-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_5988968-6151784

-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_27-snap.1467-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.102420_t
Couldn't classify 86059, 86060
Couldn't classify 88377, 88378
Sorry, prediction CodingQuarry_transcript_41823-T1 fails validation.
(ATG)	 AG	86059-86060	GT	ATG
(GTC)	 AG	86163-86219	GT	GTG
(ACT)	 AG	86577-86634	GT	AAG
(TTC)	 AG	87486-87525	GT	CGG
(ATG)	 AG	87817-87990	GT	TTG
(GAA)	 AG	88377-88378	AA	GAA
add_exon() Sorry, CodingQuarry_transcript_41823-T1 87817-87990-initial-1 is invalid.
-recovered CodingQuarry_transcript_41823-T1, initial, 87817, 87990
-recovered CodingQuarry_transcript_41823-T1, internal, 86059, 86060
-recovered CodingQuarry_transcript_41823-T1, internal, 86163, 86219
-recovered CodingQuarry_transcript_41823-T1, internal, 86577, 86634
-recovered CodingQuarry_transcript_41823-T1, internal, 87486, 87525
-recovered CodingQuarry_transcript_41823-T1, internal, 87817, 87990
Valid prediction for GeneMark_model.102377_t
Valid prediction for snap_scaffold_27-snap.1452-T1
Valid prediction for snap_scaffold_27-snap.1466-T1
Valid prediction for snap_scaffold_27-snap.1440-T1
Valid prediction for GeneMark_model.102384_t
Valid prediction for Augustus_model.g39163.t1
Valid prediction for GlimmerHMM_glimmerT_58798-T1
Valid prediction for snap_scaffold_27-snap.1471-T1
Valid prediction for GeneMark_model.102402_t
Valid prediction for snap_scaffold_27-snap.1449-T1
Valid prediction for Augustus_model.g39165.t1
Valid prediction for GeneMark_model.102398_t
Valid prediction for GeneMark_model.102423_t
Valid prediction for GeneMark_model.102408_t
Valid prediction for GeneMark_model.102379_t
Valid prediction for snap_scaffold_27-snap.1468-T1
Valid prediction for snap_scaffold_27-snap.1447-T1
Valid prediction for Augustus_model.g39160.t1
Valid prediction for Augustus_model.g39161.t1
Valid prediction for GlimmerHMM_glimmerT_58790-T1
Valid prediction for GeneMark_model.102405_t
Valid prediction for GeneMark_model.102419_t
Valid prediction for GlimmerHMM_glimmerT_58801-T1
Valid prediction for snap_scaffold_27-snap.1456-T1
Valid prediction for snap_scaffold_27-snap.1461-T1
Valid prediction for snap_scaffold_27-snap.1439-T1
Valid prediction for GeneMark_model.102396_t
Valid prediction for GeneMark_model.102394_t
Valid prediction for GeneMark_model.102421_t
Valid prediction for GeneMark_model.102392_t
Valid prediction for snap_scaffold_27-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_58794-T1
Valid prediction for GlimmerHMM_glimmerT_58800-T1
Valid prediction for GeneMark_model.102397_t
Valid prediction for GeneMark_model.102390_t
Valid prediction for GlimmerHMM_glimmerT_58796-T1
Valid prediction for GeneMark_model.102417_t
Valid prediction for snap_scaffold_27-snap.1441-T1
Valid prediction for Augustus_model.g39162.t1
Valid prediction for snap_scaffold_27-snap.1443-T1
Valid prediction for snap_scaffold_27-snap.1469-T1
Valid prediction for GeneMark_model.102387_t
Valid prediction for GeneMark_model.102400_t
Valid prediction for GeneMark_model.102409_t
Valid prediction for snap_scaffold_27-snap.1448-T1
Valid prediction for GeneMark_model.102411_t
Valid prediction for GeneMark_model.102393_t
Valid prediction for snap_scaffold_27-snap.1457-T1
Valid prediction for GeneMark_model.102415_t
Valid prediction for GeneMark_model.102424_t
Valid prediction for GlimmerHMM_glimmerT_58793-T1
Valid prediction for GeneMark_model.102382_t
Valid prediction for GeneMark_model.102410_t
Valid prediction for snap_scaffold_27-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_58787-T1
Valid prediction for GeneMark_model.102418_t
Valid prediction for GeneMark_model.102388_t
Valid prediction for GeneMark_model.102407_t
Valid prediction for GeneMark_model.102413_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.102406_t
Valid prediction for Augustus_model.g39157.t1
Valid prediction for GlimmerHMM_glimmerT_58786-T1
Valid prediction for snap_scaffold_27-snap.1446-T1
Valid prediction for snap_scaffold_27-snap.1445-T1
Valid prediction for GeneMark_model.102422_t
Valid prediction for snap_scaffold_27-snap.1454-T1
Valid prediction for GeneMark_model.102403_t
Valid prediction for GeneMark_model.102381_t
Valid prediction for GlimmerHMM_glimmerT_58795-T1
Valid prediction for snap_scaffold_27-snap.1464-T1
Valid prediction for GeneMark_model.102378_t
Valid prediction for GlimmerHMM_glimmerT_58799-T1
Valid prediction for GeneMark_model.102425_t
Valid prediction for Augustus_model.g39156.t1
Valid prediction for snap_scaffold_27-snap.1450-T1
Valid prediction for GeneMark_model.102385_t
Valid prediction for snap_scaffold_27-snap.1460-T1
Valid prediction for GeneMark_model.102399_t
Valid prediction for GeneMark_model.102386_t
Valid prediction for snap_scaffold_27-snap.1470-T1
Valid prediction for GeneMark_model.102376_t
Valid prediction for snap_scaffold_27-snap.1455-T1
Valid prediction for GeneMark_model.102414_t
Valid prediction for Augustus_model.g39159.t1
Valid prediction for snap_scaffold_27-snap.1459-T1
Valid prediction for snap_scaffold_27-snap.1451-T1
Valid prediction for GlimmerHMM_glimmerT_58789-T1
Valid prediction for GlimmerHMM_glimmerT_58788-T1
Valid prediction for GeneMark_model.102395_t
Valid prediction for GeneMark_model.102380_t
Valid prediction for snap_scaffold_27-snap.1442-T1
Valid prediction for GeneMark_model.102416_t
Valid prediction for GlimmerHMM_glimmerT_58797-T1
Valid prediction for snap_scaffold_27-snap.1453-T1
Valid prediction for GeneMark_model.102401_t
Valid prediction for snap_scaffold_27-snap.1444-T1
Valid prediction for snap_scaffold_27-snap.1465-T1
Valid prediction for snap_scaffold_27-snap.1463-T1
Valid prediction for Augustus_model.g39158.t1
Valid prediction for GeneMark_model.102391_t
Valid prediction for GeneMark_model.102412_t
Valid prediction for GeneMark_model.102404_t
Valid prediction for GlimmerHMM_glimmerT_58792-T1
Valid prediction for GlimmerHMM_glimmerT_58791-T1
Valid prediction for snap_scaffold_27-snap.1438-T1
Valid prediction for GeneMark_model.102375_t
Valid prediction for pasa_asmbl_37003.p3
Valid prediction for Augustus_model.g39164.t1
Valid prediction for GeneMark_model.102383_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8679, rend_intergenic: 8258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14453, rend_intergenic: 12851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35506, rend_intergenic: 27744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52459, rend_intergenic: 36270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65719, rend_intergenic: 53616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95583, rend_intergenic: 92016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138230, rend_intergenic: 113248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150966, rend_intergenic: 146028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157466, rend_intergenic: 155553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162817
-exon list size: 570


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.1    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.8    
5.9    
6.1    
6.3    
6.5    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.7    
8.9    
9.1    
9.3    
9.4    
9.6    
9.8    
10.0    
10.1    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.1    
19.2    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.2    
21.3    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.6    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.4    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
42.0    
42.1    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
44.9    
45.1    
45.3    
45.5    
45.6    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 8679, rend_intergenic: 8258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14453, rend_intergenic: 12851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35506, rend_intergenic: 27744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52459, rend_intergenic: 36270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65719, rend_intergenic: 53616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95583, rend_intergenic: 92016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138230, rend_intergenic: 113248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150966, rend_intergenic: 146028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157466, rend_intergenic: 155553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support