-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_6483928-6832608

-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_7-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_17564-T1
Valid prediction for snap_scaffold_7-snap.1340-T1
Valid prediction for pasa_asmbl_49871.p1
Valid prediction for snap_scaffold_7-snap.1374-T1
Valid prediction for HiQ_model.g11755.t1
Valid prediction for snap_scaffold_7-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_17556-T1
Valid prediction for snap_scaffold_7-snap.1380-T1
Valid prediction for Augustus_model.g11756.t1
Valid prediction for GlimmerHMM_glimmerT_17577-T1
Valid prediction for snap_scaffold_7-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_17559-T1
Valid prediction for GlimmerHMM_glimmerT_17571-T1
Valid prediction for snap_scaffold_7-snap.1390-T1
Valid prediction for snap_scaffold_7-snap.1377-T1
Couldn't classify 139469, 139602
Sorry, prediction pasa_asmbl_49868.p1 fails validation.
(CTC)	 CC	139469-139602	GT	GGG
(GTA)	 AG	141902-142031	GT	AGG
(GCC)	 AG	142526-142627	GT	AGG
(ATT)	 AG	142811-143008	GT	GGG
(GAG)	 AG	143130-143318	GT	TGG
(TTC)	 AG	144736-144747	CG	GAC
-recovered pasa_asmbl_49868.p1, terminal, 144736, 144747
-recovered pasa_asmbl_49868.p1, internal, 141902, 142031
-recovered pasa_asmbl_49868.p1, internal, 142526, 142627
-recovered pasa_asmbl_49868.p1, internal, 142811, 143008
-recovered pasa_asmbl_49868.p1, internal, 143130, 143318
Valid prediction for snap_scaffold_7-snap.1357-T1
Valid prediction for snap_scaffold_7-snap.1388-T1
Valid prediction for Augustus_model.g11754.t1
Valid prediction for snap_scaffold_7-snap.1351-T1
Valid prediction for GlimmerHMM_glimmerT_17550-T1
Valid prediction for snap_scaffold_7-snap.1384-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.1386-T1
Valid prediction for snap_scaffold_7-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_17572-T1
Valid prediction for snap_scaffold_7-snap.1379-T1
Valid prediction for Augustus_model.g11762.t1
Valid prediction for Augustus_model.g11765.t1
Valid prediction for snap_scaffold_7-snap.1339-T1
Valid prediction for snap_scaffold_7-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_17563-T1
Valid prediction for GlimmerHMM_glimmerT_17551-T1
Valid prediction for snap_scaffold_7-snap.1358-T1
Valid prediction for snap_scaffold_7-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_17569-T1
Valid prediction for snap_scaffold_7-snap.1359-T1
Valid prediction for snap_scaffold_7-snap.1382-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.1348-T1
Valid prediction for snap_scaffold_7-snap.1352-T1
Valid prediction for snap_scaffold_7-snap.1342-T1
Valid prediction for snap_scaffold_7-snap.1391-T1
Valid prediction for Augustus_model.g11766.t1
Valid prediction for CodingQuarry_transcript_57532-T1
Valid prediction for snap_scaffold_7-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_17566-T1
Valid prediction for HiQ_model.g11751.t1
Valid prediction for snap_scaffold_7-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_17580-T1
Valid prediction for snap_scaffold_7-snap.1346-T1
Valid prediction for snap_scaffold_7-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_17573-T1
Valid prediction for snap_scaffold_7-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_17562-T1
Valid prediction for snap_scaffold_7-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_17578-T1
Valid prediction for snap_scaffold_7-snap.1354-T1
Valid prediction for Augustus_model.g11761.t1
Valid prediction for GlimmerHMM_glimmerT_17555-T1
Valid prediction for snap_scaffold_7-snap.1365-T1
Valid prediction for Augustus_model.g11750.t1
Valid prediction for snap_scaffold_7-snap.1378-T1
Valid prediction for Augustus_model.g11773.t1
Valid prediction for GlimmerHMM_glimmerT_17575-T1
Valid prediction for HiQ_model.g11760.t1
Couldn't classify 254116, 254901
Sorry, prediction pasa_asmbl_50919.p1 fails validation.
(GAC)	 AG	254116-254901	GC	CCG
-recovered pasa_asmbl_50919.p1, internal, 254116, 254901
Valid prediction for snap_scaffold_7-snap.1355-T1
Valid prediction for snap_scaffold_7-snap.1375-T1
Valid prediction for Augustus_model.g11752.t1
Valid prediction for snap_scaffold_7-snap.1347-T1
Valid prediction for Augustus_model.g11747.t1
Valid prediction for Augustus_model.g11774.t1
Valid prediction for CodingQuarry_transcript_57535-T1
Valid prediction for pasa_asmbl_50916.p1
Valid prediction for GlimmerHMM_glimmerT_17581-T1
Valid prediction for GlimmerHMM_glimmerT_17554-T1
Valid prediction for Augustus_model.g11757.t1
Valid prediction for Augustus_model.g11744.t1
Valid prediction for snap_scaffold_7-snap.1385-T1
Valid prediction for snap_scaffold_7-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_17576-T1
Couldn't classify 255124, 255308
Sorry, prediction pasa_asmbl_50918.p1 fails validation.
(GCC)	 AG	255124-255308	GT	TGG
(GAT)	 AG	255448-255574	GT	TTG
(CTT)	 AG	256128-256184	GT	TTG
(GGT)	 AG	256420-256536	GT	AGG
(GCA)	 AG	256773-256850	CT	GAC
-recovered pasa_asmbl_50918.p1, terminal, 256773, 256850
-recovered pasa_asmbl_50918.p1, internal, 255124, 255308
-recovered pasa_asmbl_50918.p1, internal, 255448, 255574
-recovered pasa_asmbl_50918.p1, internal, 256128, 256184
-recovered pasa_asmbl_50918.p1, internal, 256420, 256536
Valid prediction for GlimmerHMM_glimmerT_17579-T1
Valid prediction for Augustus_model.g11742.t1
Couldn't classify 253405, 253764
Sorry, prediction pasa_asmbl_50920.p1 fails validation.
(ATG)	 CC	253405-253764	AA	AGA
Valid prediction for snap_scaffold_7-snap.1371-T1
Valid prediction for Augustus_model.g11748.t1
Valid prediction for GlimmerHMM_glimmerT_17568-T1
Valid prediction for Augustus_model.g11758.t1
Valid prediction for pasa_asmbl_50930.p1
Couldn't classify 187968, 188153
Couldn't classify 190620, 190754
Sorry, prediction pasa_asmbl_50925.p2 fails validation.
(ATC)	 AG	187968-188153	GT	AGG
(CAC)	 AG	190620-190754	TA	GGT
-recovered pasa_asmbl_50925.p2, internal, 187968, 188153
Valid prediction for GlimmerHMM_glimmerT_17561-T1
Valid prediction for Augustus_model.g11763.t1
Valid prediction for snap_scaffold_7-snap.1367-T1
Couldn't classify 196409, 196651
Sorry, prediction pasa_asmbl_50923.p1 fails validation.
(ACG)	 AG	196409-196651	GT	AGG
(GTC)	 AG	197892-197996	GT	AGG
(GGA)	 AG	198170-198277	GC	GAG
-recovered pasa_asmbl_50923.p1, terminal, 198170, 198277
-recovered pasa_asmbl_50923.p1, internal, 196409, 196651
-recovered pasa_asmbl_50923.p1, internal, 197892, 197996
-recovered pasa_asmbl_50923.p1, internal, 198170, 198277
Valid prediction for snap_scaffold_7-snap.1343-T1
Valid prediction for snap_scaffold_7-snap.1362-T1
Valid prediction for snap_scaffold_7-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_17558-T1
Valid prediction for snap_scaffold_7-snap.1364-T1
Valid prediction for Augustus_model.g11767.t1
Valid prediction for GlimmerHMM_glimmerT_17582-T1
Valid prediction for GlimmerHMM_glimmerT_17565-T1
Valid prediction for Augustus_model.g11764.t1
Valid prediction for Augustus_model.g11759.t1
Valid prediction for GlimmerHMM_glimmerT_17570-T1
Valid prediction for Augustus_model.g11769.t1
Valid prediction for GlimmerHMM_glimmerT_17552-T1
Valid prediction for snap_scaffold_7-snap.1381-T1
Valid prediction for snap_scaffold_7-snap.1368-T1
Valid prediction for snap_scaffold_7-snap.1353-T1
Valid prediction for Augustus_model.g11743.t1
Valid prediction for GlimmerHMM_glimmerT_17553-T1
Valid prediction for Augustus_model.g11771.t1
Valid prediction for Augustus_model.g11772.t1
Valid prediction for CodingQuarry_transcript_57533-T1
Valid prediction for GlimmerHMM_glimmerT_17560-T1
Valid prediction for Augustus_model.g11745.t1
Valid prediction for Augustus_model.g11746.t1
Valid prediction for snap_scaffold_7-snap.1376-T1
Valid prediction for snap_scaffold_7-snap.1389-T1
Valid prediction for snap_scaffold_7-snap.1349-T1
Valid prediction for snap_scaffold_7-snap.1360-T1
Valid prediction for Augustus_model.g11768.t1
Valid prediction for GlimmerHMM_glimmerT_17574-T1
Valid prediction for Augustus_model.g11753.t1
Valid prediction for CodingQuarry_transcript_57537-T1
Valid prediction for Augustus_model.g11770.t1
Valid prediction for snap_scaffold_7-snap.1373-T1
Valid prediction for GlimmerHMM_glimmerT_17567-T1
Valid prediction for snap_scaffold_7-snap.1372-T1
Valid prediction for Augustus_model.g11749.t1
Valid prediction for GlimmerHMM_glimmerT_17557-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 144900, rend_intergenic: 138634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147056, rend_intergenic: 145015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211766, rend_intergenic: 183593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222336, rend_intergenic: 215686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241675, rend_intergenic: 239757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259215, rend_intergenic: 242164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283037, rend_intergenic: 264385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293339, rend_intergenic: 284438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 313461, rend_intergenic: 297492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 325130, rend_intergenic: 315478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 327921, rend_intergenic: 325181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 348681
-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 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 144900, rend_intergenic: 138634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147056, rend_intergenic: 145015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211766, rend_intergenic: 183593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222336, rend_intergenic: 215686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241675, rend_intergenic: 239757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259215, rend_intergenic: 242164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283037, rend_intergenic: 264385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293339, rend_intergenic: 284438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 313461, rend_intergenic: 297492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 325130, rend_intergenic: 315478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 327921, rend_intergenic: 325181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10929
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 330998 - 348681
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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