-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_4940114-5168206

-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.1161-T1
Valid prediction for snap_scaffold_28-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_58765-T1
Valid prediction for GlimmerHMM_glimmerT_58761-T1
Valid prediction for snap_scaffold_28-snap.1180-T1
Valid prediction for snap_scaffold_28-snap.1182-T1
Couldn't classify 116494, 116565
Couldn't classify 122699, 122709
Sorry, prediction pasa_asmbl_37570.p1 fails validation.
(GGT)	 TA	116494-116565	GT	AGG
(CCA)	 AG	116693-116817	GT	ACG
(CTT)	 AG	116901-116982	GT	CTG
(GAC)	 AG	118083-118166	GT	AGG
(AGC)	 AG	118428-118517	GT	AGG
(GAA)	 AG	118680-118799	GT	GGG
(GCC)	 AG	120621-120713	GT	AGG
(GTT)	 AG	122373-122529	GC	AGG
(AGT)	 AG	122699-122709	CA	CTC
-recovered pasa_asmbl_37570.p1, internal, 116693, 116817
-recovered pasa_asmbl_37570.p1, internal, 116901, 116982
-recovered pasa_asmbl_37570.p1, internal, 118083, 118166
-recovered pasa_asmbl_37570.p1, internal, 118428, 118517
-recovered pasa_asmbl_37570.p1, internal, 118680, 118799
-recovered pasa_asmbl_37570.p1, internal, 120621, 120713
-recovered pasa_asmbl_37570.p1, internal, 122373, 122529
Valid prediction for HiQ_model.g38923.t1
Valid prediction for pasa_asmbl_37555.p1
Valid prediction for CodingQuarry_transcript_43648-T1
Valid prediction for pasa_asmbl_37554.p1
Valid prediction for snap_scaffold_28-snap.1174-T1
Valid prediction for Augustus_model.g38920.t1
Valid prediction for pasa_asmbl_37564.p1
Valid prediction for GlimmerHMM_glimmerT_58764-T1
Valid prediction for GlimmerHMM_glimmerT_58746-T1
Valid prediction for GlimmerHMM_glimmerT_58752-T1
Valid prediction for CodingQuarry_transcript_43652-T1
Couldn't classify 106019, 106142
Couldn't classify 106927, 107043
Sorry, prediction pasa_asmbl_37835.p2 fails validation.
(GAG)	 CG	106019-106142	GT	AGG
(GTG)	 AG	106584-106684	GT	AGG
(GGT)	 AG	106927-107043	CA	GCC
-recovered pasa_asmbl_37835.p2, internal, 106584, 106684
Valid prediction for snap_scaffold_28-snap.1193-T1
Couldn't classify 122940, 123065
Sorry, prediction pasa_asmbl_37571.p1 fails validation.
(ACG)	 TG	122940-123065	GT	AGG
(TTC)	 AG	123187-123338	GT	AGG
(GCT)	 AG	123426-123533	GT	AGG
(CAT)	 AG	123635-123762	GT	AGG
(ATC)	 AG	123878-124036	GT	AGG
(GTT)	 AG	124184-124263	GT	TGG
(GCC)	 AG	126616-126815	GT	CGG
(GTT)	 AG	127340-127430	GT	AGG
(TTC)	 AG	128201-128368	GT	CGG
(GAT)	 AG	128459-128512	GT	AGG
(ATG)	 AG	128686-128806	GT	CCG
(CTG)	 AG	128934-129063	GT	AAG
(ACC)	 AG	130500-130643	GT	AGG
(TGC)	 AG	130746-130816	GT	AGG
(GTC)	 AG	131010-131116	GT	AGG
(GAC)	 AG	131272-131376	GT	GGG
(TGT)	 AG	131547-131672	GT	AGG
(GCG)	 AG	131909-132029	GT	TGG
(ACT)	 AG	132156-132315	GT	AGG
(GCC)	 AG	132401-132490	GT	AAG
(GCA)	 AG	132614-132697	GT	AGG
(GAG)	 AG	132807-132858	TG	GAT
-recovered pasa_asmbl_37571.p1, initial, 128686, 128806
add_exon() Sorry, pasa_asmbl_37571.p1 123426-123533-terminal-1 is invalid.
-recovered pasa_asmbl_37571.p1, terminal, 123426, 123533
-recovered pasa_asmbl_37571.p1, terminal, 132807, 132858
-recovered pasa_asmbl_37571.p1, internal, 123187, 123338
-recovered pasa_asmbl_37571.p1, internal, 123426, 123533
-recovered pasa_asmbl_37571.p1, internal, 123635, 123762
-recovered pasa_asmbl_37571.p1, internal, 123878, 124036
-recovered pasa_asmbl_37571.p1, internal, 124184, 124263
-recovered pasa_asmbl_37571.p1, internal, 126616, 126815
-recovered pasa_asmbl_37571.p1, internal, 127340, 127430
-recovered pasa_asmbl_37571.p1, internal, 128201, 128368
-recovered pasa_asmbl_37571.p1, internal, 128459, 128512
-recovered pasa_asmbl_37571.p1, internal, 128686, 128806
-recovered pasa_asmbl_37571.p1, internal, 128934, 129063
-recovered pasa_asmbl_37571.p1, internal, 130500, 130643
-recovered pasa_asmbl_37571.p1, internal, 130746, 130816
-recovered pasa_asmbl_37571.p1, internal, 131010, 131116
-recovered pasa_asmbl_37571.p1, internal, 131272, 131376
-recovered pasa_asmbl_37571.p1, internal, 131547, 131672
-recovered pasa_asmbl_37571.p1, internal, 131909, 132029
-recovered pasa_asmbl_37571.p1, internal, 132156, 132315
-recovered pasa_asmbl_37571.p1, internal, 132401, 132490
-recovered pasa_asmbl_37571.p1, internal, 132614, 132697
Valid prediction for GlimmerHMM_glimmerT_58740-T1
Valid prediction for CodingQuarry_transcript_43650-T1
Valid prediction for snap_scaffold_28-snap.1154-T1
Valid prediction for snap_scaffold_28-snap.1189-T1
Valid prediction for Augustus_model.g38929.t1
Valid prediction for snap_scaffold_28-snap.1163-T1
Valid prediction for snap_scaffold_28-snap.1162-T1
Valid prediction for HiQ_model.g38934.t1
Valid prediction for GlimmerHMM_glimmerT_58755-T1
Valid prediction for GlimmerHMM_glimmerT_58750-T1
Valid prediction for snap_scaffold_28-snap.1190-T1
Valid prediction for HiQ_model.g38922.t1
Valid prediction for Augustus_model.g38936.t1
Valid prediction for CodingQuarry_transcript_43649-T1
Valid prediction for HiQ_model.g38924.t1
Valid prediction for GlimmerHMM_glimmerT_58744-T1
Valid prediction for snap_scaffold_28-snap.1192-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_37573.p1
Valid prediction for GlimmerHMM_glimmerT_58745-T1
Valid prediction for CodingQuarry_transcript_43647-T1
Valid prediction for GlimmerHMM_glimmerT_58747-T1
Valid prediction for GlimmerHMM_glimmerT_58749-T1
Valid prediction for CodingQuarry_transcript_43651-T1
Valid prediction for GlimmerHMM_glimmerT_58757-T1
Valid prediction for snap_scaffold_28-snap.1188-T1
Valid prediction for snap_scaffold_28-snap.1191-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58766-T1
Valid prediction for snap_scaffold_28-snap.1149-T1
Valid prediction for Augustus_model.g38933.t1
Valid prediction for CodingQuarry_transcript_43654-T1
Valid prediction for GlimmerHMM_glimmerT_58759-T1
Valid prediction for snap_scaffold_28-snap.1164-T1
Valid prediction for Augustus_model.g38927.t1
Valid prediction for snap_scaffold_28-snap.1179-T1
Valid prediction for snap_scaffold_28-snap.1170-T1
Valid prediction for HiQ_model.g38930.t1
Valid prediction for snap_scaffold_28-snap.1152-T1
Valid prediction for snap_scaffold_28-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_58741-T1
Valid prediction for snap_scaffold_28-snap.1171-T1
Valid prediction for snap_scaffold_28-snap.1150-T1
Valid prediction for snap_scaffold_28-snap.1184-T1
Valid prediction for Augustus_model.g38935.t1
Valid prediction for GlimmerHMM_glimmerT_58769-T1
Valid prediction for GlimmerHMM_glimmerT_58751-T1
Valid prediction for GlimmerHMM_glimmerT_58768-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1167-T1
Valid prediction for snap_scaffold_28-snap.1155-T1
Valid prediction for snap_scaffold_28-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_58758-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_58748-T1
Valid prediction for snap_scaffold_28-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_58763-T1
Valid prediction for Augustus_model.g38921.t1
Valid prediction for GlimmerHMM_glimmerT_58739-T1
Valid prediction for snap_scaffold_28-snap.1151-T1
Valid prediction for Augustus_model.g38925.t1
Valid prediction for snap_scaffold_28-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_58743-T1
Valid prediction for snap_scaffold_28-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_58760-T1
Valid prediction for CodingQuarry_transcript_43653-T1
Valid prediction for Augustus_model.g38932.t1
Valid prediction for snap_scaffold_28-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_58756-T1
Valid prediction for GlimmerHMM_glimmerT_58762-T1
Valid prediction for snap_scaffold_28-snap.1157-T1
Valid prediction for HiQ_model.g38928.t1
Valid prediction for GlimmerHMM_glimmerT_58767-T1
Valid prediction for Augustus_model.g38919.t1
Valid prediction for snap_scaffold_28-snap.1181-T1
Valid prediction for Augustus_model.g38926.t1
Valid prediction for snap_scaffold_28-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_58754-T1
Valid prediction for snap_scaffold_28-snap.1173-T1
Valid prediction for Augustus_model.g38918.t1
Valid prediction for snap_scaffold_28-snap.1158-T1
Valid prediction for snap_scaffold_28-snap.1168-T1
Valid prediction for snap_scaffold_28-snap.1187-T1
Valid prediction for snap_scaffold_28-snap.1153-T1
Couldn't classify 114086, 114264
Sorry, prediction pasa_asmbl_38238.p1 fails validation.
(CCC)	 AC	114086-114264	GT	AGG
(CGA)	 AG	114470-115113	GT	AGG
(GCA)	 AG	115310-115458	GT	AGG
(CTG)	 AG	116397-116521	GT	AGG
(GAC)	 AG	117059-117203	GT	GGG
(CTG)	 AG	117434-117625	AT	AGA
-recovered pasa_asmbl_38238.p1, terminal, 117434, 117625
-recovered pasa_asmbl_38238.p1, internal, 114470, 115113
-recovered pasa_asmbl_38238.p1, internal, 115310, 115458
-recovered pasa_asmbl_38238.p1, internal, 116397, 116521
-recovered pasa_asmbl_38238.p1, internal, 117059, 117203
Valid prediction for snap_scaffold_28-snap.1175-T1
Valid prediction for GlimmerHMM_glimmerT_58738-T1
Valid prediction for pasa_asmbl_38237.p1
Valid prediction for Augustus_model.g38931.t1
Valid prediction for GlimmerHMM_glimmerT_58753-T1
Valid prediction for snap_scaffold_28-snap.1172-T1
Valid prediction for snap_scaffold_28-snap.1177-T1
Valid prediction for snap_scaffold_28-snap.1156-T1
Valid prediction for snap_scaffold_28-snap.1183-T1
Valid prediction for snap_scaffold_28-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_58742-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8602, rend_intergenic: 7785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25889, rend_intergenic: 12000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35915, rend_intergenic: 31594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87596, rend_intergenic: 78871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114107, rend_intergenic: 106493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115351, rend_intergenic: 114363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122543, rend_intergenic: 121762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124863, rend_intergenic: 122746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129568, rend_intergenic: 126438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154633, rend_intergenic: 148121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159366, rend_intergenic: 155593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228093
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 8602, rend_intergenic: 7785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25889, rend_intergenic: 12000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35915, rend_intergenic: 31594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87596, rend_intergenic: 78871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114107, rend_intergenic: 106493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115351, rend_intergenic: 114363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122543, rend_intergenic: 121762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124863, rend_intergenic: 122746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129568, rend_intergenic: 126438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154633, rend_intergenic: 148121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159366, rend_intergenic: 155593  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