-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_4135227-4331793

-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 pasa_asmbl_37532.p1
Valid prediction for snap_scaffold_28-snap.1005-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_58617-T1
Valid prediction for snap_scaffold_28-snap.992-T1
Valid prediction for snap_scaffold_28-snap.1004-T1
Valid prediction for snap_scaffold_28-snap.1002-T1
Couldn't classify 11284, 12243
Sorry, prediction pasa_asmbl_37515.p1 fails validation.
(ATG)	 GC	11284-12243	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_58632-T1
Valid prediction for GlimmerHMM_glimmerT_58625-T1
Valid prediction for snap_scaffold_28-snap.989-T1
Valid prediction for snap_scaffold_28-snap.1017-T1
Valid prediction for Augustus_model.g38838.t1
Valid prediction for GlimmerHMM_glimmerT_58640-T1
Valid prediction for snap_scaffold_28-snap.990-T1
Valid prediction for snap_scaffold_28-snap.1008-T1
Valid prediction for snap_scaffold_28-snap.996-T1
Valid prediction for Augustus_model.g38848.t1
Valid prediction for Augustus_model.g38832.t1
Valid prediction for CodingQuarry_transcript_43632-T1
Valid prediction for pasa_asmbl_37827.p1
Valid prediction for snap_scaffold_28-snap.1007-T1
Valid prediction for snap_scaffold_28-snap.1012-T1
Valid prediction for CodingQuarry_transcript_43626-T1
Valid prediction for Augustus_model.g38849.t1
Valid prediction for GlimmerHMM_glimmerT_58626-T1
Valid prediction for GlimmerHMM_glimmerT_58628-T1
Couldn't classify 72465, 72699
Sorry, prediction pasa_asmbl_37521.p1 fails validation.
(TCC)	 AT	72465-72699	GT	CAG
(TCC)	 AG	72943-73115	GT	AGG
(CTG)	 AG	74247-74456	GT	AGG
(CTT)	 AG	74623-74823	CG	GAC
-recovered pasa_asmbl_37521.p1, terminal, 74623, 74823
-recovered pasa_asmbl_37521.p1, internal, 72943, 73115
-recovered pasa_asmbl_37521.p1, internal, 74247, 74456
Valid prediction for GlimmerHMM_glimmerT_58636-T1
Valid prediction for snap_scaffold_28-snap.1001-T1
Valid prediction for Augustus_model.g38839.t1
Valid prediction for snap_scaffold_28-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_58629-T1
Valid prediction for GlimmerHMM_glimmerT_58618-T1
Valid prediction for Augustus_model.g38845.t1
Valid prediction for snap_scaffold_28-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_58621-T1
Valid prediction for GlimmerHMM_glimmerT_58627-T1
Valid prediction for snap_scaffold_28-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_58641-T1
Couldn't classify 112815, 112922
Sorry, prediction pasa_asmbl_37530.p1 fails validation.
(ATG)	 CA	110364-110366	GT	TGG
(GGA)	 AG	110457-110510	GT	AGG
(GGT)	 AG	110758-110811	GT	AGG
(GGT)	 AG	111397-111453	GT	GAG
(GGT)	 AG	111690-111743	GT	AGG
(GGT)	 AG	111889-111942	GT	CTG
(GGA)	 AG	112035-112088	GT	AAG
(GGT)	 AG	112183-112236	GT	CAG
(GGT)	 AG	112402-112509	GT	AGG
(GGG)	 AG	112620-112727	GT	AGG
(GGG)	 AG	112815-112922	GT	TGG
-recovered pasa_asmbl_37530.p1, initial, 110364, 110366
-recovered pasa_asmbl_37530.p1, internal, 110457, 110510
-recovered pasa_asmbl_37530.p1, internal, 110758, 110811
-recovered pasa_asmbl_37530.p1, internal, 111397, 111453
-recovered pasa_asmbl_37530.p1, internal, 111690, 111743
-recovered pasa_asmbl_37530.p1, internal, 111889, 111942
-recovered pasa_asmbl_37530.p1, internal, 112035, 112088
-recovered pasa_asmbl_37530.p1, internal, 112183, 112236
-recovered pasa_asmbl_37530.p1, internal, 112402, 112509
-recovered pasa_asmbl_37530.p1, internal, 112620, 112727
-recovered pasa_asmbl_37530.p1, internal, 112815, 112922
Valid prediction for GlimmerHMM_glimmerT_58635-T1
Valid prediction for Augustus_model.g38840.t1
Valid prediction for HiQ_model.g38837.t1
Valid prediction for CodingQuarry_transcript_43635-T1
Valid prediction for snap_scaffold_28-snap.999-T1
Valid prediction for CodingQuarry_transcript_43631-T1
Valid prediction for CodingQuarry_transcript_43628-T1
Valid prediction for snap_scaffold_28-snap.1013-T1
Valid prediction for snap_scaffold_28-snap.988-T1
Valid prediction for Augustus_model.g38831.t1
Valid prediction for HiQ_model.g38844.t1
Valid prediction for CodingQuarry_transcript_43630-T1
Valid prediction for CodingQuarry_transcript_43629-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 HiQ_model.g38836.t1
Valid prediction for Augustus_model.g38834.t1
Valid prediction for GlimmerHMM_glimmerT_58634-T1
Valid prediction for snap_scaffold_28-snap.1011-T1
Valid prediction for pasa_asmbl_38201.p1
Valid prediction for GlimmerHMM_glimmerT_58622-T1
Valid prediction for snap_scaffold_28-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_58623-T1
Valid prediction for CodingQuarry_transcript_43625-T1
Valid prediction for snap_scaffold_28-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_58633-T1
Valid prediction for snap_scaffold_28-snap.1014-T1
Valid prediction for snap_scaffold_28-snap.998-T1
Valid prediction for snap_scaffold_28-snap.1018-T1
Valid prediction for Augustus_model.g38846.t1
Valid prediction for snap_scaffold_28-snap.997-T1
Valid prediction for HiQ_model.g38842.t1
Valid prediction for GlimmerHMM_glimmerT_58638-T1
Couldn't classify 168207, 168314
Couldn't classify 169051, 169377
Sorry, prediction pasa_asmbl_38197.p1 fails validation.
(CTG)	 AC	168207-168314	GT	AGG
(TTC)	 AG	168817-168837	GT	AGG
(TCT)	 AG	169051-169377	GG	GGG
-recovered pasa_asmbl_38197.p1, internal, 168817, 168837
Valid prediction for GlimmerHMM_glimmerT_58619-T1
Valid prediction for Augustus_model.g38833.t1
Valid prediction for snap_scaffold_28-snap.991-T1
Valid prediction for snap_scaffold_28-snap.1019-T1
Valid prediction for Augustus_model.g38847.t1
Valid prediction for pasa_asmbl_38204.p1
Valid prediction for Augustus_model.g38850.t1
Valid prediction for CodingQuarry_transcript_43633-T1
Valid prediction for snap_scaffold_28-snap.1021-T1
Valid prediction for snap_scaffold_28-snap.1020-T1
Valid prediction for HiQ_model.g38843.t1
Valid prediction for snap_scaffold_28-snap.993-T1
Valid prediction for pasa_asmbl_38199.p1
Valid prediction for GlimmerHMM_glimmerT_58631-T1
Valid prediction for Augustus_model.g38835.t1
Couldn't classify 69578, 70309
Sorry, prediction pasa_asmbl_38206.p1 fails validation.
(CTG)	 GG	69578-70309	GT	GAG
(ATC)	 AG	70555-70839	GG	GAG
-recovered pasa_asmbl_38206.p1, terminal, 70555, 70839
Valid prediction for snap_scaffold_28-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_58630-T1
Valid prediction for HiQ_model.g38841.t1
Valid prediction for snap_scaffold_28-snap.994-T1
Valid prediction for GlimmerHMM_glimmerT_58624-T1
Valid prediction for GlimmerHMM_glimmerT_58639-T1
Valid prediction for Augustus_model.g38830.t1
Valid prediction for CodingQuarry_transcript_43634-T1
Valid prediction for GlimmerHMM_glimmerT_58637-T1
Valid prediction for GlimmerHMM_glimmerT_58620-T1
Valid prediction for snap_scaffold_28-snap.1009-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32746, rend_intergenic: 29126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37363, rend_intergenic: 33499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51789, rend_intergenic: 51391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196567
-exon list size: 375


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 32746, rend_intergenic: 29126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37363, rend_intergenic: 33499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51789, rend_intergenic: 51391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 172227 - 196567
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 173655 - 196567
-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 173655 - 194022
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 177691 - 194022
-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 179363 - 194022
-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
	-no exons in range 179363 - 193458