-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_4660268-4816174

-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_6455-T1
Couldn't classify 62576, 62986
Sorry, prediction pasa_asmbl_40030.p1 fails validation.
(GGC)	 GA	62576-62986	AG	ACA
Valid prediction for snap_scaffold_3-snap.997-T1
Valid prediction for Augustus_model.g4178.t1
Valid prediction for snap_scaffold_3-snap.996-T1
Valid prediction for snap_scaffold_3-snap.1036-T1
Valid prediction for Augustus_model.g4174.t1
Valid prediction for snap_scaffold_3-snap.1014-T1
Couldn't classify 73655, 73859
Sorry, prediction pasa_asmbl_40032.p1 fails validation.
(TCG)	 TC	73655-73859	GT	AGG
(ATG)	 AG	75554-75601	GT	AGG
(TGG)	 AG	75961-76130	GT	CGG
(AGG)	 AG	77419-77568	TA	AAT
add_exon() Sorry, pasa_asmbl_40032.p1 75554-75601-initial-1 is invalid.
-recovered pasa_asmbl_40032.p1, initial, 75554, 75601
-recovered pasa_asmbl_40032.p1, terminal, 77419, 77568
-recovered pasa_asmbl_40032.p1, internal, 75554, 75601
-recovered pasa_asmbl_40032.p1, internal, 75961, 76130
Valid prediction for snap_scaffold_3-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_6449-T1
Valid prediction for snap_scaffold_3-snap.1000-T1
Valid prediction for snap_scaffold_3-snap.998-T1
Valid prediction for GlimmerHMM_glimmerT_6463-T1
Valid prediction for GlimmerHMM_glimmerT_6452-T1
Valid prediction for Augustus_model.g4173.t1
Valid prediction for GlimmerHMM_glimmerT_6462-T1
Valid prediction for snap_scaffold_3-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_6451-T1
Valid prediction for Augustus_model.g4191.t1
Valid prediction for snap_scaffold_3-snap.1008-T1
Couldn't classify 24058, 24237
Couldn't classify 24450, 24623
Sorry, prediction pasa_asmbl_40842.p1 fails validation.
(GAG)	 CA	24058-24237	GT	GGG
(GAC)	 AG	24450-24623	GG	CTG
Valid prediction for GlimmerHMM_glimmerT_6441-T1
Valid prediction for snap_scaffold_3-snap.1031-T1
Valid prediction for snap_scaffold_3-snap.1028-T1
Valid prediction for snap_scaffold_3-snap.1011-T1
Valid prediction for snap_scaffold_3-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_6440-T1
Valid prediction for snap_scaffold_3-snap.1007-T1
Valid prediction for Augustus_model.g4175.t1
Valid prediction for snap_scaffold_3-snap.1017-T1
Valid prediction for snap_scaffold_3-snap.1010-T1
Valid prediction for Augustus_model.g4190.t1
Couldn't classify 25158, 25205
Sorry, prediction pasa_asmbl_40829.p2 fails validation.
(CCC)	 GG	25158-25205	GT	AGG
(CCA)	 AG	25390-25576	GT	CGG
(GTC)	 AG	25927-26078	TT	GAT
-recovered pasa_asmbl_40829.p2, terminal, 25927, 26078
-recovered pasa_asmbl_40829.p2, internal, 25390, 25576
Valid prediction for GlimmerHMM_glimmerT_6445-T1
Valid prediction for snap_scaffold_3-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_6438-T1
Valid prediction for snap_scaffold_3-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_6444-T1
Valid prediction for Augustus_model.g4188.t1
Valid prediction for snap_scaffold_3-snap.1013-T1
Valid prediction for snap_scaffold_3-snap.1002-T1
Valid prediction for snap_scaffold_3-snap.1006-T1
Valid prediction for Augustus_model.g4189.t1
Valid prediction for snap_scaffold_3-snap.1026-T1
Valid prediction for snap_scaffold_3-snap.1020-T1
Valid prediction for Augustus_model.g4182.t1
Valid prediction for Augustus_model.g4179.t1
Valid prediction for GlimmerHMM_glimmerT_6448-T1
Valid prediction for Augustus_model.g4183.t1
Valid prediction for GlimmerHMM_glimmerT_6461-T1
Valid prediction for snap_scaffold_3-snap.994-T1
Valid prediction for GlimmerHMM_glimmerT_6458-T1
Valid prediction for Augustus_model.g4180.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.g4181.t1
Valid prediction for snap_scaffold_3-snap.1030-T1
Valid prediction for snap_scaffold_3-snap.1025-T1
Valid prediction for snap_scaffold_3-snap.1005-T1
Valid prediction for snap_scaffold_3-snap.1016-T1
Valid prediction for snap_scaffold_3-snap.1018-T1
Couldn't classify 73580, 73642
Couldn't classify 76046, 76162
Sorry, prediction pasa_asmbl_39784.p1 fails validation.
(AGT)	 CC	73580-73642	GT	TTG
(GGG)	 AG	73892-73949	GT	GGG
(TGA)	 AG	75086-75189	GT	TGG
(GTT)	 AG	76046-76162	GC	GGG
-recovered pasa_asmbl_39784.p1, internal, 73892, 73949
-recovered pasa_asmbl_39784.p1, internal, 75086, 75189
-recovered pasa_asmbl_39784.p1, internal, 76046, 76162
Valid prediction for snap_scaffold_3-snap.1021-T1
Valid prediction for Augustus_model.g4187.t1
Valid prediction for GlimmerHMM_glimmerT_6450-T1
Valid prediction for snap_scaffold_3-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_6439-T1
Valid prediction for GlimmerHMM_glimmerT_6442-T1
Valid prediction for GlimmerHMM_glimmerT_6453-T1
Valid prediction for snap_scaffold_3-snap.1004-T1
Valid prediction for Augustus_model.g4185.t1
Valid prediction for snap_scaffold_3-snap.1029-T1
Valid prediction for snap_scaffold_3-snap.1027-T1
Valid prediction for snap_scaffold_3-snap.1038-T1
Valid prediction for snap_scaffold_3-snap.1001-T1
Valid prediction for snap_scaffold_3-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_6446-T1
Valid prediction for GlimmerHMM_glimmerT_6447-T1
Valid prediction for Augustus_model.g4177.t1
Valid prediction for snap_scaffold_3-snap.995-T1
Valid prediction for snap_scaffold_3-snap.1019-T1
Couldn't classify 76265, 76618
Sorry, prediction pasa_asmbl_39735.p1 fails validation.
(AGA)	 GG	76265-76618	GG	AGG
Valid prediction for Augustus_model.g4184.t1
Valid prediction for snap_scaffold_3-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_6457-T1
Valid prediction for CodingQuarry_transcript_46145-T1
Valid prediction for Augustus_model.g4176.t1
Valid prediction for snap_scaffold_3-snap.1009-T1
Valid prediction for GlimmerHMM_glimmerT_6459-T1
Valid prediction for snap_scaffold_3-snap.1012-T1
Valid prediction for Augustus_model.g4186.t1
Couldn't classify 49333, 49391
Couldn't classify 52060, 52245
Sorry, prediction pasa_asmbl_39685.p1 fails validation.
(CAT)	 TG	49333-49391	GT	AGG
(TTT)	 AG	51459-51519	GT	TGG
(ATC)	 AG	52060-52245	CA	AGC
-recovered pasa_asmbl_39685.p1, internal, 51459, 51519
Valid prediction for GlimmerHMM_glimmerT_6443-T1
Valid prediction for GlimmerHMM_glimmerT_6460-T1
Couldn't classify 76289, 76588
Sorry, prediction CodingQuarry_transcript_46146-T1 fails validation.
(ATG)	 CC	76289-76588	AG	AGA
(GGC)	 AG	76619-76936	TG	AGT
-recovered CodingQuarry_transcript_46146-T1, terminal, 76619, 76936
Valid prediction for snap_scaffold_3-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_6454-T1
Valid prediction for snap_scaffold_3-snap.1033-T1
Valid prediction for snap_scaffold_3-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_6456-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9407, rend_intergenic: 4973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18154, rend_intergenic: 15765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22945, rend_intergenic: 20413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25948, rend_intergenic: 23020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31876, rend_intergenic: 31677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46697, rend_intergenic: 43333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49569, rend_intergenic: 46698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57621, rend_intergenic: 55225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64633, rend_intergenic: 57805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70428, rend_intergenic: 68227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72081, rend_intergenic: 70678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77568, rend_intergenic: 72598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84985, rend_intergenic: 77972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90991, rend_intergenic: 84985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99916, rend_intergenic: 94643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101490, rend_intergenic: 100118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106720, rend_intergenic: 102647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112458, rend_intergenic: 107410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128302, rend_intergenic: 123291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154288, rend_intergenic: 143614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155907
-exon list size: 326


building trellis

0.3    
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4.9    
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5.8    
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6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
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8.8    
9.1    
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10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
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17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
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21.3    
21.6    
22.0    
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22.6    
22.9    
23.2    
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23.8    
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24.4    
24.7    
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25.3    
25.6    
25.9    
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26.8    
27.1    
27.4    
27.7    
28.0    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
72.0    
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72.6    
72.9    
73.2    
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73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
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76.8    
77.1    
77.4    
77.7    
78.0    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9407, rend_intergenic: 4973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18154, rend_intergenic: 15765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22945, rend_intergenic: 20413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25948, rend_intergenic: 23020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31876, rend_intergenic: 31677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46697, rend_intergenic: 43333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49569, rend_intergenic: 46698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57621, rend_intergenic: 55225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64633, rend_intergenic: 57805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70428, rend_intergenic: 68227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72081, rend_intergenic: 70678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77568, rend_intergenic: 72598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84985, rend_intergenic: 77972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90991, rend_intergenic: 84985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99916, rend_intergenic: 94643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101490, rend_intergenic: 100118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106720, rend_intergenic: 102647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112458, rend_intergenic: 107410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128302, rend_intergenic: 123291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154288, rend_intergenic: 143614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support