-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_9729391-9920336

-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_50076-T1
Valid prediction for snap_scaffold_22-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_50073-T1
Valid prediction for Augustus_model.g33404.t1
Valid prediction for snap_scaffold_22-snap.2024-T1
Valid prediction for Augustus_model.g33403.t1
Valid prediction for Augustus_model.g33408.t1
Valid prediction for Augustus_model.g33396.t1
Valid prediction for snap_scaffold_22-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_50077-T1
Valid prediction for snap_scaffold_22-snap.2019-T1
Valid prediction for snap_scaffold_22-snap.2015-T1
Valid prediction for snap_scaffold_22-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_50066-T1
Valid prediction for snap_scaffold_22-snap.2004-T1
Valid prediction for snap_scaffold_22-snap.2021-T1
Valid prediction for snap_scaffold_22-snap.2008-T1
Valid prediction for snap_scaffold_22-snap.2017-T1
Valid prediction for snap_scaffold_22-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_50064-T1
Valid prediction for snap_scaffold_22-snap.1993-T1
Couldn't classify 52210, 52410
Couldn't classify 52809, 53015
Sorry, prediction pasa_asmbl_30517.p1 fails validation.
(CAG)	 CC	52210-52410	GT	AGG
(GAT)	 AG	52809-53015	CA	GTC
Valid prediction for snap_scaffold_22-snap.2028-T1
Valid prediction for HiQ_model.g33409.t1
Valid prediction for Augustus_model.g33398.t1
Valid prediction for snap_scaffold_22-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_50067-T1
Couldn't classify 118243, 118329
Sorry, prediction pasa_asmbl_30323.p1 fails validation.
(CCA)	 GC	118243-118329	GT	TGG
(TGG)	 AG	118891-118943	GT	GTG
(CTC)	 AG	119029-119119	GT	TAG
(GTG)	 AG	119569-119712	AA	AGA
-recovered pasa_asmbl_30323.p1, terminal, 119569, 119712
-recovered pasa_asmbl_30323.p1, internal, 118891, 118943
-recovered pasa_asmbl_30323.p1, internal, 119029, 119119
Valid prediction for snap_scaffold_22-snap.2013-T1
Valid prediction for snap_scaffold_22-snap.2002-T1
Valid prediction for Augustus_model.g33393.t1
Valid prediction for snap_scaffold_22-snap.1997-T1
Valid prediction for snap_scaffold_22-snap.1991-T1
Valid prediction for snap_scaffold_22-snap.2011-T1
Valid prediction for Augustus_model.g33397.t1
Valid prediction for snap_scaffold_22-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_50071-T1
Valid prediction for snap_scaffold_22-snap.1990-T1
Valid prediction for Augustus_model.g33392.t1
Valid prediction for Augustus_model.g33400.t1
Valid prediction for snap_scaffold_22-snap.1998-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_22-snap.1996-T1
Valid prediction for Augustus_model.g33395.t1
Valid prediction for snap_scaffold_22-snap.2020-T1
Valid prediction for snap_scaffold_22-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_50072-T1
Valid prediction for Augustus_model.g33406.t1
Couldn't classify 11474, 11511
Sorry, prediction pasa_asmbl_29571.p1 fails validation.
(CAG)	 CC	11474-11511	GT	AGG
(GTA)	 AG	11731-11942	GT	CGG
(TGT)	 AG	12151-12407	GT	AGG
(GTG)	 AG	12702-12821	GT	AGG
(AAA)	 AG	13875-14034	GT	TGG
(AAA)	 AG	14555-14856	AC	AAA
-recovered pasa_asmbl_29571.p1, terminal, 14555, 14856
-recovered pasa_asmbl_29571.p1, internal, 11731, 11942
-recovered pasa_asmbl_29571.p1, internal, 12151, 12407
-recovered pasa_asmbl_29571.p1, internal, 12702, 12821
-recovered pasa_asmbl_29571.p1, internal, 13875, 14034
Valid prediction for Augustus_model.g33391.t1
Valid prediction for Augustus_model.g33399.t1
Couldn't classify 8313, 8401
Couldn't classify 9132, 9198
Sorry, prediction pasa_asmbl_29572.p1 fails validation.
(ACC)	 CC	8313-8401	GT	AGG
(AAT)	 AG	8619-8882	GT	AGG
(GTT)	 AG	9132-9198	GG	AGG
-recovered pasa_asmbl_29572.p1, internal, 8619, 8882
Valid prediction for snap_scaffold_22-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_50074-T1
Valid prediction for pasa_asmbl_29558.p1
Valid prediction for snap_scaffold_22-snap.1989-T1
Couldn't classify 18438, 18505
Sorry, prediction pasa_asmbl_29569.p1 fails validation.
(AGC)	 GC	18438-18505	GT	AAG
(TGA)	 AG	18849-19020	GT	AGG
(GAC)	 AG	19339-19503	GT	AGG
(GAG)	 AG	20637-20825	GT	TGG
(GCC)	 AG	21222-21319	GT	AGG
(GTA)	 AG	21449-21581	GT	AGG
(AAC)	 AG	21752-21958	GT	AGG
(GGA)	 AG	23083-23310	GA	AGG
-recovered pasa_asmbl_29569.p1, terminal, 23083, 23310
-recovered pasa_asmbl_29569.p1, internal, 18849, 19020
-recovered pasa_asmbl_29569.p1, internal, 19339, 19503
-recovered pasa_asmbl_29569.p1, internal, 20637, 20825
-recovered pasa_asmbl_29569.p1, internal, 21222, 21319
-recovered pasa_asmbl_29569.p1, internal, 21449, 21581
-recovered pasa_asmbl_29569.p1, internal, 21752, 21958
Valid prediction for snap_scaffold_22-snap.2023-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50065-T1
Valid prediction for GlimmerHMM_glimmerT_50080-T1
Valid prediction for GlimmerHMM_glimmerT_50079-T1
Valid prediction for snap_scaffold_22-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_50069-T1
Valid prediction for Augustus_model.g33405.t1
Valid prediction for snap_scaffold_22-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_50063-T1
Valid prediction for snap_scaffold_22-snap.2005-T1
Valid prediction for snap_scaffold_22-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_50070-T1
Valid prediction for snap_scaffold_22-snap.2025-T1
Valid prediction for Augustus_model.g33402.t1
Valid prediction for GlimmerHMM_glimmerT_50068-T1
Valid prediction for Augustus_model.g33401.t1
Valid prediction for Augustus_model.g33411.t1
Valid prediction for snap_scaffold_22-snap.2026-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.2009-T1
Valid prediction for Augustus_model.g33407.t1
Valid prediction for snap_scaffold_22-snap.2022-T1
Valid prediction for snap_scaffold_22-snap.2014-T1
Valid prediction for snap_scaffold_22-snap.2030-T1
Valid prediction for Augustus_model.g33390.t1
Valid prediction for snap_scaffold_22-snap.2012-T1
Valid prediction for snap_scaffold_22-snap.2027-T1
Valid prediction for snap_scaffold_22-snap.1988-T1
Couldn't classify 49840, 50010
Couldn't classify 50565, 50738
Sorry, prediction pasa_asmbl_29566.p1 fails validation.
(CCA)	 CC	49840-50010	GC	AGG
(GTG)	 AG	50565-50738	GT	CGG
-recovered pasa_asmbl_29566.p1, internal, 50565, 50738
Valid prediction for CodingQuarry_transcript_34263-T1
Valid prediction for snap_scaffold_22-snap.2029-T1
Valid prediction for Augustus_model.g33410.t1
Valid prediction for GlimmerHMM_glimmerT_50075-T1
Valid prediction for snap_scaffold_22-snap.2007-T1
Valid prediction for snap_scaffold_22-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_50078-T1
Valid prediction for Augustus_model.g33412.t1
Valid prediction for GlimmerHMM_glimmerT_50062-T1
Valid prediction for Augustus_model.g33394.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8996, rend_intergenic: 3178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14946, rend_intergenic: 9041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30702, rend_intergenic: 17280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33929, rend_intergenic: 30729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40549, rend_intergenic: 37217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46214, rend_intergenic: 45574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65857, rend_intergenic: 46422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69030, rend_intergenic: 66889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75456, rend_intergenic: 69676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85928, rend_intergenic: 78319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102980, rend_intergenic: 86013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111895, rend_intergenic: 103999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114967, rend_intergenic: 113063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123282, rend_intergenic: 121730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131887, rend_intergenic: 127927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143344, rend_intergenic: 134645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156284, rend_intergenic: 146863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165751, rend_intergenic: 156475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174712, rend_intergenic: 167637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182760, rend_intergenic: 178774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190946
-exon list size: 407


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    
4.2    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
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7.1    
7.3    
7.6    
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8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
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10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.5    
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65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
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 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 8996, rend_intergenic: 3178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14946, rend_intergenic: 9041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30702, rend_intergenic: 17280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33929, rend_intergenic: 30729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40549, rend_intergenic: 37217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46214, rend_intergenic: 45574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65857, rend_intergenic: 46422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69030, rend_intergenic: 66889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75456, rend_intergenic: 69676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85928, rend_intergenic: 78319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102980, rend_intergenic: 86013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111895, rend_intergenic: 103999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114967, rend_intergenic: 113063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123282, rend_intergenic: 121730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131887, rend_intergenic: 127927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143344, rend_intergenic: 134645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156284, rend_intergenic: 146863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165751, rend_intergenic: 156475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174712, rend_intergenic: 167637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182760, rend_intergenic: 178774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support