-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_8710924-9260607

-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_6993-T1
Valid prediction for snap_scaffold_3-snap.1813-T1
Valid prediction for snap_scaffold_3-snap.1801-T1
Valid prediction for snap_scaffold_3-snap.1768-T1
Valid prediction for snap_scaffold_3-snap.1811-T1
Valid prediction for snap_scaffold_3-snap.1779-T1
Valid prediction for Augustus_model.g4576.t1
Valid prediction for GlimmerHMM_glimmerT_7018-T1
Valid prediction for snap_scaffold_3-snap.1816-T1
Valid prediction for snap_scaffold_3-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_7001-T1
Valid prediction for snap_scaffold_3-snap.1773-T1
Valid prediction for GlimmerHMM_glimmerT_7008-T1
Valid prediction for GlimmerHMM_glimmerT_6994-T1
Valid prediction for snap_scaffold_3-snap.1774-T1
Valid prediction for Augustus_model.g4575.t1
Valid prediction for snap_scaffold_3-snap.1772-T1
Valid prediction for snap_scaffold_3-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_7019-T1
Valid prediction for GlimmerHMM_glimmerT_7014-T1
Valid prediction for CodingQuarry_transcript_46233-T1
Valid prediction for snap_scaffold_3-snap.1785-T1
Valid prediction for Augustus_model.g4582.t1
Valid prediction for GlimmerHMM_glimmerT_7023-T1
Valid prediction for GlimmerHMM_glimmerT_6999-T1
Valid prediction for GlimmerHMM_glimmerT_7017-T1
Valid prediction for snap_scaffold_3-snap.1766-T1
Valid prediction for snap_scaffold_3-snap.1817-T1
Valid prediction for snap_scaffold_3-snap.1800-T1
Valid prediction for snap_scaffold_3-snap.1809-T1
Valid prediction for GlimmerHMM_glimmerT_7004-T1
Valid prediction for GlimmerHMM_glimmerT_6998-T1
Valid prediction for GlimmerHMM_glimmerT_7012-T1
Valid prediction for GlimmerHMM_glimmerT_7026-T1
Valid prediction for snap_scaffold_3-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_7011-T1
Valid prediction for GlimmerHMM_glimmerT_7003-T1
Valid prediction for snap_scaffold_3-snap.1786-T1
Valid prediction for snap_scaffold_3-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_7021-T1
Valid prediction for snap_scaffold_3-snap.1798-T1
Valid prediction for snap_scaffold_3-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_7013-T1
Valid prediction for snap_scaffold_3-snap.1780-T1
Valid prediction for snap_scaffold_3-snap.1815-T1
Valid prediction for snap_scaffold_3-snap.1806-T1
Valid prediction for GlimmerHMM_glimmerT_7024-T1
Valid prediction for snap_scaffold_3-snap.1794-T1
Valid prediction for snap_scaffold_3-snap.1787-T1
Valid prediction for HiQ_model.g4584.t1
Valid prediction for CodingQuarry_transcript_46235-T1
Valid prediction for pasa_asmbl_40223.p1
Valid prediction for snap_scaffold_3-snap.1802-T1
Valid prediction for HiQ_model.g4574.t1
Valid prediction for Augustus_model.g4590.t1
Valid prediction for snap_scaffold_3-snap.1808-T1
Valid prediction for snap_scaffold_3-snap.1764-T1
Valid prediction for Augustus_model.g4578.t1
Valid prediction for GlimmerHMM_glimmerT_7009-T1
Valid prediction for GlimmerHMM_glimmerT_7020-T1
Valid prediction for snap_scaffold_3-snap.1783-T1
Valid prediction for snap_scaffold_3-snap.1775-T1
Valid prediction for snap_scaffold_3-snap.1807-T1
Couldn't classify 331200, 331393
Sorry, prediction pasa_asmbl_40224.p1 fails validation.
(AAA)	 GA	331200-331393	GT	CGG
(GTA)	 AG	331669-331919	GT	TGG
(AGT)	 AG	332076-332220	GT	AGG
(AGG)	 AG	332413-332523	GT	ATG
(GTC)	 AG	332662-332728	GC	ATG
(ACT)	 AG	333135-333260	GC	TGG
(GCT)	 AG	333388-333568	GT	AGG
(ACC)	 AG	333947-334070	GT	AGG
(GTT)	 AG	334559-334712	CA	GAC
-recovered pasa_asmbl_40224.p1, terminal, 334559, 334712
-recovered pasa_asmbl_40224.p1, internal, 331669, 331919
-recovered pasa_asmbl_40224.p1, internal, 332076, 332220
-recovered pasa_asmbl_40224.p1, internal, 332413, 332523
-recovered pasa_asmbl_40224.p1, internal, 332662, 332728
-recovered pasa_asmbl_40224.p1, internal, 333135, 333260
-recovered pasa_asmbl_40224.p1, internal, 333388, 333568
-recovered pasa_asmbl_40224.p1, internal, 333947, 334070
Valid prediction for snap_scaffold_3-snap.1814-T1
Valid prediction for snap_scaffold_3-snap.1796-T1
Valid prediction for snap_scaffold_3-snap.1771-T1
Valid prediction for snap_scaffold_3-snap.1778-T1
Valid prediction for snap_scaffold_3-snap.1805-T1
Valid prediction for Augustus_model.g4577.t1
Valid prediction for snap_scaffold_3-snap.1799-T1
Valid prediction for snap_scaffold_3-snap.1781-T1
Valid prediction for Augustus_model.g4586.t1
Valid prediction for GlimmerHMM_glimmerT_7016-T1
Valid prediction for snap_scaffold_3-snap.1804-T1
Valid prediction for snap_scaffold_3-snap.1776-T1
Valid prediction for Augustus_model.g4589.t1
Valid prediction for Augustus_model.g4585.t1
Valid prediction for GlimmerHMM_glimmerT_7006-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 Augustus_model.g4583.t1
Valid prediction for pasa_asmbl_39044.p1
Valid prediction for HiQ_model.g4579.t1
Valid prediction for snap_scaffold_3-snap.1791-T1
Valid prediction for CodingQuarry_transcript_46234-T1
Valid prediction for Augustus_model.g4581.t1
Valid prediction for GlimmerHMM_glimmerT_7015-T1
Valid prediction for GlimmerHMM_glimmerT_6995-T1
Valid prediction for snap_scaffold_3-snap.1767-T1
Valid prediction for snap_scaffold_3-snap.1789-T1
Valid prediction for HiQ_model.g4573.t1
Valid prediction for snap_scaffold_3-snap.1810-T1
Valid prediction for snap_scaffold_3-snap.1790-T1
Couldn't classify 242363, 242456
Sorry, prediction pasa_asmbl_39052.p1 fails validation.
(TAT)	 GC	242363-242456	GT	CGG
(AGG)	 AG	244877-244981	GT	AGG
(CTT)	 AG	246235-246281	GT	TTG
(GGA)	 AG	248535-248598	GT	TTG
(ACC)	 AG	250796-250894	GT	GAG
(AGA)	 AG	251305-251408	GT	GGG
(AAC)	 AG	252467-252614	GT	TGG
(ACC)	 AG	253780-253898	GT	AGG
(GCA)	 AG	254973-255059	GT	AGG
(GCT)	 AG	255167-255232	GT	AGG
(GAC)	 AG	256890-256994	GT	AGG
(GAC)	 AG	258140-258202	GT	ATG
(AAC)	 AG	258503-258703	GT	AGG
(GTA)	 AG	259250-259476	GT	AGG
(GTG)	 AG	259609-259809	GT	AGG
(GGA)	 AG	261095-261188	GT	CGG
(CTG)	 AG	261903-262052	GT	CGG
(CAA)	 AG	262157-262225	GT	AGG
(GCT)	 AG	262343-262429	GT	AGG
(GCG)	 AG	262818-262904	GT	AGG
(GCT)	 AG	265217-265303	GT	AGG
(GTC)	 AG	266315-266389	GT	TTG
(ATG)	 AG	266545-266679	GT	GGG
(TGC)	 AG	266812-266918	GT	AGG
(TGT)	 AG	267041-267173	GT	AGG
(GGT)	 AG	267454-267606	GT	AGG
(GGC)	 AG	267796-267926	GT	GAG
(GTT)	 AG	268042-268171	AG	AAA
-recovered pasa_asmbl_39052.p1, initial, 266545, 266679
add_exon() Sorry, pasa_asmbl_39052.p1 250796-250894-terminal-1 is invalid.
-recovered pasa_asmbl_39052.p1, terminal, 250796, 250894
add_exon() Sorry, pasa_asmbl_39052.p1 259609-259809-terminal-1 is invalid.
-recovered pasa_asmbl_39052.p1, terminal, 259609, 259809
-recovered pasa_asmbl_39052.p1, terminal, 268042, 268171
-recovered pasa_asmbl_39052.p1, internal, 244877, 244981
-recovered pasa_asmbl_39052.p1, internal, 246235, 246281
-recovered pasa_asmbl_39052.p1, internal, 248535, 248598
-recovered pasa_asmbl_39052.p1, internal, 250796, 250894
-recovered pasa_asmbl_39052.p1, internal, 251305, 251408
-recovered pasa_asmbl_39052.p1, internal, 252467, 252614
-recovered pasa_asmbl_39052.p1, internal, 253780, 253898
-recovered pasa_asmbl_39052.p1, internal, 254973, 255059
-recovered pasa_asmbl_39052.p1, internal, 255167, 255232
-recovered pasa_asmbl_39052.p1, internal, 256890, 256994
-recovered pasa_asmbl_39052.p1, internal, 258140, 258202
-recovered pasa_asmbl_39052.p1, internal, 258503, 258703
-recovered pasa_asmbl_39052.p1, internal, 259250, 259476
-recovered pasa_asmbl_39052.p1, internal, 259609, 259809
-recovered pasa_asmbl_39052.p1, internal, 261095, 261188
-recovered pasa_asmbl_39052.p1, internal, 261903, 262052
-recovered pasa_asmbl_39052.p1, internal, 262157, 262225
-recovered pasa_asmbl_39052.p1, internal, 262343, 262429
-recovered pasa_asmbl_39052.p1, internal, 262818, 262904
-recovered pasa_asmbl_39052.p1, internal, 265217, 265303
-recovered pasa_asmbl_39052.p1, internal, 266315, 266389
-recovered pasa_asmbl_39052.p1, internal, 266545, 266679
-recovered pasa_asmbl_39052.p1, internal, 266812, 266918
-recovered pasa_asmbl_39052.p1, internal, 267041, 267173
-recovered pasa_asmbl_39052.p1, internal, 267454, 267606
-recovered pasa_asmbl_39052.p1, internal, 267796, 267926
Valid prediction for Augustus_model.g4587.t1
Valid prediction for GlimmerHMM_glimmerT_7010-T1
Valid prediction for snap_scaffold_3-snap.1765-T1
Valid prediction for Augustus_model.g4572.t1
Valid prediction for GlimmerHMM_glimmerT_7027-T1
Valid prediction for snap_scaffold_3-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_6996-T1
Valid prediction for GlimmerHMM_glimmerT_7007-T1
Valid prediction for Augustus_model.g4588.t1
Valid prediction for GlimmerHMM_glimmerT_7002-T1
Valid prediction for pasa_asmbl_39045.p1
Valid prediction for GlimmerHMM_glimmerT_6997-T1
Valid prediction for snap_scaffold_3-snap.1769-T1
Valid prediction for snap_scaffold_3-snap.1797-T1
Valid prediction for snap_scaffold_3-snap.1788-T1
Valid prediction for snap_scaffold_3-snap.1795-T1
Valid prediction for pasa_asmbl_39048.p1
Valid prediction for HiQ_model.g4580.t1
Valid prediction for GlimmerHMM_glimmerT_7005-T1
Valid prediction for snap_scaffold_3-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_7000-T1
Valid prediction for snap_scaffold_3-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_7025-T1
Valid prediction for CodingQuarry_transcript_46232-T1
Valid prediction for GlimmerHMM_glimmerT_7022-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13850, rend_intergenic: 8846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 312920, rend_intergenic: 310961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 549684
-exon list size: 531


building trellis

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8.1    
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8.8    
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14.8    
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17.8    
18.0    
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18.4    
18.6    
18.8    
18.9    
19.1    
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20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
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21.6    
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22.0    
22.1    
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22.5    
22.7    
22.9    
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23.3    
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23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13850, rend_intergenic: 8846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 312920, rend_intergenic: 310961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 536002 - 549684
-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 536417 - 549684
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 536417 - 547578
-exon list size: 1


building trellis

33.3    
66.7    
-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