-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_7204241-7388453

-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_1-snap.1257-T1
Valid prediction for CodingQuarry_transcript_2681-T1
Valid prediction for pasa_asmbl_1899.p1
Valid prediction for snap_scaffold_1-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_1011-T1
Valid prediction for snap_scaffold_1-snap.1264-T1
Valid prediction for Augustus_model.g742.t1
Valid prediction for GlimmerHMM_glimmerT_1017-T1
Valid prediction for GlimmerHMM_glimmerT_995-T1
Valid prediction for Augustus_model.g756.t1
Valid prediction for snap_scaffold_1-snap.1233-T1
Valid prediction for snap_scaffold_1-snap.1234-T1
Valid prediction for GlimmerHMM_glimmerT_994-T1
Valid prediction for Augustus_model.g741.t1
Valid prediction for pasa_asmbl_1890.p1
Valid prediction for Augustus_model.g746.t1
Valid prediction for snap_scaffold_1-snap.1274-T1
Valid prediction for snap_scaffold_1-snap.1260-T1
Valid prediction for snap_scaffold_1-snap.1256-T1
Valid prediction for snap_scaffold_1-snap.1262-T1
Valid prediction for snap_scaffold_1-snap.1250-T1
Valid prediction for GlimmerHMM_glimmerT_1009-T1
Valid prediction for GlimmerHMM_glimmerT_1016-T1
Valid prediction for Augustus_model.g750.t1
Valid prediction for GlimmerHMM_glimmerT_998-T1
Valid prediction for CodingQuarry_transcript_2689-T1
Valid prediction for GlimmerHMM_glimmerT_1002-T1
Valid prediction for snap_scaffold_1-snap.1249-T1
Valid prediction for snap_scaffold_1-snap.1238-T1
Valid prediction for Augustus_model.g758.t1
Valid prediction for snap_scaffold_1-snap.1247-T1
Valid prediction for snap_scaffold_1-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_1013-T1
Valid prediction for snap_scaffold_1-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_1018-T1
Valid prediction for Augustus_model.g745.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.1272-T1
Couldn't classify 152333, 152668
Sorry, prediction pasa_asmbl_1894.p1 fails validation.
(ATG)	 CA	152333-152668	GG	CAG
Valid prediction for pasa_asmbl_421.p1
Valid prediction for pasa_asmbl_422.p1
Valid prediction for GlimmerHMM_glimmerT_1003-T1
Valid prediction for GlimmerHMM_glimmerT_997-T1
Valid prediction for GlimmerHMM_glimmerT_1000-T1
Valid prediction for snap_scaffold_1-snap.1265-T1
Valid prediction for HiQ_model.g759.t1
Valid prediction for GlimmerHMM_glimmerT_1007-T1
Couldn't classify 126866, 126973
Sorry, prediction pasa_asmbl_414.p1 fails validation.
(GAC)	 TG	126866-126973	GT	AGG
(GGA)	 AG	127413-127482	GT	AGG
(AGT)	 AG	127621-127695	GT	CGG
(TTT)	 AG	127914-128048	GT	GGG
(GTG)	 AG	128411-128531	GT	GAG
(CAA)	 AG	128642-128710	GT	AGG
(GGT)	 AG	128837-128943	GT	GGG
(GCT)	 AG	129104-129231	GT	TGG
(TTC)	 AG	129740-129922	GT	AAG
(TCT)	 AG	130233-130453	GT	AGG
(GGA)	 AG	130551-130616	GT	AAG
(TGA)	 AG	130763-130826	GT	AGG
(CAT)	 AG	130949-131020	GT	GGG
(GGG)	 AG	131134-131208	GT	TGG
(ATT)	 AG	131348-131445	GT	CCG
(GAC)	 AG	131564-131690	GT	AGG
(TTC)	 AG	131803-131903	GT	AGG
(CAT)	 AG	132045-132111	GT	TGG
(GAA)	 AG	132556-132660	GT	TGG
(ATG)	 AG	132864-133068	GT	CGG
(ACC)	 AG	133225-133472	GA	GAG
-recovered pasa_asmbl_414.p1, initial, 132864, 133068
-recovered pasa_asmbl_414.p1, terminal, 133225, 133472
-recovered pasa_asmbl_414.p1, internal, 127413, 127482
-recovered pasa_asmbl_414.p1, internal, 127621, 127695
-recovered pasa_asmbl_414.p1, internal, 127914, 128048
-recovered pasa_asmbl_414.p1, internal, 128411, 128531
-recovered pasa_asmbl_414.p1, internal, 128642, 128710
-recovered pasa_asmbl_414.p1, internal, 128837, 128943
-recovered pasa_asmbl_414.p1, internal, 129104, 129231
-recovered pasa_asmbl_414.p1, internal, 129740, 129922
-recovered pasa_asmbl_414.p1, internal, 130233, 130453
-recovered pasa_asmbl_414.p1, internal, 130551, 130616
-recovered pasa_asmbl_414.p1, internal, 130763, 130826
-recovered pasa_asmbl_414.p1, internal, 130949, 131020
-recovered pasa_asmbl_414.p1, internal, 131134, 131208
-recovered pasa_asmbl_414.p1, internal, 131348, 131445
-recovered pasa_asmbl_414.p1, internal, 131564, 131690
-recovered pasa_asmbl_414.p1, internal, 131803, 131903
-recovered pasa_asmbl_414.p1, internal, 132045, 132111
-recovered pasa_asmbl_414.p1, internal, 132556, 132660
-recovered pasa_asmbl_414.p1, internal, 132864, 133068
Valid prediction for pasa_asmbl_426.p1
Valid prediction for snap_scaffold_1-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_1019-T1
Valid prediction for snap_scaffold_1-snap.1261-T1
Valid prediction for CodingQuarry_transcript_2687-T1
Valid prediction for snap_scaffold_1-snap.1236-T1
Valid prediction for snap_scaffold_1-snap.1237-T1
Valid prediction for snap_scaffold_1-snap.1246-T1
Valid prediction for HiQ_model.g753.t1
Valid prediction for snap_scaffold_1-snap.1255-T1
Valid prediction for snap_scaffold_1-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_996-T1
Valid prediction for CodingQuarry_transcript_2690-T1
Valid prediction for CodingQuarry_transcript_2684-T1
Valid prediction for Augustus_model.g744.t1
Valid prediction for GlimmerHMM_glimmerT_1014-T1
Valid prediction for GlimmerHMM_glimmerT_1020-T1
Valid prediction for HiQ_model.g755.t1
Valid prediction for snap_scaffold_1-snap.1253-T1
Valid prediction for CodingQuarry_transcript_2688-T1
Valid prediction for snap_scaffold_1-snap.1263-T1
Valid prediction for pasa_asmbl_424.p1
Valid prediction for CodingQuarry_transcript_2691-T1
Valid prediction for snap_scaffold_1-snap.1269-T1
Valid prediction for snap_scaffold_1-snap.1251-T1
Valid prediction for Augustus_model.g743.t1
Valid prediction for HiQ_model.g754.t1
Valid prediction for snap_scaffold_1-snap.1258-T1
Valid prediction for Augustus_model.g747.t1
Valid prediction for GlimmerHMM_glimmerT_1004-T1
Valid prediction for snap_scaffold_1-snap.1271-T1
Valid prediction for CodingQuarry_transcript_2685-T1
Valid prediction for GlimmerHMM_glimmerT_999-T1
Valid prediction for CodingQuarry_transcript_2683-T1
Valid prediction for snap_scaffold_1-snap.1248-T1
Valid prediction for HiQ_model.g752.t1
Valid prediction for CodingQuarry_transcript_2686-T1
Valid prediction for GlimmerHMM_glimmerT_1001-T1
Valid prediction for snap_scaffold_1-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_1015-T1
Valid prediction for snap_scaffold_1-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_1008-T1
Valid prediction for snap_scaffold_1-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_1010-T1
Valid prediction for Augustus_model.g748.t1
Valid prediction for snap_scaffold_1-snap.1273-T1
Valid prediction for Augustus_model.g749.t1
Couldn't classify 8507, 8720
Sorry, prediction pasa_asmbl_432.p1 fails validation.
(AAG)	 AG	8507-8720	GT	AGG
(GTG)	 AG	8846-8980	GT	CGG
(GTA)	 AG	9945-10179	GT	GAG
(GCG)	 AG	10383-10515	GT	AGG
(GTG)	 AG	11422-11556	GT	AGG
(GTG)	 AG	11714-11817	GT	AGG
(GGA)	 AG	11923-12047	GT	AGG
(GCC)	 AG	14057-14169	GT	AGG
(TTT)	 AG	14304-14441	GT	AGG
(GGT)	 AG	14590-14692	GT	TGG
(GCG)	 AG	14842-14942	GT	TGG
(GGC)	 AG	15362-15532	GT	AGG
(CGT)	 AG	15763-15921	TA	AGT
-recovered pasa_asmbl_432.p1, terminal, 15763, 15921
-recovered pasa_asmbl_432.p1, internal, 8507, 8720
-recovered pasa_asmbl_432.p1, internal, 8846, 8980
-recovered pasa_asmbl_432.p1, internal, 9945, 10179
-recovered pasa_asmbl_432.p1, internal, 10383, 10515
-recovered pasa_asmbl_432.p1, internal, 11422, 11556
-recovered pasa_asmbl_432.p1, internal, 11714, 11817
-recovered pasa_asmbl_432.p1, internal, 11923, 12047
-recovered pasa_asmbl_432.p1, internal, 14057, 14169
-recovered pasa_asmbl_432.p1, internal, 14304, 14441
-recovered pasa_asmbl_432.p1, internal, 14590, 14692
-recovered pasa_asmbl_432.p1, internal, 14842, 14942
-recovered pasa_asmbl_432.p1, internal, 15362, 15532
Valid prediction for snap_scaffold_1-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_1005-T1
Valid prediction for GlimmerHMM_glimmerT_1012-T1
Valid prediction for snap_scaffold_1-snap.1270-T1
Valid prediction for snap_scaffold_1-snap.1267-T1
Valid prediction for HiQ_model.g751.t1
Valid prediction for snap_scaffold_1-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_1006-T1
Valid prediction for snap_scaffold_1-snap.1268-T1
Valid prediction for snap_scaffold_1-snap.1259-T1
Valid prediction for Augustus_model.g757.t1
Valid prediction for snap_scaffold_1-snap.1266-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13991, rend_intergenic: 10329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18547, rend_intergenic: 16801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24587, rend_intergenic: 19780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30152, rend_intergenic: 26553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57351, rend_intergenic: 51392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72417, rend_intergenic: 64057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74579, rend_intergenic: 73551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93818, rend_intergenic: 89213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98335, rend_intergenic: 95497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111685, rend_intergenic: 100548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116106, rend_intergenic: 114224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119223, rend_intergenic: 118516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125338, rend_intergenic: 119232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163144, rend_intergenic: 127463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181330, rend_intergenic: 176991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184213
-exon list size: 449


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 13991, rend_intergenic: 10329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18547, rend_intergenic: 16801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24587, rend_intergenic: 19780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30152, rend_intergenic: 26553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57351, rend_intergenic: 51392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72417, rend_intergenic: 64057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74579, rend_intergenic: 73551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93818, rend_intergenic: 89213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98335, rend_intergenic: 95497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111685, rend_intergenic: 100548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116106, rend_intergenic: 114224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119223, rend_intergenic: 118516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125338, rend_intergenic: 119232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163144, rend_intergenic: 127463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181330, rend_intergenic: 176991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support