-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_9347401-9520151

-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 GeneMark_model.52632_t
Valid prediction for GlimmerHMM_glimmerT_30437-T1
Valid prediction for GeneMark_model.52617_t
Valid prediction for GeneMark_model.52614_t
Valid prediction for snap_scaffold_12-snap.1796-T1
Valid prediction for GeneMark_model.52599_t
Valid prediction for snap_scaffold_12-snap.1799-T1
Valid prediction for GeneMark_model.52621_t
Valid prediction for snap_scaffold_12-snap.1809-T1
Valid prediction for snap_scaffold_12-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_30451-T1
Valid prediction for GlimmerHMM_glimmerT_30438-T1
Valid prediction for snap_scaffold_12-snap.1805-T1
Valid prediction for GeneMark_model.52598_t
Valid prediction for GeneMark_model.52634_t
Valid prediction for GeneMark_model.52603_t
Valid prediction for GeneMark_model.52609_t
Valid prediction for GlimmerHMM_glimmerT_30455-T1
Valid prediction for GlimmerHMM_glimmerT_30444-T1
Valid prediction for snap_scaffold_12-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_30457-T1
Valid prediction for snap_scaffold_12-snap.1786-T1
Valid prediction for Augustus_model.g20286.t1
Valid prediction for snap_scaffold_12-snap.1794-T1
Valid prediction for Augustus_model.g20295.t1
Valid prediction for GlimmerHMM_glimmerT_30434-T1
Valid prediction for snap_scaffold_12-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_30456-T1
Valid prediction for snap_scaffold_12-snap.1779-T1
Valid prediction for GlimmerHMM_glimmerT_30445-T1
Valid prediction for GlimmerHMM_glimmerT_30435-T1
Valid prediction for snap_scaffold_12-snap.1806-T1
Valid prediction for snap_scaffold_12-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_30441-T1
Couldn't classify 157347, 157559
Couldn't classify 158472, 158611
Sorry, prediction pasa_asmbl_8827.p1 fails validation.
(TAT)	 GC	157347-157559	GT	CGG
(ATG)	 AG	157636-157660	GT	AGG
(ATG)	 AG	157899-158012	GT	AGG
(AGA)	 AG	158199-158333	GT	AGG
(TGG)	 AG	158472-158611	CC	CCC
-recovered pasa_asmbl_8827.p1, initial, 157636, 157660
add_exon() Sorry, pasa_asmbl_8827.p1 157899-158012-initial-1 is invalid.
-recovered pasa_asmbl_8827.p1, initial, 157899, 158012
-recovered pasa_asmbl_8827.p1, terminal, 157899, 158012
-recovered pasa_asmbl_8827.p1, internal, 157636, 157660
-recovered pasa_asmbl_8827.p1, internal, 157899, 158012
-recovered pasa_asmbl_8827.p1, internal, 158199, 158333
Couldn't classify 158708, 158824
Sorry, prediction pasa_asmbl_8830.p1 fails validation.
(CCC)	 TC	158708-158824	GT	AGG
(GTG)	 AG	158970-159096	GT	GGG
(GTG)	 AG	159215-159795	GT	AAG
-recovered pasa_asmbl_8830.p1, terminal, 159215, 159795
-recovered pasa_asmbl_8830.p1, internal, 158970, 159096
-recovered pasa_asmbl_8830.p1, internal, 159215, 159795
Valid prediction for GlimmerHMM_glimmerT_30454-T1
Valid prediction for GeneMark_model.52607_t
Valid prediction for GlimmerHMM_glimmerT_30433-T1
Valid prediction for GeneMark_model.52605_t
Valid prediction for Augustus_model.g20288.t1
Valid prediction for Augustus_model.g20285.t1
Valid prediction for snap_scaffold_12-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_30452-T1
Valid prediction for GeneMark_model.52627_t
Valid prediction for GeneMark_model.52622_t
Valid prediction for Augustus_model.g20296.t1
Valid prediction for GlimmerHMM_glimmerT_30436-T1
Valid prediction for snap_scaffold_12-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_30447-T1
Valid prediction for GeneMark_model.52619_t
Valid prediction for GeneMark_model.52630_t
Valid prediction for snap_scaffold_12-snap.1790-T1
Valid prediction for GeneMark_model.52628_t
Valid prediction for snap_scaffold_12-snap.1798-T1
Valid prediction for snap_scaffold_12-snap.1788-T1
Valid prediction for GeneMark_model.52629_t
Valid prediction for GlimmerHMM_glimmerT_30449-T1
Valid prediction for GeneMark_model.52636_t
Valid prediction for GeneMark_model.52612_t
Valid prediction for GeneMark_model.52601_t
Valid prediction for GeneMark_model.52624_t
Valid prediction for snap_scaffold_12-snap.1787-T1
Valid prediction for HiQ_model.g20298.t1
Valid prediction for snap_scaffold_12-snap.1782-T1
Valid prediction for GeneMark_model.52610_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 GeneMark_model.52631_t
Valid prediction for snap_scaffold_12-snap.1800-T1
Valid prediction for Augustus_model.g20292.t1
Valid prediction for GeneMark_model.52616_t
Valid prediction for GlimmerHMM_glimmerT_30442-T1
Valid prediction for GlimmerHMM_glimmerT_30458-T1
Valid prediction for GlimmerHMM_glimmerT_30439-T1
Valid prediction for Augustus_model.g20294.t1
Valid prediction for GeneMark_model.52602_t
Valid prediction for GeneMark_model.52625_t
Valid prediction for GlimmerHMM_glimmerT_30431-T1
Valid prediction for GeneMark_model.52606_t
Valid prediction for GlimmerHMM_glimmerT_30446-T1
Valid prediction for snap_scaffold_12-snap.1807-T1
Valid prediction for Augustus_model.g20284.t1
Valid prediction for GlimmerHMM_glimmerT_30453-T1
Valid prediction for GeneMark_model.52623_t
Valid prediction for snap_scaffold_12-snap.1781-T1
Valid prediction for GeneMark_model.52604_t
Valid prediction for GeneMark_model.52633_t
Couldn't classify 5949, 5972
Sorry, prediction pasa_asmbl_7802.p1 fails validation.
(TTC)	 AG	5949-5972	GT	AGG
(GAG)	 AG	6067-6159	GT	AGG
(GAG)	 AG	6408-6533	GT	AGG
(GGA)	 AG	6670-6891	GT	AGG
(ATG)	 AG	7382-7474	GT	AGG
(GCT)	 AG	7665-7743	GT	AGG
(ACG)	 AG	7886-7949	GT	AGG
(CAA)	 AG	9237-9337	GT	GAG
(GCT)	 AG	9541-9653	GT	TGG
(TCA)	 AG	10161-10273	GT	TGG
(GCT)	 AG	10420-10523	GT	AGG
(ATC)	 AG	10789-10829	TG	AGT
-recovered pasa_asmbl_7802.p1, initial, 7382, 7474
-recovered pasa_asmbl_7802.p1, terminal, 10789, 10829
-recovered pasa_asmbl_7802.p1, internal, 5949, 5972
-recovered pasa_asmbl_7802.p1, internal, 6067, 6159
-recovered pasa_asmbl_7802.p1, internal, 6408, 6533
-recovered pasa_asmbl_7802.p1, internal, 6670, 6891
-recovered pasa_asmbl_7802.p1, internal, 7382, 7474
-recovered pasa_asmbl_7802.p1, internal, 7665, 7743
-recovered pasa_asmbl_7802.p1, internal, 7886, 7949
-recovered pasa_asmbl_7802.p1, internal, 9237, 9337
-recovered pasa_asmbl_7802.p1, internal, 9541, 9653
-recovered pasa_asmbl_7802.p1, internal, 10161, 10273
-recovered pasa_asmbl_7802.p1, internal, 10420, 10523
Valid prediction for Augustus_model.g20287.t1
Couldn't classify 102934, 103132
Sorry, prediction pasa_asmbl_7800.p2 fails validation.
(GAA)	 AG	102934-103132	GT	AGG
(TGG)	 AG	105961-106097	CC	AGC
-recovered pasa_asmbl_7800.p2, terminal, 105961, 106097
-recovered pasa_asmbl_7800.p2, internal, 102934, 103132
Valid prediction for GlimmerHMM_glimmerT_30440-T1
Valid prediction for snap_scaffold_12-snap.1804-T1
Valid prediction for GeneMark_model.52620_t
Valid prediction for snap_scaffold_12-snap.1795-T1
Valid prediction for snap_scaffold_12-snap.1801-T1
Valid prediction for GeneMark_model.52626_t
Valid prediction for snap_scaffold_12-snap.1789-T1
Valid prediction for snap_scaffold_12-snap.1783-T1
Valid prediction for GeneMark_model.52613_t
Valid prediction for GeneMark_model.52635_t
Valid prediction for Augustus_model.g20293.t1
Valid prediction for Augustus_model.g20290.t1
Valid prediction for snap_scaffold_12-snap.1793-T1
Valid prediction for Augustus_model.g20291.t1
Valid prediction for GlimmerHMM_glimmerT_30432-T1
Valid prediction for GeneMark_model.52618_t
Valid prediction for Augustus_model.g20297.t1
Valid prediction for GlimmerHMM_glimmerT_30450-T1
Valid prediction for GeneMark_model.52600_t
Valid prediction for snap_scaffold_12-snap.1784-T1
Valid prediction for Augustus_model.g20289.t1
Valid prediction for snap_scaffold_12-snap.1803-T1
Valid prediction for GeneMark_model.52615_t
Valid prediction for GeneMark_model.52611_t
Valid prediction for snap_scaffold_12-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_30443-T1
Valid prediction for GlimmerHMM_glimmerT_30448-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 161926, rend_intergenic: 161923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56843, rend_intergenic: 44683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71296, rend_intergenic: 66655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83547, rend_intergenic: 73791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102897, rend_intergenic: 98182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114219, rend_intergenic: 103233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136653, rend_intergenic: 131821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141704, rend_intergenic: 136676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159548, rend_intergenic: 157287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163191, rend_intergenic: 161127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172751
-exon list size: 507


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 161926, rend_intergenic: 161923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56843, rend_intergenic: 44683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71296, rend_intergenic: 66655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83547, rend_intergenic: 73791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102897, rend_intergenic: 98182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114219, rend_intergenic: 103233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136653, rend_intergenic: 131821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141704, rend_intergenic: 136676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159548, rend_intergenic: 157287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163191, rend_intergenic: 161127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support