-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_6915829-7144544

-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_24944-T1
Valid prediction for snap_scaffold_10-snap.1450-T1
Valid prediction for snap_scaffold_10-snap.1430-T1
Valid prediction for Augustus_model.g16611.t1
Valid prediction for snap_scaffold_10-snap.1460-T1
Valid prediction for Augustus_model.g16622.t1
Couldn't classify 187733, 187753
Couldn't classify 189403, 189424
Sorry, prediction pasa_asmbl_3256.p1 fails validation.
(GAC)	 CG	187733-187753	GT	AGG
(ACT)	 AG	188115-188348	GT	CGG
(AAC)	 AG	188640-188815	GT	CGG
(GGA)	 AG	189403-189424	CG	AGC
-recovered pasa_asmbl_3256.p1, internal, 188115, 188348
-recovered pasa_asmbl_3256.p1, internal, 188640, 188815
Valid prediction for snap_scaffold_10-snap.1452-T1
Valid prediction for snap_scaffold_10-snap.1467-T1
Valid prediction for snap_scaffold_10-snap.1455-T1
Valid prediction for snap_scaffold_10-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_24955-T1
Valid prediction for snap_scaffold_10-snap.1447-T1
Valid prediction for Augustus_model.g16610.t1
Valid prediction for Augustus_model.g16609.t1
Valid prediction for snap_scaffold_10-snap.1429-T1
Valid prediction for snap_scaffold_10-snap.1440-T1
Valid prediction for Augustus_model.g16625.t1
Valid prediction for snap_scaffold_10-snap.1438-T1
Valid prediction for snap_scaffold_10-snap.1469-T1
Valid prediction for snap_scaffold_10-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_24952-T1
Valid prediction for snap_scaffold_10-snap.1470-T1
Valid prediction for Augustus_model.g16626.t1
Couldn't classify 194271, 194526
Sorry, prediction pasa_asmbl_3262.p1 fails validation.
(CCC)	 CT	194271-194526	GT	AGG
(GTG)	 AG	195264-195546	GT	AGG
(TGA)	 AG	195670-195856	GT	GAG
(CCC)	 AG	196057-196296	GT	AGG
(ATG)	 AG	196487-197492	GT	AGG
(ATG)	 AG	197614-197695	GT	AGG
(GTT)	 AG	197836-197929	CA	GAC
-recovered pasa_asmbl_3262.p1, initial, 196487, 197492
-recovered pasa_asmbl_3262.p1, initial, 197614, 197695
add_exon() Sorry, pasa_asmbl_3262.p1 196487-197492-terminal-3 is invalid.
-recovered pasa_asmbl_3262.p1, terminal, 196487, 197492
-recovered pasa_asmbl_3262.p1, terminal, 197836, 197929
-recovered pasa_asmbl_3262.p1, internal, 195264, 195546
-recovered pasa_asmbl_3262.p1, internal, 195670, 195856
-recovered pasa_asmbl_3262.p1, internal, 196057, 196296
-recovered pasa_asmbl_3262.p1, internal, 196487, 197492
-recovered pasa_asmbl_3262.p1, internal, 197614, 197695
Valid prediction for GlimmerHMM_glimmerT_24960-T1
Valid prediction for snap_scaffold_10-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_24950-T1
Valid prediction for snap_scaffold_10-snap.1453-T1
Valid prediction for snap_scaffold_10-snap.1468-T1
Valid prediction for snap_scaffold_10-snap.1441-T1
Valid prediction for snap_scaffold_10-snap.1444-T1
Valid prediction for Augustus_model.g16615.t1
Valid prediction for GlimmerHMM_glimmerT_24949-T1
Valid prediction for snap_scaffold_10-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_24953-T1
Valid prediction for snap_scaffold_10-snap.1432-T1
Valid prediction for snap_scaffold_10-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_24945-T1
Valid prediction for GlimmerHMM_glimmerT_24954-T1
Valid prediction for GlimmerHMM_glimmerT_24964-T1
Valid prediction for snap_scaffold_10-snap.1456-T1
Valid prediction for GlimmerHMM_glimmerT_24962-T1
Valid prediction for Augustus_model.g16617.t1
Valid prediction for GlimmerHMM_glimmerT_24948-T1
Valid prediction for snap_scaffold_10-snap.1466-T1
Valid prediction for snap_scaffold_10-snap.1434-T1
Valid prediction for Augustus_model.g16616.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_10-snap.1454-T1
Valid prediction for CodingQuarry_transcript_5458-T1
Valid prediction for snap_scaffold_10-snap.1446-T1
Valid prediction for snap_scaffold_10-snap.1443-T1
Valid prediction for HiQ_model.g16623.t1
Valid prediction for Augustus_model.g16612.t1
Valid prediction for CodingQuarry_transcript_5460-T1
Valid prediction for GlimmerHMM_glimmerT_24957-T1
Valid prediction for GlimmerHMM_glimmerT_24958-T1
Valid prediction for snap_scaffold_10-snap.1439-T1
Valid prediction for snap_scaffold_10-snap.1451-T1
Valid prediction for HiQ_model.g16618.t1
Valid prediction for pasa_asmbl_4527.p1
Valid prediction for snap_scaffold_10-snap.1436-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24959-T1
Valid prediction for Augustus_model.g16619.t1
Valid prediction for snap_scaffold_10-snap.1442-T1
Valid prediction for GlimmerHMM_glimmerT_24956-T1
Valid prediction for GlimmerHMM_glimmerT_24963-T1
Valid prediction for snap_scaffold_10-snap.1437-T1
Valid prediction for snap_scaffold_10-snap.1465-T1
Valid prediction for GlimmerHMM_glimmerT_24947-T1
Valid prediction for Augustus_model.g16621.t1
Valid prediction for Augustus_model.g16614.t1
Valid prediction for GlimmerHMM_glimmerT_24951-T1
Valid prediction for snap_scaffold_10-snap.1431-T1
Valid prediction for pasa_asmbl_4528.p1
Valid prediction for GlimmerHMM_glimmerT_24946-T1
Valid prediction for GlimmerHMM_glimmerT_24961-T1
Valid prediction for snap_scaffold_10-snap.1458-T1
Valid prediction for Augustus_model.g16613.t1
Valid prediction for snap_scaffold_10-snap.1457-T1
Valid prediction for snap_scaffold_10-snap.1435-T1
Valid prediction for snap_scaffold_10-snap.1448-T1
Valid prediction for snap_scaffold_10-snap.1461-T1
Valid prediction for CodingQuarry_transcript_5459-T1
Valid prediction for Augustus_model.g16624.t1
Valid prediction for snap_scaffold_10-snap.1462-T1
Valid prediction for snap_scaffold_10-snap.1464-T1
Valid prediction for Augustus_model.g16620.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35206, rend_intergenic: 30342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46532, rend_intergenic: 37687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60378, rend_intergenic: 56080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69773, rend_intergenic: 61092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101400, rend_intergenic: 88963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103923, rend_intergenic: 103047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106504, rend_intergenic: 104068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114698, rend_intergenic: 109213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131753, rend_intergenic: 126810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141437, rend_intergenic: 131755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162051, rend_intergenic: 158005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228716
-exon list size: 376


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 35206, rend_intergenic: 30342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46532, rend_intergenic: 37687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60378, rend_intergenic: 56080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69773, rend_intergenic: 61092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101400, rend_intergenic: 88963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103923, rend_intergenic: 103047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106504, rend_intergenic: 104068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114698, rend_intergenic: 109213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131753, rend_intergenic: 126810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141437, rend_intergenic: 131755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162051, rend_intergenic: 158005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support