-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_7386152-7529012

-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 Augustus_model.g770.t1
Valid prediction for Augustus_model.g761.t1
Valid prediction for Augustus_model.g766.t1
Valid prediction for GlimmerHMM_glimmerT_1038-T1
Valid prediction for snap_scaffold_1-snap.1283-T1
Valid prediction for snap_scaffold_1-snap.1292-T1
Valid prediction for snap_scaffold_1-snap.1280-T1
Valid prediction for GlimmerHMM_glimmerT_1029-T1
Valid prediction for GlimmerHMM_glimmerT_1023-T1
Valid prediction for snap_scaffold_1-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_1021-T1
Valid prediction for GlimmerHMM_glimmerT_1033-T1
Valid prediction for snap_scaffold_1-snap.1290-T1
Valid prediction for snap_scaffold_1-snap.1302-T1
Valid prediction for Augustus_model.g763.t1
Valid prediction for snap_scaffold_1-snap.1287-T1
Valid prediction for Augustus_model.g769.t1
Valid prediction for snap_scaffold_1-snap.1282-T1
Valid prediction for snap_scaffold_1-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_1037-T1
Valid prediction for Augustus_model.g771.t1
Valid prediction for Augustus_model.g767.t1
Valid prediction for GlimmerHMM_glimmerT_1026-T1
Valid prediction for GlimmerHMM_glimmerT_1035-T1
Valid prediction for snap_scaffold_1-snap.1301-T1
Valid prediction for snap_scaffold_1-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_1032-T1
Valid prediction for GlimmerHMM_glimmerT_1039-T1
Valid prediction for GlimmerHMM_glimmerT_1034-T1
Valid prediction for snap_scaffold_1-snap.1276-T1
Valid prediction for Augustus_model.g760.t1
Valid prediction for snap_scaffold_1-snap.1288-T1
Valid prediction for snap_scaffold_1-snap.1303-T1
Valid prediction for Augustus_model.g772.t1
Valid prediction for snap_scaffold_1-snap.1289-T1
Valid prediction for snap_scaffold_1-snap.1295-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_1-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_1022-T1
Valid prediction for CodingQuarry_transcript_2692-T1
Valid prediction for snap_scaffold_1-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_1028-T1
Valid prediction for snap_scaffold_1-snap.1299-T1
Valid prediction for snap_scaffold_1-snap.1284-T1
Couldn't classify 108794, 108820
Sorry, prediction pasa_asmbl_437.p1 fails validation.
(TTG)	 AT	108794-108820	GT	AGG
(CAA)	 AG	109257-109367	GT	ACG
(GCT)	 AG	109559-109654	GT	AGG
(TCC)	 AG	109891-109971	CT	AGC
-recovered pasa_asmbl_437.p1, terminal, 109891, 109971
-recovered pasa_asmbl_437.p1, internal, 109257, 109367
-recovered pasa_asmbl_437.p1, internal, 109559, 109654
Valid prediction for GlimmerHMM_glimmerT_1025-T1
Valid prediction for snap_scaffold_1-snap.1281-T1
Valid prediction for snap_scaffold_1-snap.1277-T1
Valid prediction for Augustus_model.g765.t1
Valid prediction for snap_scaffold_1-snap.1300-T1
Valid prediction for HiQ_model.g762.t1
Valid prediction for CodingQuarry_transcript_2693-T1
Valid prediction for GlimmerHMM_glimmerT_1024-T1
Valid prediction for GlimmerHMM_glimmerT_1036-T1
Valid prediction for snap_scaffold_1-snap.1291-T1
Valid prediction for snap_scaffold_1-snap.1298-T1
Valid prediction for Augustus_model.g768.t1
Valid prediction for GlimmerHMM_glimmerT_1031-T1
Valid prediction for CodingQuarry_transcript_2694-T1
Valid prediction for snap_scaffold_1-snap.1279-T1
Valid prediction for snap_scaffold_1-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_1030-T1
Valid prediction for Augustus_model.g773.t1
Valid prediction for Augustus_model.g764.t1
Valid prediction for snap_scaffold_1-snap.1304-T1
Valid prediction for snap_scaffold_1-snap.1293-T1
Valid prediction for pasa_asmbl_438.p1
Valid prediction for snap_scaffold_1-snap.1275-T1
Valid prediction for snap_scaffold_1-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_1027-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14511, rend_intergenic: 13757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17621, rend_intergenic: 15336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23484, rend_intergenic: 21289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27307, rend_intergenic: 26283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44896, rend_intergenic: 40382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88849, rend_intergenic: 88216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96310, rend_intergenic: 91302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102672, rend_intergenic: 102221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104157, rend_intergenic: 103179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121499, rend_intergenic: 106397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139048, rend_intergenic: 134133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142861
-exon list size: 247


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.4    
6.8    
7.2    
7.6    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.1    
22.5    
22.9    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.9    
27.3    
27.7    
28.1    
28.5    
28.9    
29.3    
29.7    
30.1    
30.5    
30.9    
31.3    
31.7    
32.1    
32.5    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.8    
44.2    
44.6    
45.0    
45.4    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.6    
55.0    
55.4    
55.8    
56.2    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.5    
67.9    
68.3    
68.7    
69.1    
69.5    
69.9    
70.3    
70.7    
71.1    
71.5    
71.9    
72.3    
72.7    
73.1    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.1    
77.5    
77.9    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.4    
92.8    
93.2    
93.6    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 14511, rend_intergenic: 13757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17621, rend_intergenic: 15336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23484, rend_intergenic: 21289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27307, rend_intergenic: 26283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44896, rend_intergenic: 40382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88849, rend_intergenic: 88216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96310, rend_intergenic: 91302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102672, rend_intergenic: 102221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104157, rend_intergenic: 103179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121499, rend_intergenic: 106397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139048, rend_intergenic: 134133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 13412
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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