-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_7114943-7271970

-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 GlimmerHMM_glimmerT_27931-T1
Valid prediction for GeneMark_model.48285_t
Valid prediction for GlimmerHMM_glimmerT_27922-T1
Valid prediction for snap_scaffold_11-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_27930-T1
Valid prediction for HiQ_model.g18614.t1
Valid prediction for snap_scaffold_11-snap.1692-T1
Valid prediction for GeneMark_model.48277_t
Valid prediction for GlimmerHMM_glimmerT_27932-T1
Valid prediction for HiQ_model.g18617.t1
Valid prediction for snap_scaffold_11-snap.1679-T1
Valid prediction for GlimmerHMM_glimmerT_27919-T1
Valid prediction for GlimmerHMM_glimmerT_27936-T1
Valid prediction for GeneMark_model.48269_t
Valid prediction for snap_scaffold_11-snap.1669-T1
Valid prediction for Augustus_model.g18619.t1
Valid prediction for snap_scaffold_11-snap.1687-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.48282_t
Valid prediction for Augustus_model.g18615.t1
Valid prediction for GeneMark_model.48249_t
Valid prediction for snap_scaffold_11-snap.1690-T1
Valid prediction for GeneMark_model.48270_t
Valid prediction for GeneMark_model.48263_t
Valid prediction for GeneMark_model.48267_t
Valid prediction for snap_scaffold_11-snap.1682-T1
Valid prediction for GeneMark_model.48259_t
Valid prediction for GeneMark_model.48272_t
Valid prediction for GlimmerHMM_glimmerT_27929-T1
Valid prediction for snap_scaffold_11-snap.1673-T1
Valid prediction for GeneMark_model.48273_t
Valid prediction for GeneMark_model.48253_t
Valid prediction for GeneMark_model.48255_t
Couldn't classify 1109, 6249
Sorry, prediction pasa_asmbl_5627.p1 fails validation.
(TCT)	 TC	1109-6249	GT	GGG
(ACA)	 AG	6343-6543	GT	AGG
(GAT)	 AG	6707-6890	GT	AGG
(GAT)	 AG	7029-7175	GT	AGG
(GCA)	 AG	7299-7398	GT	AGG
(ATG)	 AG	7510-7673	GT	AGG
(GTG)	 AG	7858-7922	GT	AGG
(GTA)	 AG	8245-8447	GT	GGG
(TGT)	 AG	8789-8868	GT	AGG
(GGC)	 AG	9061-9219	GT	AGG
(GTG)	 AG	9444-9545	AA	GAA
-recovered pasa_asmbl_5627.p1, initial, 7510, 7673
-recovered pasa_asmbl_5627.p1, terminal, 9444, 9545
-recovered pasa_asmbl_5627.p1, internal, 6343, 6543
-recovered pasa_asmbl_5627.p1, internal, 6707, 6890
-recovered pasa_asmbl_5627.p1, internal, 7029, 7175
-recovered pasa_asmbl_5627.p1, internal, 7299, 7398
-recovered pasa_asmbl_5627.p1, internal, 7510, 7673
-recovered pasa_asmbl_5627.p1, internal, 7858, 7922
-recovered pasa_asmbl_5627.p1, internal, 8245, 8447
-recovered pasa_asmbl_5627.p1, internal, 8789, 8868
-recovered pasa_asmbl_5627.p1, internal, 9061, 9219
Valid prediction for snap_scaffold_11-snap.1675-T1
Couldn't classify 542, 841
Sorry, prediction pasa_asmbl_6303.p1 fails validation.
(GAC)	 CA	542-841	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_27933-T1
Valid prediction for GeneMark_model.48251_t
Valid prediction for GeneMark_model.48261_t
Valid prediction for GlimmerHMM_glimmerT_27923-T1
Valid prediction for GlimmerHMM_glimmerT_27920-T1
Valid prediction for GeneMark_model.48280_t
Valid prediction for snap_scaffold_11-snap.1671-T1
Valid prediction for snap_scaffold_11-snap.1693-T1
Valid prediction for GeneMark_model.48279_t
Valid prediction for pasa_asmbl_5630.p1
Valid prediction for snap_scaffold_11-snap.1677-T1
Valid prediction for snap_scaffold_11-snap.1686-T1
Valid prediction for snap_scaffold_11-snap.1668-T1
Valid prediction for snap_scaffold_11-snap.1684-T1
Valid prediction for GeneMark_model.48275_t

-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 Augustus_model.g18626.t1
Valid prediction for GeneMark_model.48268_t
Valid prediction for snap_scaffold_11-snap.1695-T1
Valid prediction for GeneMark_model.48257_t
Valid prediction for snap_scaffold_11-snap.1688-T1
Valid prediction for Augustus_model.g18622.t1
Valid prediction for Augustus_model.g18618.t1
Valid prediction for GlimmerHMM_glimmerT_27928-T1
Valid prediction for GeneMark_model.48256_t
Valid prediction for snap_scaffold_11-snap.1680-T1
Valid prediction for GeneMark_model.48254_t
Valid prediction for GeneMark_model.48250_t
Valid prediction for GeneMark_model.48252_t
Valid prediction for snap_scaffold_11-snap.1670-T1
Valid prediction for GeneMark_model.48276_t
Valid prediction for Augustus_model.g18625.t1
Valid prediction for snap_scaffold_11-snap.1667-T1
Valid prediction for GeneMark_model.48260_t
Valid prediction for GlimmerHMM_glimmerT_27937-T1
Valid prediction for GeneMark_model.48271_t
Valid prediction for GeneMark_model.48265_t
Valid prediction for Augustus_model.g18621.t1
Valid prediction for Augustus_model.g18623.t1
Valid prediction for snap_scaffold_11-snap.1683-T1
Couldn't classify 48083, 48143
Couldn't classify 50573, 50734
Sorry, prediction pasa_asmbl_6742.p1 fails validation.
(AGG)	 AG	48083-48143	GT	AGG
(CCA)	 AG	48297-48469	GT	AGG
(GCC)	 AG	48916-49062	GT	TGG
(CGG)	 AG	49425-49613	GT	AGG
(ATC)	 AG	49927-50037	GT	TGG
(TCT)	 AG	50573-50734	AT	CCA
-recovered pasa_asmbl_6742.p1, internal, 48083, 48143
-recovered pasa_asmbl_6742.p1, internal, 48297, 48469
-recovered pasa_asmbl_6742.p1, internal, 48916, 49062
-recovered pasa_asmbl_6742.p1, internal, 49425, 49613
-recovered pasa_asmbl_6742.p1, internal, 49927, 50037
Valid prediction for snap_scaffold_11-snap.1691-T1
Valid prediction for GeneMark_model.48262_t
Valid prediction for snap_scaffold_11-snap.1689-T1
Valid prediction for snap_scaffold_11-snap.1672-T1
Valid prediction for GeneMark_model.48283_t
Valid prediction for Augustus_model.g18616.t1
Valid prediction for pasa_asmbl_6737.p1
Valid prediction for GlimmerHMM_glimmerT_27921-T1
Valid prediction for snap_scaffold_11-snap.1694-T1
Valid prediction for snap_scaffold_11-snap.1676-T1
Valid prediction for snap_scaffold_11-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_27934-T1
Valid prediction for GlimmerHMM_glimmerT_27925-T1
Valid prediction for Augustus_model.g18624.t1
Valid prediction for Augustus_model.g18620.t1
Valid prediction for GeneMark_model.48278_t
Valid prediction for GlimmerHMM_glimmerT_27927-T1
Valid prediction for GeneMark_model.48284_t
Couldn't classify 51491, 51547
Sorry, prediction pasa_asmbl_6740.p1 fails validation.
(TCA)	 TA	51491-51547	GT	AGG
(AGC)	 AG	53087-53120	GT	CGG
(GTG)	 AG	54224-54316	GT	AGG
(CAA)	 AG	54760-54976	GT	CCG
(GCC)	 AG	55135-55212	GT	CAG
(GAA)	 AG	55346-55478	AA	AGA
add_exon() Sorry, pasa_asmbl_6740.p1 54224-54316-terminal-1 is invalid.
-recovered pasa_asmbl_6740.p1, terminal, 54224, 54316
-recovered pasa_asmbl_6740.p1, terminal, 55346, 55478
-recovered pasa_asmbl_6740.p1, internal, 53087, 53120
-recovered pasa_asmbl_6740.p1, internal, 54224, 54316
-recovered pasa_asmbl_6740.p1, internal, 54760, 54976
-recovered pasa_asmbl_6740.p1, internal, 55135, 55212
Valid prediction for GeneMark_model.48258_t
Valid prediction for snap_scaffold_11-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_27924-T1
Valid prediction for GeneMark_model.48264_t
Valid prediction for GeneMark_model.48281_t
Valid prediction for GeneMark_model.48274_t
Valid prediction for GeneMark_model.48286_t
Valid prediction for GlimmerHMM_glimmerT_27935-T1
Valid prediction for snap_scaffold_11-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_27926-T1
Valid prediction for GeneMark_model.48266_t
Valid prediction for snap_scaffold_11-snap.1681-T1
Couldn't classify 32182, 32297
Couldn't classify 32730, 32932
Sorry, prediction pasa_asmbl_6745.p1 fails validation.
(TCT)	 AG	32182-32297	GT	AGG
(GCT)	 AG	32407-32477	GT	AGG
(GTG)	 AG	32730-32932	GC	AGG
-recovered pasa_asmbl_6745.p1, internal, 32182, 32297
-recovered pasa_asmbl_6745.p1, internal, 32407, 32477
-recovered pasa_asmbl_6745.p1, internal, 32730, 32932

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18439, rend_intergenic: 13045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23473, rend_intergenic: 20256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24412, rend_intergenic: 24207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39371, rend_intergenic: 31326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47777, rend_intergenic: 43289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56962, rend_intergenic: 51635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68219, rend_intergenic: 57612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73761, rend_intergenic: 69586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80446, rend_intergenic: 78427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87850, rend_intergenic: 84621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94400, rend_intergenic: 91662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109467, rend_intergenic: 105925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133211, rend_intergenic: 123914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148872, rend_intergenic: 147318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157028
-exon list size: 619


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
1.0    
1.1    
1.3    
1.4    
1.6    
1.8    
1.9    
2.1    
2.3    
2.4    
2.6    
2.7    
2.9    
3.1    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.3    
5.5    
5.6    
5.8    
6.0    
6.1    
6.3    
6.4    
6.6    
6.8    
6.9    
7.1    
7.2    
7.4    
7.6    
7.7    
7.9    
8.1    
8.2    
8.4    
8.5    
8.7    
8.9    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.1    
11.3    
11.4    
11.6    
11.8    
11.9    
12.1    
12.2    
12.4    
12.6    
12.7    
12.9    
13.0    
13.2    
13.4    
13.5    
13.7    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.8    
15.0    
15.1    
15.3    
15.5    
15.6    
15.8    
15.9    
16.1    
16.3    
16.4    
16.6    
16.7    
16.9    
17.1    
17.2    
17.4    
17.6    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.8    
19.0    
19.2    
19.3    
19.5    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.6    
20.8    
20.9    
21.1    
21.3    
21.4    
21.6    
21.7    
21.9    
22.1    
22.2    
22.4    
22.5    
22.7    
22.9    
23.0    
23.2    
23.3    
23.5    
23.7    
23.8    
24.0    
24.2    
24.3    
24.5    
24.6    
24.8    
25.0    
25.1    
25.3    
25.4    
25.6    
25.8    
25.9    
26.1    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.2    
27.4    
27.5    
27.7    
27.9    
28.0    
28.2    
28.3    
28.5    
28.7    
28.8    
29.0    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.1    
30.3    
30.4    
30.6    
30.8    
30.9    
31.1    
31.2    
31.4    
31.6    
31.7    
31.9    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.0    
33.2    
33.3    
33.5    
33.7    
33.8    
34.0    
34.1    
34.3    
34.5    
34.6    
34.8    
34.9    
35.1    
35.3    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.8    
38.0    
38.2    
38.3    
38.5    
38.6    
38.8    
39.0    
39.1    
39.3    
39.5    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.7    
40.9    
41.1    
41.2    
41.4    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.5    
42.7    
42.8    
43.0    
43.2    
43.3    
43.5    
43.6    
43.8    
44.0    
44.1    
44.3    
44.4    
44.6    
44.8    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.5    
46.7    
46.9    
47.0    
47.2    
47.3    
47.5    
47.7    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.3    
52.5    
52.7    
52.8    
53.0    
53.1    
53.3    
53.5    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.2    
55.4    
55.6    
55.7    
55.9    
56.0    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.2    
57.3    
57.5    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.6    
58.8    
58.9    
59.1    
59.3    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 18439, rend_intergenic: 13045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23473, rend_intergenic: 20256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24412, rend_intergenic: 24207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39371, rend_intergenic: 31326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47777, rend_intergenic: 43289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56962, rend_intergenic: 51635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68219, rend_intergenic: 57612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73761, rend_intergenic: 69586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80446, rend_intergenic: 78427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87850, rend_intergenic: 84621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94400, rend_intergenic: 91662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109467, rend_intergenic: 105925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133211, rend_intergenic: 123914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148872, rend_intergenic: 147318  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