-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_5425406-5762946

-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_6570-T1
Valid prediction for Augustus_model.g4282.t1
Valid prediction for pasa_asmbl_40075.p1
Valid prediction for GlimmerHMM_glimmerT_6596-T1
Couldn't classify 253456, 253591
Sorry, prediction pasa_asmbl_40074.p1 fails validation.
(CCC)	 AA	253456-253591	GT	GGG
(TCC)	 AG	253793-253950	GT	GCG
(CTT)	 AG	254078-254248	GT	AGG
(AGC)	 AG	254383-254453	GT	AGG
(CAT)	 AG	254667-254712	GC	GAG
-recovered pasa_asmbl_40074.p1, terminal, 254667, 254712
-recovered pasa_asmbl_40074.p1, internal, 253793, 253950
-recovered pasa_asmbl_40074.p1, internal, 254078, 254248
-recovered pasa_asmbl_40074.p1, internal, 254383, 254453
-recovered pasa_asmbl_40074.p1, internal, 254667, 254712
Valid prediction for GlimmerHMM_glimmerT_6577-T1
Valid prediction for GlimmerHMM_glimmerT_6583-T1
Valid prediction for GlimmerHMM_glimmerT_6569-T1
Valid prediction for Augustus_model.g4263.t1
Valid prediction for GlimmerHMM_glimmerT_6573-T1
Valid prediction for GlimmerHMM_glimmerT_6561-T1
Couldn't classify 233833, 233887
Sorry, prediction pasa_asmbl_40070.p1 fails validation.
(TAC)	 GC	233833-233887	GT	CAG
(ACT)	 AG	233985-234104	GT	GGG
(ATA)	 AG	234479-234613	GT	TGG
(ATA)	 AG	234721-234843	GT	AGG
(TCA)	 AG	235357-235416	GT	CGG
(CCA)	 AG	235969-236202	GT	TGG
(TTC)	 AG	238740-238814	GT	AGG
(ATT)	 AG	238903-238998	GT	TGG
(GTC)	 AG	239112-239374	GT	CTG
(GTC)	 AG	239589-239693	AG	AAA
-recovered pasa_asmbl_40070.p1, terminal, 239589, 239693
-recovered pasa_asmbl_40070.p1, internal, 233985, 234104
-recovered pasa_asmbl_40070.p1, internal, 234479, 234613
-recovered pasa_asmbl_40070.p1, internal, 234721, 234843
-recovered pasa_asmbl_40070.p1, internal, 235357, 235416
-recovered pasa_asmbl_40070.p1, internal, 235969, 236202
-recovered pasa_asmbl_40070.p1, internal, 238740, 238814
-recovered pasa_asmbl_40070.p1, internal, 238903, 238998
-recovered pasa_asmbl_40070.p1, internal, 239112, 239374
Valid prediction for snap_scaffold_3-snap.1188-T1
Couldn't classify 250852, 251166
Sorry, prediction pasa_asmbl_40073.p1 fails validation.
(GTG)	 AG	250852-251166	AT	ACA
Valid prediction for GlimmerHMM_glimmerT_6580-T1
Valid prediction for Augustus_model.g4275.t1
Valid prediction for Augustus_model.g4270.t1
Valid prediction for snap_scaffold_3-snap.1206-T1
Valid prediction for Augustus_model.g4273.t1
Valid prediction for GlimmerHMM_glimmerT_6589-T1
Valid prediction for GlimmerHMM_glimmerT_6591-T1
Valid prediction for snap_scaffold_3-snap.1191-T1
Valid prediction for snap_scaffold_3-snap.1185-T1
Valid prediction for Augustus_model.g4279.t1
Valid prediction for snap_scaffold_3-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_6574-T1
Valid prediction for snap_scaffold_3-snap.1183-T1
Valid prediction for Augustus_model.g4277.t1
Valid prediction for GlimmerHMM_glimmerT_6575-T1
Valid prediction for GlimmerHMM_glimmerT_6585-T1
Valid prediction for snap_scaffold_3-snap.1170-T1
Valid prediction for pasa_asmbl_40082.p1
Valid prediction for Augustus_model.g4265.t1
Valid prediction for snap_scaffold_3-snap.1187-T1
Valid prediction for Augustus_model.g4271.t1
Valid prediction for GlimmerHMM_glimmerT_6565-T1
Valid prediction for GlimmerHMM_glimmerT_6568-T1
Couldn't classify 235357, 235413
Couldn't classify 235967, 236043
Sorry, prediction CodingQuarry_transcript_46165-T1 fails validation.
(ATG)	 TC	233866-233887	GT	CAG
(ACT)	 AG	233985-234104	GT	GGG
(ATA)	 AG	234479-234613	GT	TGG
(ATA)	 AG	234721-234843	GT	AGG
(TCA)	 AG	235357-235413	AC	CAA
(AGC)	 GC	235967-236043	CC	GAC
-recovered CodingQuarry_transcript_46165-T1, initial, 233866, 233887
-recovered CodingQuarry_transcript_46165-T1, internal, 233985, 234104
-recovered CodingQuarry_transcript_46165-T1, internal, 234479, 234613
-recovered CodingQuarry_transcript_46165-T1, internal, 234721, 234843
Valid prediction for snap_scaffold_3-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_6566-T1
Valid prediction for snap_scaffold_3-snap.1198-T1
Valid prediction for Augustus_model.g4283.t1
Valid prediction for snap_scaffold_3-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_6584-T1
Valid prediction for GlimmerHMM_glimmerT_6578-T1
Valid prediction for snap_scaffold_3-snap.1200-T1
Valid prediction for snap_scaffold_3-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_6582-T1
Valid prediction for Augustus_model.g4278.t1
Valid prediction for snap_scaffold_3-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_6590-T1
Valid prediction for GlimmerHMM_glimmerT_6595-T1
Valid prediction for snap_scaffold_3-snap.1172-T1
Valid prediction for snap_scaffold_3-snap.1173-T1
Valid prediction for GlimmerHMM_glimmerT_6579-T1
Valid prediction for snap_scaffold_3-snap.1199-T1
Valid prediction for snap_scaffold_3-snap.1190-T1
Valid prediction for Augustus_model.g4266.t1
Valid prediction for CodingQuarry_transcript_46167-T1
Valid prediction for CodingQuarry_transcript_46164-T1
Valid prediction for snap_scaffold_3-snap.1186-T1
Valid prediction for snap_scaffold_3-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_6581-T1
Valid prediction for snap_scaffold_3-snap.1184-T1
Valid prediction for Augustus_model.g4262.t1
Valid prediction for snap_scaffold_3-snap.1180-T1
Valid prediction for snap_scaffold_3-snap.1201-T1
Valid prediction for HiQ_model.g4272.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_3-snap.1204-T1
Valid prediction for Augustus_model.g4269.t1
Valid prediction for GlimmerHMM_glimmerT_6587-T1
Valid prediction for snap_scaffold_3-snap.1189-T1
Valid prediction for snap_scaffold_3-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_6562-T1
Valid prediction for HiQ_model.g4274.t1
Valid prediction for Augustus_model.g4259.t1
Couldn't classify 20890, 21010
Sorry, prediction pasa_asmbl_38857.p1 fails validation.
(GGC)	 AG	20890-21010	GT	AGG
(ACA)	 AG	21176-21416	GT	AGG
(CCC)	 AG	21591-22005	TC	GAT
-recovered pasa_asmbl_38857.p1, terminal, 21591, 22005
-recovered pasa_asmbl_38857.p1, internal, 20890, 21010
-recovered pasa_asmbl_38857.p1, internal, 21176, 21416
Couldn't classify 18244, 18294
Couldn't classify 20607, 20736
Sorry, prediction pasa_asmbl_38858.p1 fails validation.
(AAT)	 AT	18244-18294	GT	CAG
(TGT)	 AG	18442-18531	GT	AGG
(AGC)	 AG	18670-18798	GT	AAG
(GAA)	 AG	18949-19121	GT	CTG
(ACC)	 AG	20607-20736	GA	CAG
-recovered pasa_asmbl_38858.p1, internal, 18442, 18531
-recovered pasa_asmbl_38858.p1, internal, 18670, 18798
-recovered pasa_asmbl_38858.p1, internal, 18949, 19121
Valid prediction for snap_scaffold_3-snap.1163-T1
Valid prediction for Augustus_model.g4280.t1
Valid prediction for snap_scaffold_3-snap.1171-T1
Valid prediction for snap_scaffold_3-snap.1195-T1
Valid prediction for snap_scaffold_3-snap.1166-T1
Valid prediction for Augustus_model.g4260.t1
Valid prediction for Augustus_model.g4264.t1
Valid prediction for snap_scaffold_3-snap.1177-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6594-T1
Valid prediction for snap_scaffold_3-snap.1168-T1
Valid prediction for snap_scaffold_3-snap.1174-T1
Valid prediction for snap_scaffold_3-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_6586-T1
Valid prediction for pasa_asmbl_38852.p1
Valid prediction for Augustus_model.g4268.t1
Valid prediction for GlimmerHMM_glimmerT_6588-T1
Valid prediction for GlimmerHMM_glimmerT_6593-T1
Valid prediction for GlimmerHMM_glimmerT_6571-T1
Valid prediction for snap_scaffold_3-snap.1167-T1
Valid prediction for snap_scaffold_3-snap.1175-T1
Valid prediction for snap_scaffold_3-snap.1197-T1
Valid prediction for snap_scaffold_3-snap.1202-T1
Valid prediction for GlimmerHMM_glimmerT_6592-T1
Valid prediction for snap_scaffold_3-snap.1194-T1
Valid prediction for snap_scaffold_3-snap.1181-T1
Valid prediction for snap_scaffold_3-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_6572-T1
Valid prediction for snap_scaffold_3-snap.1164-T1
Valid prediction for Augustus_model.g4276.t1
Valid prediction for GlimmerHMM_glimmerT_6563-T1
Valid prediction for GlimmerHMM_glimmerT_6567-T1
Valid prediction for snap_scaffold_3-snap.1179-T1
Valid prediction for snap_scaffold_3-snap.1178-T1
Valid prediction for Augustus_model.g4281.t1
Couldn't classify 75220, 75407
Sorry, prediction pasa_asmbl_38855.p1 fails validation.
(GGT)	 CA	75220-75407	GT	ATG
(AGT)	 AG	76308-76464	GT	TGG
(TTT)	 AG	76573-76741	GT	CGG
(GAA)	 AG	77379-77452	GT	AGG
(TTC)	 AG	77603-77668	GT	TGG
(CTG)	 AG	78133-78213	TT	AAT
-recovered pasa_asmbl_38855.p1, terminal, 78133, 78213
-recovered pasa_asmbl_38855.p1, internal, 76308, 76464
-recovered pasa_asmbl_38855.p1, internal, 76573, 76741
-recovered pasa_asmbl_38855.p1, internal, 77379, 77452
-recovered pasa_asmbl_38855.p1, internal, 77603, 77668
Valid prediction for pasa_asmbl_38851.p1
Valid prediction for snap_scaffold_3-snap.1165-T1
Valid prediction for HiQ_model.g4267.t1
Valid prediction for snap_scaffold_3-snap.1182-T1
Valid prediction for pasa_asmbl_38850.p3
Valid prediction for GlimmerHMM_glimmerT_6564-T1
Valid prediction for Augustus_model.g4261.t1
Valid prediction for GlimmerHMM_glimmerT_6576-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 269668, rend_intergenic: 265201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 337541
-exon list size: 453


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    
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7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.7    
13.0    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.7    
24.0    
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    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.8    
51.0    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
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    
76.0    
76.3    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
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 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 269668, rend_intergenic: 265201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 22078
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2335 - 22078
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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

-building DP trellis

-building trellis in range 7155 - 22078
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 7155 - 17474
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support