-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_17547396-17733179

-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 CodingQuarry_transcript_57747-T1
Valid prediction for snap_scaffold_7-snap.3384-T1
Valid prediction for snap_scaffold_7-snap.3362-T1
Valid prediction for snap_scaffold_7-snap.3371-T1
Valid prediction for snap_scaffold_7-snap.3374-T1
Valid prediction for snap_scaffold_7-snap.3389-T1
Valid prediction for snap_scaffold_7-snap.3387-T1
Valid prediction for snap_scaffold_7-snap.3376-T1
Valid prediction for GlimmerHMM_glimmerT_18910-T1
Valid prediction for pasa_asmbl_50490.p1
Valid prediction for snap_scaffold_7-snap.3356-T1
Valid prediction for Augustus_model.g12676.t1
Valid prediction for snap_scaffold_7-snap.3360-T1
Valid prediction for GlimmerHMM_glimmerT_18894-T1
Valid prediction for GlimmerHMM_glimmerT_18896-T1
Valid prediction for snap_scaffold_7-snap.3358-T1
Valid prediction for snap_scaffold_7-snap.3386-T1
Valid prediction for GlimmerHMM_glimmerT_18900-T1
Valid prediction for snap_scaffold_7-snap.3390-T1
Couldn't classify 59745, 59853
Couldn't classify 65583, 65695
Sorry, prediction pasa_asmbl_50487.p1 fails validation.
(GAC)	 TA	59745-59853	GT	AGG
(ACG)	 AG	60205-60318	GT	CAG
(ATA)	 AG	61327-61373	GT	AGG
(GAC)	 AG	61806-61979	GT	AGG
(CTG)	 AG	62083-62233	GT	AGG
(TGA)	 AG	63398-63562	GT	GAG
(ACA)	 AG	64832-64945	GT	CAG
(ACA)	 AG	65187-65300	GT	TCG
(GTG)	 AG	65583-65695	GG	TAG
-recovered pasa_asmbl_50487.p1, internal, 60205, 60318
-recovered pasa_asmbl_50487.p1, internal, 61327, 61373
-recovered pasa_asmbl_50487.p1, internal, 61806, 61979
-recovered pasa_asmbl_50487.p1, internal, 62083, 62233
-recovered pasa_asmbl_50487.p1, internal, 63398, 63562
-recovered pasa_asmbl_50487.p1, internal, 64832, 64945
-recovered pasa_asmbl_50487.p1, internal, 65187, 65300
Valid prediction for snap_scaffold_7-snap.3382-T1
Valid prediction for snap_scaffold_7-snap.3379-T1
Valid prediction for snap_scaffold_7-snap.3378-T1
Couldn't classify 53819, 53871
Couldn't classify 59023, 59066
Sorry, prediction pasa_asmbl_50484.p1 fails validation.
(CGT)	 GT	53819-53871	GT	AAG
(GTG)	 AG	56653-56783	GT	AGG
(ATC)	 AG	57021-57140	GT	AGG
(CGG)	 AG	59023-59066	TG	GCT
-recovered pasa_asmbl_50484.p1, internal, 56653, 56783
-recovered pasa_asmbl_50484.p1, internal, 57021, 57140
Valid prediction for snap_scaffold_7-snap.3372-T1
Valid prediction for GlimmerHMM_glimmerT_18903-T1
Valid prediction for snap_scaffold_7-snap.3393-T1
Valid prediction for GlimmerHMM_glimmerT_18908-T1
Valid prediction for snap_scaffold_7-snap.3391-T1
Valid prediction for Augustus_model.g12685.t1
Valid prediction for GlimmerHMM_glimmerT_18898-T1
Valid prediction for Augustus_model.g12683.t1
Valid prediction for GlimmerHMM_glimmerT_18893-T1
Valid prediction for GlimmerHMM_glimmerT_18905-T1
Valid prediction for GlimmerHMM_glimmerT_18891-T1
Couldn't classify 72800, 73309
Sorry, prediction pasa_asmbl_50488.p1 fails validation.
(TGC)	 CG	72800-73309	CA	AGC
Valid prediction for snap_scaffold_7-snap.3364-T1
Valid prediction for GlimmerHMM_glimmerT_18886-T1
Valid prediction for GlimmerHMM_glimmerT_18906-T1
Valid prediction for HiQ_model.g12681.t1
Valid prediction for Augustus_model.g12675.t1
Valid prediction for GlimmerHMM_glimmerT_18884-T1
Valid prediction for GlimmerHMM_glimmerT_18888-T1
Valid prediction for Augustus_model.g12682.t1
Valid prediction for snap_scaffold_7-snap.3361-T1
Valid prediction for Augustus_model.g12678.t1
Valid prediction for Augustus_model.g12684.t1
Valid prediction for snap_scaffold_7-snap.3394-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_7-snap.3367-T1
Valid prediction for Augustus_model.g12679.t1
Valid prediction for snap_scaffold_7-snap.3357-T1
Valid prediction for snap_scaffold_7-snap.3366-T1
Valid prediction for pasa_asmbl_51431.p1
Valid prediction for snap_scaffold_7-snap.3369-T1
Valid prediction for snap_scaffold_7-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_18902-T1
Valid prediction for snap_scaffold_7-snap.3375-T1
Valid prediction for GlimmerHMM_glimmerT_18885-T1
Valid prediction for snap_scaffold_7-snap.3396-T1
Valid prediction for GlimmerHMM_glimmerT_18887-T1
Valid prediction for snap_scaffold_7-snap.3355-T1
Valid prediction for GlimmerHMM_glimmerT_18904-T1
Valid prediction for HiQ_model.g12680.t1
Valid prediction for snap_scaffold_7-snap.3377-T1
Valid prediction for snap_scaffold_7-snap.3359-T1
Valid prediction for GlimmerHMM_glimmerT_18899-T1
Valid prediction for snap_scaffold_7-snap.3370-T1
Valid prediction for snap_scaffold_7-snap.3381-T1
Valid prediction for snap_scaffold_7-snap.3395-T1
Valid prediction for GlimmerHMM_glimmerT_18907-T1
Couldn't classify 65377, 65458
Sorry, prediction pasa_asmbl_51430.p1 fails validation.
(AAC)	 TC	65377-65458	GT	TGG
(GTT)	 AG	65594-65695	GT	AGG
(GAG)	 AG	65803-65953	GT	AGG
(GTA)	 AG	66035-66101	AA	GAA
-recovered pasa_asmbl_51430.p1, terminal, 66035, 66101
-recovered pasa_asmbl_51430.p1, internal, 65594, 65695
-recovered pasa_asmbl_51430.p1, internal, 65803, 65953
Valid prediction for Augustus_model.g12677.t1
Valid prediction for GlimmerHMM_glimmerT_18889-T1
Valid prediction for GlimmerHMM_glimmerT_18890-T1
Valid prediction for GlimmerHMM_glimmerT_18892-T1
Valid prediction for GlimmerHMM_glimmerT_18897-T1
Valid prediction for CodingQuarry_transcript_57746-T1
Valid prediction for CodingQuarry_transcript_57745-T1
Valid prediction for GlimmerHMM_glimmerT_18909-T1
Valid prediction for snap_scaffold_7-snap.3383-T1
Valid prediction for snap_scaffold_7-snap.3363-T1
Valid prediction for snap_scaffold_7-snap.3388-T1
Valid prediction for snap_scaffold_7-snap.3385-T1
Valid prediction for GlimmerHMM_glimmerT_18895-T1
Valid prediction for snap_scaffold_7-snap.3368-T1
Valid prediction for snap_scaffold_7-snap.3380-T1
Valid prediction for GlimmerHMM_glimmerT_18901-T1
Valid prediction for snap_scaffold_7-snap.3365-T1
Valid prediction for snap_scaffold_7-snap.3373-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9997, rend_intergenic: 9295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10988, rend_intergenic: 10850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14686, rend_intergenic: 12470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20941, rend_intergenic: 18370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26162, rend_intergenic: 21994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45614, rend_intergenic: 42109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70262, rend_intergenic: 46869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83435, rend_intergenic: 76650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87254, rend_intergenic: 84915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88352, rend_intergenic: 87671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95182, rend_intergenic: 92317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98506, rend_intergenic: 96320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105595, rend_intergenic: 103039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114017, rend_intergenic: 107835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129860, rend_intergenic: 127414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159978, rend_intergenic: 158008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167474, rend_intergenic: 160511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182896, rend_intergenic: 177108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185784
-exon list size: 360


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.7    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.3    
13.5    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.1    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.1    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.1    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
51.9    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.9    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
80.9    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.3    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9997, rend_intergenic: 9295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10988, rend_intergenic: 10850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14686, rend_intergenic: 12470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20941, rend_intergenic: 18370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26162, rend_intergenic: 21994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45614, rend_intergenic: 42109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70262, rend_intergenic: 46869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83435, rend_intergenic: 76650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87254, rend_intergenic: 84915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88352, rend_intergenic: 87671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95182, rend_intergenic: 92317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98506, rend_intergenic: 96320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105595, rend_intergenic: 103039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114017, rend_intergenic: 107835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129860, rend_intergenic: 127414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159978, rend_intergenic: 158008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167474, rend_intergenic: 160511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182896, rend_intergenic: 177108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19596
-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

-building DP trellis

-building trellis in range 1 - 18369
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 1 - 12469
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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