-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_6111256-6322307

-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_17504-T1
Valid prediction for Augustus_model.g11725.t1
Valid prediction for snap_scaffold_7-snap.1265-T1
Valid prediction for Augustus_model.g11723.t1
Valid prediction for snap_scaffold_7-snap.1279-T1
Valid prediction for snap_scaffold_7-snap.1297-T1
Valid prediction for Augustus_model.g11719.t1
Valid prediction for GlimmerHMM_glimmerT_17522-T1
Valid prediction for GlimmerHMM_glimmerT_17493-T1
Valid prediction for GlimmerHMM_glimmerT_17495-T1
Valid prediction for GlimmerHMM_glimmerT_17511-T1
Valid prediction for Augustus_model.g11717.t1
Valid prediction for snap_scaffold_7-snap.1274-T1
Valid prediction for Augustus_model.g11721.t1
Valid prediction for snap_scaffold_7-snap.1280-T1
Valid prediction for snap_scaffold_7-snap.1277-T1
Valid prediction for snap_scaffold_7-snap.1294-T1
Valid prediction for snap_scaffold_7-snap.1284-T1
Valid prediction for snap_scaffold_7-snap.1273-T1
Valid prediction for snap_scaffold_7-snap.1271-T1
Valid prediction for Augustus_model.g11722.t1
Couldn't classify 85896, 85984
Couldn't classify 89211, 89277
Sorry, prediction pasa_asmbl_49849.p1 fails validation.
(ATT)	 AT	85896-85984	GT	AAG
(TAT)	 AG	86129-86234	GT	AGG
(ATT)	 AG	86438-86520	GT	AGG
(GGT)	 AG	86689-86758	GT	AGG
(GCT)	 AG	86938-87093	GT	AGG
(ATC)	 AG	88861-88970	GT	GAG
(GCT)	 AG	89211-89277	AG	GCA
-recovered pasa_asmbl_49849.p1, internal, 86129, 86234
-recovered pasa_asmbl_49849.p1, internal, 86438, 86520
-recovered pasa_asmbl_49849.p1, internal, 86689, 86758
-recovered pasa_asmbl_49849.p1, internal, 86938, 87093
-recovered pasa_asmbl_49849.p1, internal, 88861, 88970
Valid prediction for snap_scaffold_7-snap.1283-T1
Valid prediction for snap_scaffold_7-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_17519-T1
Valid prediction for GlimmerHMM_glimmerT_17507-T1
Couldn't classify 78225, 78479
Sorry, prediction pasa_asmbl_49845.p2 fails validation.
(ATG)	 TT	76715-76810	GT	TGG
(GTG)	 AG	78225-78479	GA	TAG
-recovered pasa_asmbl_49845.p2, initial, 76715, 76810
Valid prediction for GlimmerHMM_glimmerT_17501-T1
Couldn't classify 118595, 118726
Sorry, prediction pasa_asmbl_49857.p1 fails validation.
(GTG)	 CA	118595-118726	GT	CGG
(ACA)	 AG	120237-120431	GT	GGG
(GAT)	 AG	120859-120977	GT	CGG
(GTA)	 AG	121292-121514	GT	AGG
-recovered pasa_asmbl_49857.p1, terminal, 121292, 121514
-recovered pasa_asmbl_49857.p1, internal, 120237, 120431
-recovered pasa_asmbl_49857.p1, internal, 120859, 120977
-recovered pasa_asmbl_49857.p1, internal, 121292, 121514
Valid prediction for snap_scaffold_7-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_17499-T1
Valid prediction for HiQ_model.g11724.t1
Valid prediction for CodingQuarry_transcript_57530-T1
Valid prediction for Augustus_model.g11714.t1
Valid prediction for Augustus_model.g11720.t1
Valid prediction for snap_scaffold_7-snap.1269-T1
Valid prediction for GlimmerHMM_glimmerT_17500-T1
Valid prediction for Augustus_model.g11712.t1
Valid prediction for snap_scaffold_7-snap.1263-T1
Valid prediction for snap_scaffold_7-snap.1278-T1
Valid prediction for snap_scaffold_7-snap.1268-T1
Valid prediction for GlimmerHMM_glimmerT_17494-T1
Valid prediction for GlimmerHMM_glimmerT_17516-T1
Valid prediction for snap_scaffold_7-snap.1264-T1
Valid prediction for snap_scaffold_7-snap.1261-T1
Valid prediction for Augustus_model.g11715.t1
Valid prediction for GlimmerHMM_glimmerT_17509-T1
Valid prediction for Augustus_model.g11718.t1
Valid prediction for Augustus_model.g11726.t1
Valid prediction for GlimmerHMM_glimmerT_17497-T1
Valid prediction for snap_scaffold_7-snap.1292-T1
Couldn't classify 112579, 112749
Sorry, prediction pasa_asmbl_49855.p1 fails validation.
(ATG)	 AC	110813-110893	GT	TGG
(ACC)	 AG	111580-111804	GT	CTG
(GGT)	 AG	112579-112749	GT	GGG
-recovered pasa_asmbl_49855.p1, initial, 110813, 110893
-recovered pasa_asmbl_49855.p1, internal, 111580, 111804
-recovered pasa_asmbl_49855.p1, internal, 112579, 112749

-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 GlimmerHMM_glimmerT_17506-T1
Valid prediction for Augustus_model.g11728.t1
Valid prediction for snap_scaffold_7-snap.1291-T1
Valid prediction for GlimmerHMM_glimmerT_17498-T1
Valid prediction for snap_scaffold_7-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_17512-T1
Valid prediction for GlimmerHMM_glimmerT_17502-T1
Valid prediction for GlimmerHMM_glimmerT_17514-T1
Valid prediction for snap_scaffold_7-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_17503-T1
Valid prediction for GlimmerHMM_glimmerT_17517-T1
Valid prediction for GlimmerHMM_glimmerT_17520-T1
Valid prediction for Augustus_model.g11713.t1
Valid prediction for snap_scaffold_7-snap.1290-T1
Valid prediction for snap_scaffold_7-snap.1272-T1
Valid prediction for Augustus_model.g11731.t1
Valid prediction for snap_scaffold_7-snap.1281-T1
Valid prediction for snap_scaffold_7-snap.1262-T1
Valid prediction for GlimmerHMM_glimmerT_17496-T1
Valid prediction for snap_scaffold_7-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_17513-T1
Valid prediction for Augustus_model.g11727.t1
Valid prediction for snap_scaffold_7-snap.1275-T1
Valid prediction for snap_scaffold_7-snap.1299-T1
Valid prediction for snap_scaffold_7-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_17523-T1
Valid prediction for GlimmerHMM_glimmerT_17508-T1
Valid prediction for Augustus_model.g11730.t1
Valid prediction for snap_scaffold_7-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_17510-T1
Valid prediction for snap_scaffold_7-snap.1295-T1
Valid prediction for snap_scaffold_7-snap.1267-T1
Valid prediction for Augustus_model.g11729.t1
Valid prediction for snap_scaffold_7-snap.1282-T1
Valid prediction for GlimmerHMM_glimmerT_17521-T1
Valid prediction for snap_scaffold_7-snap.1298-T1
Valid prediction for snap_scaffold_7-snap.1285-T1
Valid prediction for snap_scaffold_7-snap.1266-T1
Valid prediction for Augustus_model.g11716.t1
Valid prediction for snap_scaffold_7-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_17518-T1
Valid prediction for GlimmerHMM_glimmerT_17505-T1
Valid prediction for GlimmerHMM_glimmerT_17515-T1
Valid prediction for snap_scaffold_7-snap.1270-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 158744, rend_intergenic: 158741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37513, rend_intergenic: 32929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41899, rend_intergenic: 38727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53483, rend_intergenic: 50503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67042, rend_intergenic: 64267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82813, rend_intergenic: 71596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183045, rend_intergenic: 177200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211052
-exon list size: 322


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 158744, rend_intergenic: 158741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37513, rend_intergenic: 32929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41899, rend_intergenic: 38727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53483, rend_intergenic: 50503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67042, rend_intergenic: 64267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82813, rend_intergenic: 71596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183045, rend_intergenic: 177200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support