-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_9107481-9301031

-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 CodingQuarry_transcript_32690-T1
Valid prediction for snap_scaffold_21-snap.1975-T1
Valid prediction for snap_scaffold_21-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_48329-T1
Valid prediction for snap_scaffold_21-snap.1987-T1
Valid prediction for snap_scaffold_21-snap.1986-T1
Valid prediction for Augustus_model.g32298.t1
Valid prediction for GlimmerHMM_glimmerT_48337-T1
Valid prediction for GlimmerHMM_glimmerT_48343-T1
Valid prediction for snap_scaffold_21-snap.1991-T1
Valid prediction for Augustus_model.g32299.t1
Valid prediction for snap_scaffold_21-snap.1996-T1
Valid prediction for Augustus_model.g32297.t1
Valid prediction for pasa_asmbl_28841.p1
Valid prediction for snap_scaffold_21-snap.1994-T1
Valid prediction for snap_scaffold_21-snap.1988-T1
Valid prediction for snap_scaffold_21-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_48341-T1
Valid prediction for GlimmerHMM_glimmerT_48334-T1
Valid prediction for snap_scaffold_21-snap.2003-T1
Valid prediction for HiQ_model.g32295.t1
Valid prediction for snap_scaffold_21-snap.1979-T1
Valid prediction for Augustus_model.g32290.t1
Valid prediction for snap_scaffold_21-snap.1966-T1
Valid prediction for snap_scaffold_21-snap.1985-T1
Valid prediction for snap_scaffold_21-snap.1999-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 GlimmerHMM_glimmerT_48342-T1
Valid prediction for snap_scaffold_21-snap.1963-T1
Valid prediction for snap_scaffold_21-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_48328-T1
Valid prediction for Augustus_model.g32285.t1
Couldn't classify 110321, 110430
Sorry, prediction pasa_asmbl_27958.p1 fails validation.
(TTG)	 GG	110321-110430	GT	GGG
(CAA)	 AG	112299-112377	GT	TGG
(GAG)	 AG	112510-112671	CA	AGC
-recovered pasa_asmbl_27958.p1, terminal, 112510, 112671
-recovered pasa_asmbl_27958.p1, internal, 112299, 112377
Valid prediction for Augustus_model.g32293.t1
Valid prediction for snap_scaffold_21-snap.1995-T1
Valid prediction for snap_scaffold_21-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_48327-T1
Valid prediction for GlimmerHMM_glimmerT_48336-T1
Valid prediction for GlimmerHMM_glimmerT_48345-T1
Valid prediction for snap_scaffold_21-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_48344-T1
Couldn't classify 110066, 110160
Sorry, prediction GlimmerHMM_glimmerT_48331-T1 fails validation.
(ATG)	 AT	104690-104728	GT	TGG
(AAC)	 AG	106487-106549	GT	AGG
(ATC)	 AG	107048-107267	GT	TGG
(CTC)	 AG	107470-107656	GT	TGG
(GGA)	 AG	107910-108000	GT	AGG
(ACC)	 AG	108308-108445	GT	AGG
(ATC)	 AG	108544-108662	GT	AGG
(GGT)	 AG	108928-109218	GT	GGG
(AGC)	 AG	109313-109505	GT	TGG
(GTG)	 AG	110066-110160	NT	AGN
(GTT)	 AG	110320-110430	GT	GGG
(CAA)	 AG	110859-110937	GT	TGG
(GAG)	 AG	111070-111231	CA	AGC
-recovered GlimmerHMM_glimmerT_48331-T1, initial, 104690, 104728
-recovered GlimmerHMM_glimmerT_48331-T1, terminal, 111070, 111231
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 106487, 106549
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 107048, 107267
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 107470, 107656
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 107910, 108000
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 108308, 108445
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 108544, 108662
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 108928, 109218
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 109313, 109505
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 110320, 110430
-recovered GlimmerHMM_glimmerT_48331-T1, internal, 110859, 110937
Valid prediction for Augustus_model.g32288.t1
Couldn't classify 110066, 110158
Sorry, prediction pasa_asmbl_28168.p1 fails validation.
(ATG)	 AT	104690-104728	GT	TGG
(AAC)	 AG	106487-106549	GT	AGG
(ATC)	 AG	107048-107267	GT	TGG
(CTC)	 AG	107470-107656	GT	TGG
(GGA)	 AG	107910-108000	GT	AGG
(ACC)	 AG	108308-108445	GT	AGG
(ATC)	 AG	108544-108662	GT	AGG
(GGT)	 AG	108928-109177	GC	AGG
(GTG)	 AG	110066-110158	AG	TCA
-recovered pasa_asmbl_28168.p1, initial, 104690, 104728
-recovered pasa_asmbl_28168.p1, internal, 106487, 106549
-recovered pasa_asmbl_28168.p1, internal, 107048, 107267
-recovered pasa_asmbl_28168.p1, internal, 107470, 107656
-recovered pasa_asmbl_28168.p1, internal, 107910, 108000
-recovered pasa_asmbl_28168.p1, internal, 108308, 108445
-recovered pasa_asmbl_28168.p1, internal, 108544, 108662
-recovered pasa_asmbl_28168.p1, internal, 108928, 109177
Valid prediction for Augustus_model.g32296.t1
Valid prediction for snap_scaffold_21-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_48326-T1
Valid prediction for GlimmerHMM_glimmerT_48324-T1
Valid prediction for GlimmerHMM_glimmerT_48323-T1
Valid prediction for snap_scaffold_21-snap.1964-T1
Valid prediction for snap_scaffold_21-snap.1977-T1
Valid prediction for snap_scaffold_21-snap.1972-T1
Valid prediction for snap_scaffold_21-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_48339-T1
Valid prediction for GlimmerHMM_glimmerT_48340-T1
Valid prediction for snap_scaffold_21-snap.2000-T1
Valid prediction for Augustus_model.g32294.t1
Valid prediction for CodingQuarry_transcript_32689-T1
Valid prediction for GlimmerHMM_glimmerT_48335-T1
Valid prediction for snap_scaffold_21-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_48338-T1
Valid prediction for Augustus_model.g32289.t1
Valid prediction for snap_scaffold_21-snap.1974-T1
Couldn't classify 184293, 184482
Couldn't classify 185022, 185212
Sorry, prediction pasa_asmbl_28187.p1 fails validation.
(TAT)	 CG	184293-184482	GT	AGG
(GTG)	 AG	185022-185212	CA	CCC
Valid prediction for pasa_asmbl_27959.p1
Valid prediction for snap_scaffold_21-snap.1984-T1
Valid prediction for snap_scaffold_21-snap.1992-T1
Valid prediction for snap_scaffold_21-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_48330-T1
Valid prediction for GlimmerHMM_glimmerT_48325-T1
Valid prediction for snap_scaffold_21-snap.1969-T1
Valid prediction for snap_scaffold_21-snap.1973-T1
Valid prediction for snap_scaffold_21-snap.1978-T1
Valid prediction for Augustus_model.g32287.t1
Valid prediction for snap_scaffold_21-snap.1980-T1
Valid prediction for snap_scaffold_21-snap.1967-T1
Valid prediction for HiQ_model.g32292.t1
Valid prediction for Augustus_model.g32291.t1
Valid prediction for snap_scaffold_21-snap.1965-T1
Valid prediction for Augustus_model.g32286.t1
Valid prediction for snap_scaffold_21-snap.1998-T1
Valid prediction for GlimmerHMM_glimmerT_48332-T1
Valid prediction for snap_scaffold_21-snap.1989-T1
Valid prediction for GlimmerHMM_glimmerT_48333-T1
Valid prediction for snap_scaffold_21-snap.1961-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1981-T1
Valid prediction for GlimmerHMM_glimmerT_48322-T1
Valid prediction for snap_scaffold_21-snap.1982-T1
Valid prediction for Augustus_model.g32284.t1
Valid prediction for snap_scaffold_21-snap.1976-T1
Valid prediction for snap_scaffold_21-snap.1971-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57950, rend_intergenic: 53843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139224, rend_intergenic: 133295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173200, rend_intergenic: 169117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182192, rend_intergenic: 179860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193551
-exon list size: 305


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
2.9    
3.3    
3.6    
3.9    
4.2    
4.6    
4.9    
5.2    
5.5    
5.9    
6.2    
6.5    
6.8    
7.2    
7.5    
7.8    
8.1    
8.5    
8.8    
9.1    
9.4    
9.8    
10.1    
10.4    
10.7    
11.1    
11.4    
11.7    
12.1    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.3    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.2    
18.6    
18.9    
19.2    
19.5    
19.9    
20.2    
20.5    
20.8    
21.2    
21.5    
21.8    
22.1    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.1    
26.4    
26.7    
27.0    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
30.0    
30.3    
30.6    
30.9    
31.3    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.5    
34.9    
35.2    
35.5    
35.8    
36.2    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.4    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.7    
43.0    
43.3    
43.6    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.3    
46.6    
46.9    
47.2    
47.6    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.4    
52.8    
53.1    
53.4    
53.7    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.4    
56.7    
57.0    
57.3    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.6    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.8    
64.2    
64.5    
64.8    
65.1    
65.5    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.7    
69.1    
69.4    
69.7    
70.0    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
73.9    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.9    
78.2    
78.5    
78.8    
79.2    
79.5    
79.8    
80.1    
80.5    
80.8    
81.1    
81.4    
81.8    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.7    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
87.9    
88.3    
88.6    
88.9    
89.3    
89.6    
89.9    
90.2    
90.6    
90.9    
91.2    
91.5    
91.9    
92.2    
92.5    
92.8    
93.2    
93.5    
93.8    
94.1    
94.5    
94.8    
95.1    
95.4    
95.8    
96.1    
96.4    
96.7    
97.1    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 57950, rend_intergenic: 53843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139224, rend_intergenic: 133295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173200, rend_intergenic: 169117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182192, rend_intergenic: 179860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support