-snap.39-T1
Valid prediction for HiQ_model.g11156.t1
Valid prediction for snap_scaffold_7-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_16688-T1
Valid prediction for snap_scaffold_7-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_16678-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_16674-T1
Valid prediction for GlimmerHMM_glimmerT_16686-T1
Valid prediction for snap_scaffold_7-snap.25-T1
Couldn't classify 92320, 92406
Couldn't classify 97771, 97890
Sorry, prediction pasa_asmbl_50660.p1 fails validation.
(GAG)	 AG	92320-92406	GT	AGG
(TAC)	 AG	92726-92805	GT	AGG
(TGC)	 AG	92935-93018	GT	GGG
(GGT)	 AG	93563-93680	GT	AGG
(GTG)	 AG	93852-93959	GT	AGG
(GTG)	 AG	96399-96524	GT	TGG
(GAC)	 AG	97771-97890	GT	GGG
-recovered pasa_asmbl_50660.p1, internal, 92320, 92406
-recovered pasa_asmbl_50660.p1, internal, 92726, 92805
-recovered pasa_asmbl_50660.p1, internal, 92935, 93018
-recovered pasa_asmbl_50660.p1, internal, 93563, 93680
-recovered pasa_asmbl_50660.p1, internal, 93852, 93959
-recovered pasa_asmbl_50660.p1, internal, 96399, 96524
-recovered pasa_asmbl_50660.p1, internal, 97771, 97890
Valid prediction for Augustus_model.g11167.t1
Valid prediction for snap_scaffold_7-snap.42-T1
Valid prediction for Augustus_model.g11154.t1
Valid prediction for snap_scaffold_7-snap.26-T1
Valid prediction for Augustus_model.g11160.t1
Valid prediction for snap_scaffold_7-snap.2-T1
Valid prediction for snap_scaffold_7-snap.40-T1
Valid prediction for snap_scaffold_7-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_16675-T1
Valid prediction for snap_scaffold_7-snap.37-T1
Valid prediction for snap_scaffold_7-snap.6-T1
Valid prediction for snap_scaffold_7-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_16680-T1
Valid prediction for snap_scaffold_7-snap.10-T1
Valid prediction for Augustus_model.g11165.t1
Valid prediction for GlimmerHMM_glimmerT_16693-T1
Valid prediction for snap_scaffold_7-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_16682-T1
Valid prediction for Augustus_model.g11151.t1
Valid prediction for GlimmerHMM_glimmerT_16694-T1
Valid prediction for CodingQuarry_transcript_57415-T1
Valid prediction for Augustus_model.g11159.t1
Valid prediction for snap_scaffold_7-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_16684-T1
Valid prediction for Augustus_model.g11157.t1
Valid prediction for snap_scaffold_7-snap.20-T1
Valid prediction for snap_scaffold_7-snap.34-T1
Couldn't classify 17992, 18306
Sorry, prediction pasa_asmbl_50675.p1 fails validation.
(CTC)	 CT	17992-18306	GA	ACG
Valid prediction for snap_scaffold_7-snap.5-T1
Valid prediction for snap_scaffold_7-snap.18-T1
Valid prediction for snap_scaffold_7-snap.32-T1
Valid prediction for Augustus_model.g11155.t1
Valid prediction for GlimmerHMM_glimmerT_16689-T1
Valid prediction for GlimmerHMM_glimmerT_16681-T1
Valid prediction for pasa_asmbl_50667.p1
Couldn't classify 41947, 43232
Sorry, prediction GlimmerHMM_glimmerT_16690-T1 fails validation.
(ATN)	 GA	41947-43232	GT	CAG
(ACT)	 AG	43846-44056	AT	AGA
-recovered GlimmerHMM_glimmerT_16690-T1, terminal, 43846, 44056
Valid prediction for HiQ_model.g11161.t1
Valid prediction for Augustus_model.g11163.t1
Valid prediction for snap_scaffold_7-snap.12-T1
Valid prediction for Augustus_model.g11153.t1
Valid prediction for Augustus_model.g11162.t1
Valid prediction for snap_scaffold_7-snap.46-T1
Valid prediction for snap_scaffold_7-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_16673-T1
Valid prediction for snap_scaffold_7-snap.28-T1
Valid prediction for snap_scaffold_7-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_16687-T1
Valid prediction for GlimmerHMM_glimmerT_16691-T1
Couldn't classify 25733, 25792
Couldn't classify 30591, 30702
Sorry, prediction pasa_asmbl_50673.p1 fails validation.
(TCT)	 TC	25733-25792	GT	AGG
(GTT)	 AG	25991-26047	GT	AGG
(GAG)	 AG	27541-27639	GT	AGG
(GTG)	 AG	28756-28903	GT	TGG
(CAG)	 AG	29703-29781	GT	AGG
(GTG)	 AG	30591-30702	GT	AGG
-recovered pasa_asmbl_50673.p1, internal, 25991, 26047
-recovered pasa_asmbl_50673.p1, internal, 27541, 27639
-recovered pasa_asmbl_50673.p1, internal, 28756, 28903
-recovered pasa_asmbl_50673.p1, internal, 29703, 29781
-recovered pasa_asmbl_50673.p1, internal, 30591, 30702
Valid prediction for Augustus_model.g11166.t1
Valid prediction for Augustus_model.g11164.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10697, rend_intergenic: 8990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42887, rend_intergenic: 34826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66266, rend_intergenic: 58674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72868, rend_intergenic: 67981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75467, rend_intergenic: 73833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90824, rend_intergenic: 77791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103304, rend_intergenic: 94763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107913, rend_intergenic: 104103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108650, rend_intergenic: 108391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114685, rend_intergenic: 109097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118205, rend_intergenic: 116862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126811, rend_intergenic: 125150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138992, rend_intergenic: 128501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144479, rend_intergenic: 139699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146556, rend_intergenic: 144625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150824, rend_intergenic: 146835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167174, rend_intergenic: 165367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171736
-exon list size: 350


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 10697, rend_intergenic: 8990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42887, rend_intergenic: 34826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66266, rend_intergenic: 58674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72868, rend_intergenic: 67981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75467, rend_intergenic: 73833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90824, rend_intergenic: 77791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103304, rend_intergenic: 94763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107913, rend_intergenic: 104103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108650, rend_intergenic: 108391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114685, rend_intergenic: 109097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118205, rend_intergenic: 116862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126811, rend_intergenic: 125150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138992, rend_intergenic: 128501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144479, rend_intergenic: 139699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146556, rend_intergenic: 144625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150824, rend_intergenic: 146835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167174, rend_intergenic: 165367  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