-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_4498480-4700941

-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_28-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_58701-T1
Valid prediction for snap_scaffold_28-snap.1067-T1
Valid prediction for snap_scaffold_28-snap.1094-T1
Valid prediction for snap_scaffold_28-snap.1101-T1
Valid prediction for snap_scaffold_28-snap.1062-T1
Valid prediction for CodingQuarry_transcript_43637-T1
Valid prediction for snap_scaffold_28-snap.1078-T1
Valid prediction for GlimmerHMM_glimmerT_58702-T1
Couldn't classify 46917, 47055
Sorry, prediction pasa_asmbl_37537.p1 fails validation.
(CTG)	 AC	46917-47055	GT	CTG
(TCT)	 AG	47938-47999	GT	AGG
(GTA)	 AG	48145-48252	GT	TGG
(GGT)	 AG	48381-48428	GT	AGG
(ATT)	 AG	48507-48590	GA	GAG
-recovered pasa_asmbl_37537.p1, terminal, 48507, 48590
-recovered pasa_asmbl_37537.p1, internal, 47938, 47999
-recovered pasa_asmbl_37537.p1, internal, 48145, 48252
-recovered pasa_asmbl_37537.p1, internal, 48381, 48428
Valid prediction for GlimmerHMM_glimmerT_58683-T1
Valid prediction for GlimmerHMM_glimmerT_58698-T1
Valid prediction for Augustus_model.g38866.t1
Valid prediction for snap_scaffold_28-snap.1079-T1
Valid prediction for CodingQuarry_transcript_43640-T1
Valid prediction for pasa_asmbl_37540.p1
Valid prediction for GlimmerHMM_glimmerT_58694-T1
Valid prediction for Augustus_model.g38869.t1
Valid prediction for GlimmerHMM_glimmerT_58688-T1
Valid prediction for snap_scaffold_28-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_58671-T1
Valid prediction for GlimmerHMM_glimmerT_58680-T1
Valid prediction for snap_scaffold_28-snap.1063-T1
Valid prediction for snap_scaffold_28-snap.1073-T1
Valid prediction for CodingQuarry_transcript_43639-T1
Valid prediction for snap_scaffold_28-snap.1072-T1
Valid prediction for pasa_asmbl_37538.p1
Valid prediction for snap_scaffold_28-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_58700-T1
Valid prediction for Augustus_model.g38881.t1
Valid prediction for HiQ_model.g38888.t1
Valid prediction for GlimmerHMM_glimmerT_58673-T1
Valid prediction for HiQ_model.g38868.t1
Valid prediction for snap_scaffold_28-snap.1100-T1
Valid prediction for Augustus_model.g38885.t1
Valid prediction for snap_scaffold_28-snap.1058-T1
Valid prediction for snap_scaffold_28-snap.1077-T1
Valid prediction for snap_scaffold_28-snap.1087-T1
Valid prediction for HiQ_model.g38873.t1
Valid prediction for snap_scaffold_28-snap.1069-T1
Valid prediction for snap_scaffold_28-snap.1056-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_37536.p1
Valid prediction for snap_scaffold_28-snap.1095-T1
Valid prediction for snap_scaffold_28-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_58676-T1
Valid prediction for snap_scaffold_28-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_58677-T1
Valid prediction for GlimmerHMM_glimmerT_58684-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 GlimmerHMM_glimmerT_58699-T1
Valid prediction for snap_scaffold_28-snap.1071-T1
Couldn't classify 149661, 149788
Sorry, prediction pasa_asmbl_38212.p1 fails validation.
(GTG)	 AG	149661-149788	GT	AGG
(GGT)	 AG	152334-152507	GT	AGG
(GCA)	 AG	152722-152838	GT	AGG
(ACA)	 AG	153099-153264	AC	GAA
-recovered pasa_asmbl_38212.p1, terminal, 149661, 149788
-recovered pasa_asmbl_38212.p1, terminal, 153099, 153264
-recovered pasa_asmbl_38212.p1, internal, 149661, 149788
-recovered pasa_asmbl_38212.p1, internal, 152334, 152507
-recovered pasa_asmbl_38212.p1, internal, 152722, 152838
Valid prediction for GlimmerHMM_glimmerT_58687-T1
Valid prediction for Augustus_model.g38867.t1
Valid prediction for snap_scaffold_28-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_58693-T1
Valid prediction for snap_scaffold_28-snap.1068-T1
Valid prediction for CodingQuarry_transcript_43638-T1
Valid prediction for GlimmerHMM_glimmerT_58678-T1
Valid prediction for snap_scaffold_28-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_58692-T1
Couldn't classify 144545, 144739
Sorry, prediction pasa_asmbl_38214.p1 fails validation.
(ATG)	 TC	141719-141890	GT	AGG
(GAA)	 AG	141969-142204	GT	TGG
(AAT)	 AG	142520-142624	GT	AGG
(GTG)	 AG	142729-142893	GT	AAG
(AAC)	 AG	143047-143135	GT	GGG
(GTA)	 AG	143808-143965	GT	CGG
(ACT)	 AG	144191-144387	GT	CTG
(GTG)	 AG	144545-144739	AT	CCA
-recovered pasa_asmbl_38214.p1, initial, 141719, 141890
-recovered pasa_asmbl_38214.p1, internal, 141969, 142204
-recovered pasa_asmbl_38214.p1, internal, 142520, 142624
-recovered pasa_asmbl_38214.p1, internal, 142729, 142893
-recovered pasa_asmbl_38214.p1, internal, 143047, 143135
-recovered pasa_asmbl_38214.p1, internal, 143808, 143965
-recovered pasa_asmbl_38214.p1, internal, 144191, 144387
Valid prediction for Augustus_model.g38887.t1
Valid prediction for snap_scaffold_28-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_58691-T1
Valid prediction for GlimmerHMM_glimmerT_58697-T1
Valid prediction for snap_scaffold_28-snap.1061-T1
Valid prediction for Augustus_model.g38876.t1
Valid prediction for snap_scaffold_28-snap.1076-T1
Valid prediction for Augustus_model.g38875.t1
Valid prediction for GlimmerHMM_glimmerT_58679-T1
Valid prediction for GlimmerHMM_glimmerT_58682-T1
Valid prediction for Augustus_model.g38870.t1
Valid prediction for snap_scaffold_28-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_58685-T1
Valid prediction for snap_scaffold_28-snap.1091-T1
Valid prediction for snap_scaffold_28-snap.1070-T1
Valid prediction for GlimmerHMM_glimmerT_58686-T1
Valid prediction for GlimmerHMM_glimmerT_58695-T1
Valid prediction for snap_scaffold_28-snap.1086-T1
Valid prediction for Augustus_model.g38879.t1
Valid prediction for Augustus_model.g38886.t1
Valid prediction for Augustus_model.g38882.t1
Valid prediction for snap_scaffold_28-snap.1066-T1
Valid prediction for snap_scaffold_28-snap.1093-T1
Valid prediction for snap_scaffold_28-snap.1075-T1
Valid prediction for Augustus_model.g38874.t1
Valid prediction for GlimmerHMM_glimmerT_58696-T1
Valid prediction for GlimmerHMM_glimmerT_58681-T1
Valid prediction for snap_scaffold_28-snap.1060-T1
Valid prediction for HiQ_model.g38871.t1
Valid prediction for GlimmerHMM_glimmerT_58675-T1
Valid prediction for snap_scaffold_28-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_58690-T1
Valid prediction for snap_scaffold_28-snap.1088-T1
Valid prediction for snap_scaffold_28-snap.1081-T1
Valid prediction for pasa_asmbl_38215.p1
Valid prediction for snap_scaffold_28-snap.1084-T1
Valid prediction for Augustus_model.g38884.t1
Valid prediction for snap_scaffold_28-snap.1065-T1
Valid prediction for Augustus_model.g38878.t1
Valid prediction for GlimmerHMM_glimmerT_58672-T1
Valid prediction for snap_scaffold_28-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_58689-T1
Valid prediction for Augustus_model.g38880.t1
Valid prediction for snap_scaffold_28-snap.1089-T1
Valid prediction for snap_scaffold_28-snap.1098-T1
Couldn't classify 176684, 176791
Couldn't classify 179958, 179997
Sorry, prediction pasa_asmbl_38211.p1 fails validation.
(GGG)	 TG	176684-176791	GT	AGG
(TTT)	 AG	177055-177129	GT	TGG
(ATC)	 AG	177441-177554	GT	AGG
(GCG)	 AG	177809-177931	GT	TGG
(ATG)	 AG	179059-179276	GT	AGG
(GGC)	 AG	179958-179997	GC	AGG
-recovered pasa_asmbl_38211.p1, initial, 179059, 179276
-recovered pasa_asmbl_38211.p1, internal, 177055, 177129
-recovered pasa_asmbl_38211.p1, internal, 177441, 177554
-recovered pasa_asmbl_38211.p1, internal, 177809, 177931
-recovered pasa_asmbl_38211.p1, internal, 179059, 179276
-recovered pasa_asmbl_38211.p1, internal, 179958, 179997
Couldn't classify 117938, 118067
Sorry, prediction pasa_asmbl_38218.p1 fails validation.
(TTT)	 CT	117938-118067	GT	AGG
(AAC)	 AG	118805-118998	GT	TGG
(GTG)	 AG	119766-119901	GT	AGG
(TTA)	 AG	120160-120283	GT	AGG
(TCC)	 AG	120477-120587	GT	CGG
(ATT)	 AG	121052-121134	GT	TGG
(ACG)	 AG	121375-121469	GT	TGG
(GTT)	 AG	123733-123801	TG	GAT
-recovered pasa_asmbl_38218.p1, terminal, 123733, 123801
-recovered pasa_asmbl_38218.p1, internal, 118805, 118998
-recovered pasa_asmbl_38218.p1, internal, 119766, 119901
-recovered pasa_asmbl_38218.p1, internal, 120160, 120283
-recovered pasa_asmbl_38218.p1, internal, 120477, 120587
-recovered pasa_asmbl_38218.p1, internal, 121052, 121134
-recovered pasa_asmbl_38218.p1, internal, 121375, 121469
Valid prediction for GlimmerHMM_glimmerT_58674-T1
Valid prediction for Augustus_model.g38883.t1
Valid prediction for snap_scaffold_28-snap.1083-T1
Valid prediction for Augustus_model.g38872.t1
Valid prediction for snap_scaffold_28-snap.1090-T1
Valid prediction for snap_scaffold_28-snap.1074-T1
Valid prediction for Augustus_model.g38877.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 117008, rend_intergenic: 117005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7604, rend_intergenic: 2804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17909, rend_intergenic: 16879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29324, rend_intergenic: 18698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53595, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60390, rend_intergenic: 54477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87685, rend_intergenic: 81000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91827, rend_intergenic: 89660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103763, rend_intergenic: 96799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108843, rend_intergenic: 106626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116336, rend_intergenic: 112263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130884, rend_intergenic: 126693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144371, rend_intergenic: 143139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179399, rend_intergenic: 166315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202462
-exon list size: 452


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.4    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
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    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
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    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 117008, rend_intergenic: 117005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7604, rend_intergenic: 2804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17909, rend_intergenic: 16879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29324, rend_intergenic: 18698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53595, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60390, rend_intergenic: 54477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87685, rend_intergenic: 81000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91827, rend_intergenic: 89660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103763, rend_intergenic: 96799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108843, rend_intergenic: 106626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116336, rend_intergenic: 112263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130884, rend_intergenic: 126693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144371, rend_intergenic: 143139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179399, rend_intergenic: 166315  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