-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_8598805-8778362

-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 Augustus_model.g39300.t1
Valid prediction for GlimmerHMM_glimmerT_59296-T1
Valid prediction for snap_scaffold_28-snap.1970-T1
Valid prediction for snap_scaffold_28-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_59289-T1
Valid prediction for Augustus_model.g39299.t1
Valid prediction for snap_scaffold_28-snap.1981-T1
Valid prediction for snap_scaffold_28-snap.1988-T1
Valid prediction for snap_scaffold_28-snap.1963-T1
Valid prediction for GlimmerHMM_glimmerT_59286-T1
Valid prediction for snap_scaffold_28-snap.1961-T1
Valid prediction for GlimmerHMM_glimmerT_59283-T1
Valid prediction for snap_scaffold_28-snap.1977-T1
Valid prediction for snap_scaffold_28-snap.1948-T1
Valid prediction for snap_scaffold_28-snap.1950-T1
Valid prediction for snap_scaffold_28-snap.1958-T1
Valid prediction for snap_scaffold_28-snap.1974-T1
Valid prediction for snap_scaffold_28-snap.1968-T1
Couldn't classify 166020, 167534
Sorry, prediction pasa_asmbl_37765.p1 fails validation.
(GGC)	 AC	166020-167534	CA	GAC
Valid prediction for snap_scaffold_28-snap.1984-T1
Valid prediction for snap_scaffold_28-snap.1986-T1
Valid prediction for snap_scaffold_28-snap.1985-T1
Valid prediction for snap_scaffold_28-snap.1952-T1
Valid prediction for snap_scaffold_28-snap.1946-T1
Valid prediction for snap_scaffold_28-snap.1969-T1
Valid prediction for GlimmerHMM_glimmerT_59282-T1
Valid prediction for snap_scaffold_28-snap.1951-T1
Valid prediction for GlimmerHMM_glimmerT_59285-T1
Valid prediction for GlimmerHMM_glimmerT_59297-T1
Valid prediction for snap_scaffold_28-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_59287-T1
Valid prediction for snap_scaffold_28-snap.1965-T1
Valid prediction for snap_scaffold_28-snap.1980-T1
Valid prediction for GlimmerHMM_glimmerT_59298-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_28-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_59288-T1
Valid prediction for snap_scaffold_28-snap.1957-T1
Valid prediction for CodingQuarry_transcript_43749-T1
Valid prediction for pasa_asmbl_38475.p1
Valid prediction for snap_scaffold_28-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_59290-T1
Valid prediction for GlimmerHMM_glimmerT_59299-T1
Valid prediction for snap_scaffold_28-snap.1967-T1
Valid prediction for snap_scaffold_28-snap.1956-T1
Valid prediction for Augustus_model.g39292.t1
Valid prediction for GlimmerHMM_glimmerT_59280-T1
Valid prediction for GlimmerHMM_glimmerT_59284-T1
Valid prediction for snap_scaffold_28-snap.1982-T1
Valid prediction for GlimmerHMM_glimmerT_59292-T1
Valid prediction for pasa_asmbl_38482.p1
Valid prediction for snap_scaffold_28-snap.1953-T1
Valid prediction for Augustus_model.g39296.t1
Valid prediction for snap_scaffold_28-snap.1978-T1
Valid prediction for snap_scaffold_28-snap.1955-T1
Valid prediction for Augustus_model.g39294.t1
Valid prediction for Augustus_model.g39293.t1
Valid prediction for Augustus_model.g39297.t1
Valid prediction for snap_scaffold_28-snap.1976-T1
Valid prediction for snap_scaffold_28-snap.1960-T1
Couldn't classify 92764, 92883
Couldn't classify 94610, 94660
Sorry, prediction pasa_asmbl_38478.p1 fails validation.
(TTC)	 AG	92764-92883	GT	CGG
(AAG)	 AG	93692-93857	GT	AGG
(GCC)	 AG	94326-94519	GT	AGG
(ATC)	 AG	94610-94660	GG	AGG
-recovered pasa_asmbl_38478.p1, internal, 92764, 92883
-recovered pasa_asmbl_38478.p1, internal, 93692, 93857
-recovered pasa_asmbl_38478.p1, internal, 94326, 94519
Valid prediction for snap_scaffold_28-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_59281-T1
Valid prediction for snap_scaffold_28-snap.1979-T1
Valid prediction for snap_scaffold_28-snap.1945-T1
Valid prediction for snap_scaffold_28-snap.1975-T1
Valid prediction for Augustus_model.g39291.t1
Valid prediction for snap_scaffold_28-snap.1959-T1
Valid prediction for Augustus_model.g39295.t1
Valid prediction for snap_scaffold_28-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_59295-T1
Valid prediction for Augustus_model.g39290.t1
Couldn't classify 66846, 67030
Couldn't classify 68167, 68278
Sorry, prediction pasa_asmbl_38577.p1 fails validation.
(AGT)	 GC	66846-67030	GT	AGG
(GGA)	 AG	68167-68278	AG	GGA
Valid prediction for GlimmerHMM_glimmerT_59293-T1
Valid prediction for snap_scaffold_28-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_59294-T1
Valid prediction for GlimmerHMM_glimmerT_59291-T1
Valid prediction for snap_scaffold_28-snap.1949-T1
Valid prediction for snap_scaffold_28-snap.1983-T1
Valid prediction for snap_scaffold_28-snap.1962-T1
Valid prediction for Augustus_model.g39298.t1
Couldn't classify 88345, 88541
Couldn't classify 92653, 92691
Sorry, prediction pasa_asmbl_38480.p1 fails validation.
(GCT)	 AT	88345-88541	GT	AGG
(TAG)	 AG	89244-89353	GT	AGG
(GCC)	 AG	89829-90011	GT	GGG
(CTC)	 AG	90657-90814	GT	AGG
(GAG)	 AG	91896-91973	GT	AGG
(AGG)	 AG	92653-92691	GC	GGG
-recovered pasa_asmbl_38480.p1, internal, 89244, 89353
-recovered pasa_asmbl_38480.p1, internal, 89829, 90011
-recovered pasa_asmbl_38480.p1, internal, 90657, 90814
-recovered pasa_asmbl_38480.p1, internal, 91896, 91973
-recovered pasa_asmbl_38480.p1, internal, 92653, 92691
Valid prediction for snap_scaffold_28-snap.1964-T1
Couldn't classify 95119, 95154
Couldn't classify 101809, 101969
Sorry, prediction pasa_asmbl_38476.p1 fails validation.
(ATC)	 AC	95119-95154	GT	AGG
(CCG)	 AG	95269-95354	GT	AGG
(GTT)	 AG	95514-95594	GT	GGG
(GTC)	 AG	95729-95783	GT	AGG
(CGA)	 AG	95886-96005	GT	AGG
(GAG)	 AG	96417-96534	GT	CGG
(GAG)	 AG	96698-96804	GT	AGG
(GGA)	 AG	97193-97346	GT	GGG
(GAA)	 AG	97465-97556	GT	AGG
(GCG)	 AG	98666-98878	GT	AGG
(CTG)	 AG	99036-99183	GT	AGG
(AGC)	 AG	99382-99536	GT	AGG
(GCG)	 AG	100047-100205	GT	AGG
(GCT)	 AG	100482-100661	GT	CGG
(GGA)	 AG	100944-101126	GT	GGG
(TTC)	 AG	101380-101470	GT	GGG
(TTG)	 AG	101809-101969	AC	GTA
-recovered pasa_asmbl_38476.p1, internal, 95269, 95354
-recovered pasa_asmbl_38476.p1, internal, 95514, 95594
-recovered pasa_asmbl_38476.p1, internal, 95729, 95783
-recovered pasa_asmbl_38476.p1, internal, 95886, 96005
-recovered pasa_asmbl_38476.p1, internal, 96417, 96534
-recovered pasa_asmbl_38476.p1, internal, 96698, 96804
-recovered pasa_asmbl_38476.p1, internal, 97193, 97346
-recovered pasa_asmbl_38476.p1, internal, 97465, 97556
-recovered pasa_asmbl_38476.p1, internal, 98666, 98878
-recovered pasa_asmbl_38476.p1, internal, 99036, 99183
-recovered pasa_asmbl_38476.p1, internal, 99382, 99536
-recovered pasa_asmbl_38476.p1, internal, 100047, 100205
-recovered pasa_asmbl_38476.p1, internal, 100482, 100661
-recovered pasa_asmbl_38476.p1, internal, 100944, 101126
-recovered pasa_asmbl_38476.p1, internal, 101380, 101470
Valid prediction for snap_scaffold_28-snap.1947-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12958, rend_intergenic: 10182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28390, rend_intergenic: 24748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34678, rend_intergenic: 33067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47554, rend_intergenic: 43509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67272, rend_intergenic: 66029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78274, rend_intergenic: 75587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90781, rend_intergenic: 78425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100416, rend_intergenic: 91014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106598, rend_intergenic: 100487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106697, rend_intergenic: 106683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115573, rend_intergenic: 113156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118720, rend_intergenic: 117271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123901, rend_intergenic: 118721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132227, rend_intergenic: 127688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174005, rend_intergenic: 172117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179558
-exon list size: 374


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    
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3.7    
4.0    
4.3    
4.5    
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5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
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7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
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60.1    
60.4    
60.6    
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75.0    
75.3    
75.5    
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76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
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78.5    
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79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.6    
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82.2    
82.4    
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83.2    
83.5    
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84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
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86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
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    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
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96.0    
96.3    
96.5    
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 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 12958, rend_intergenic: 10182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28390, rend_intergenic: 24748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34678, rend_intergenic: 33067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47554, rend_intergenic: 43509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67272, rend_intergenic: 66029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78274, rend_intergenic: 75587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90781, rend_intergenic: 78425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100416, rend_intergenic: 91014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106598, rend_intergenic: 100487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106697, rend_intergenic: 106683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115573, rend_intergenic: 113156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118720, rend_intergenic: 117271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123901, rend_intergenic: 118721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132227, rend_intergenic: 127688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174005, rend_intergenic: 172117  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