-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_10297539-10437532

-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 snap_scaffold_23-snap.1990-T1
Valid prediction for snap_scaffold_23-snap.1991-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51716-T1
Valid prediction for CodingQuarry_transcript_35798-T1
Valid prediction for snap_scaffold_23-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_51720-T1
Valid prediction for snap_scaffold_23-snap.1994-T1
Valid prediction for snap_scaffold_23-snap.2000-T1
Valid prediction for snap_scaffold_23-snap.1981-T1
Valid prediction for snap_scaffold_23-snap.1983-T1
Couldn't classify 104777, 104818
Couldn't classify 107460, 107542
Sorry, prediction pasa_asmbl_31859.p2 fails validation.
(AGG)	 AG	104777-104818	GT	AGG
(GGA)	 AG	105111-105189	GT	AAG
(ACG)	 AG	105729-105850	GT	GGG
(CAC)	 AG	106497-106578	GT	AAG
(CAG)	 AG	107460-107542	GA	GGG
-recovered pasa_asmbl_31859.p2, internal, 104777, 104818
-recovered pasa_asmbl_31859.p2, internal, 105111, 105189
-recovered pasa_asmbl_31859.p2, internal, 105729, 105850
-recovered pasa_asmbl_31859.p2, internal, 106497, 106578
Valid prediction for Augustus_model.g34564.t1
Valid prediction for GlimmerHMM_glimmerT_51711-T1
Valid prediction for Augustus_model.g34565.t1
Valid prediction for Augustus_model.g34563.t1
Valid prediction for GlimmerHMM_glimmerT_51723-T1
Valid prediction for GlimmerHMM_glimmerT_51718-T1
Valid prediction for pasa_asmbl_31850.p1
Valid prediction for CodingQuarry_transcript_35797-T1
Valid prediction for snap_scaffold_23-snap.1987-T1
Valid prediction for snap_scaffold_23-snap.1998-T1
Valid prediction for snap_scaffold_23-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_51713-T1
Valid prediction for snap_scaffold_23-snap.1979-T1
Valid prediction for Augustus_model.g34561.t1
Valid prediction for pasa_asmbl_31857.p1
Couldn't classify 46687, 46920
Sorry, prediction pasa_asmbl_31855.p1 fails validation.
(ATG)	 AC	44633-44702	GT	AGG
(GCT)	 AG	46311-46438	GT	AGG
(GCA)	 AG	46687-46920	TC	GGT
-recovered pasa_asmbl_31855.p1, initial, 44633, 44702
-recovered pasa_asmbl_31855.p1, internal, 46311, 46438
Valid prediction for GlimmerHMM_glimmerT_51717-T1
Valid prediction for CodingQuarry_transcript_35796-T1
Couldn't classify 115677, 115809
Couldn't classify 116368, 116513
Sorry, prediction pasa_asmbl_31862.p2 fails validation.
(CCA)	 GG	115677-115809	GT	GGG
(ACT)	 AG	116031-116189	GT	AGG
(ACG)	 AG	116368-116513	AC	CTA
-recovered pasa_asmbl_31862.p2, internal, 116031, 116189
Couldn't classify 113892, 113964
Sorry, prediction pasa_asmbl_31861.p1 fails validation.
(ATG)	 AG	109870-109891	GT	CGG
(GCT)	 AG	111859-112082	GT	AGG
(ACG)	 AG	112815-113004	GT	AGG
(CTC)	 AG	113338-113644	GT	ATG
(GAC)	 AG	113892-113964	AT	CCA
-recovered pasa_asmbl_31861.p1, initial, 109870, 109891
add_exon() Sorry, pasa_asmbl_31861.p1 112815-113004-terminal-3 is invalid.
-recovered pasa_asmbl_31861.p1, terminal, 112815, 113004
-recovered pasa_asmbl_31861.p1, internal, 109870, 109891
-recovered pasa_asmbl_31861.p1, internal, 111859, 112082
-recovered pasa_asmbl_31861.p1, internal, 112815, 113004
-recovered pasa_asmbl_31861.p1, internal, 113338, 113644

-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 GlimmerHMM_glimmerT_51722-T1
Valid prediction for Augustus_model.g34562.t1
Valid prediction for HiQ_model.g34560.t1
Valid prediction for snap_scaffold_23-snap.1980-T1
Valid prediction for snap_scaffold_23-snap.2002-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1986-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1985-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_51709-T1
Valid prediction for snap_scaffold_23-snap.1982-T1
Valid prediction for snap_scaffold_23-snap.1993-T1
Valid prediction for snap_scaffold_23-snap.1992-T1
Valid prediction for CodingQuarry_transcript_35795-T1
Valid prediction for GlimmerHMM_glimmerT_51714-T1
Valid prediction for snap_scaffold_23-snap.2004-T1
Valid prediction for snap_scaffold_23-snap.1997-T1
Valid prediction for snap_scaffold_23-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_51719-T1
Valid prediction for GlimmerHMM_glimmerT_51710-T1
Valid prediction for snap_scaffold_23-snap.2006-T1
Valid prediction for Augustus_model.g34566.t1
Valid prediction for snap_scaffold_23-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_51712-T1
Valid prediction for snap_scaffold_23-snap.1989-T1
Valid prediction for CodingQuarry_transcript_35794-T1
Valid prediction for GlimmerHMM_glimmerT_51715-T1
Valid prediction for snap_scaffold_23-snap.1995-T1
Valid prediction for snap_scaffold_23-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_51721-T1
Valid prediction for snap_scaffold_23-snap.2005-T1
Valid prediction for pasa_asmbl_31145.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27558, rend_intergenic: 24623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36015, rend_intergenic: 30072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43651, rend_intergenic: 39022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48147, rend_intergenic: 45579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57417, rend_intergenic: 51954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78188, rend_intergenic: 60492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88986, rend_intergenic: 78253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92515, rend_intergenic: 89025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93526, rend_intergenic: 92522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119074, rend_intergenic: 93569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139994
-exon list size: 236


building trellis

0.4    
0.8    
1.3    
1.7    
2.1    
2.5    
2.9    
3.4    
3.8    
4.2    
4.6    
5.0    
5.5    
5.9    
6.3    
6.7    
7.1    
7.6    
8.0    
8.4    
8.8    
9.2    
9.7    
10.1    
10.5    
10.9    
11.3    
11.8    
12.2    
12.6    
13.0    
13.4    
13.9    
14.3    
14.7    
15.1    
15.5    
16.0    
16.4    
16.8    
17.2    
17.6    
18.1    
18.5    
18.9    
19.3    
19.7    
20.2    
20.6    
21.0    
21.4    
21.8    
22.3    
22.7    
23.1    
23.5    
23.9    
24.4    
24.8    
25.2    
25.6    
26.1    
26.5    
26.9    
27.3    
27.7    
28.2    
28.6    
29.0    
29.4    
29.8    
30.3    
30.7    
31.1    
31.5    
31.9    
32.4    
32.8    
33.2    
33.6    
34.0    
34.5    
34.9    
35.3    
35.7    
36.1    
36.6    
37.0    
37.4    
37.8    
38.2    
38.7    
39.1    
39.5    
39.9    
40.3    
40.8    
41.2    
41.6    
42.0    
42.4    
42.9    
43.3    
43.7    
44.1    
44.5    
45.0    
45.4    
45.8    
46.2    
46.6    
47.1    
47.5    
47.9    
48.3    
48.7    
49.2    
49.6    
50.0    
50.4    
50.8    
51.3    
51.7    
52.1    
52.5    
52.9    
53.4    
53.8    
54.2    
54.6    
55.0    
55.5    
55.9    
56.3    
56.7    
57.1    
57.6    
58.0    
58.4    
58.8    
59.2    
59.7    
60.1    
60.5    
60.9    
61.3    
61.8    
62.2    
62.6    
63.0    
63.4    
63.9    
64.3    
64.7    
65.1    
65.5    
66.0    
66.4    
66.8    
67.2    
67.6    
68.1    
68.5    
68.9    
69.3    
69.7    
70.2    
70.6    
71.0    
71.4    
71.8    
72.3    
72.7    
73.1    
73.5    
73.9    
74.4    
74.8    
75.2    
75.6    
76.1    
76.5    
76.9    
77.3    
77.7    
78.2    
78.6    
79.0    
79.4    
79.8    
80.3    
80.7    
81.1    
81.5    
81.9    
82.4    
82.8    
83.2    
83.6    
84.0    
84.5    
84.9    
85.3    
85.7    
86.1    
86.6    
87.0    
87.4    
87.8    
88.2    
88.7    
89.1    
89.5    
89.9    
90.3    
90.8    
91.2    
91.6    
92.0    
92.4    
92.9    
93.3    
93.7    
94.1    
94.5    
95.0    
95.4    
95.8    
96.2    
96.6    
97.1    
97.5    
97.9    
98.3    
98.7    
99.2    
99.6    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 27558, rend_intergenic: 24623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36015, rend_intergenic: 30072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43651, rend_intergenic: 39022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48147, rend_intergenic: 45579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57417, rend_intergenic: 51954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78188, rend_intergenic: 60492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88986, rend_intergenic: 78253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92515, rend_intergenic: 89025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93526, rend_intergenic: 92522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119074, rend_intergenic: 93569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21462
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 2 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 1 - 15850
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 2 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 1 - 14484
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 2 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 119120 - 139994
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 119528 - 139994
-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
	-no exons in range 125810 - 139994