-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_8894727-9068350

-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_4-snap.1901-T1
Couldn't classify 46556, 46662
Couldn't classify 47469, 47489
Sorry, prediction pasa_asmbl_42210.p1 fails validation.
(GCC)	 AT	46556-46662	GT	TCG
(GGA)	 AG	46834-47029	GT	AGG
(GCC)	 AG	47152-47229	GT	GGG
(GTT)	 AG	47469-47489	TG	ACT
-recovered pasa_asmbl_42210.p1, internal, 46834, 47029
-recovered pasa_asmbl_42210.p1, internal, 47152, 47229
Valid prediction for GlimmerHMM_glimmerT_9851-T1
Valid prediction for GlimmerHMM_glimmerT_9852-T1
Valid prediction for snap_scaffold_4-snap.1897-T1
Valid prediction for Augustus_model.g6407.t1
Valid prediction for GlimmerHMM_glimmerT_9864-T1
Valid prediction for snap_scaffold_4-snap.1882-T1
Valid prediction for snap_scaffold_4-snap.1876-T1
Valid prediction for Augustus_model.g6413.t1
Valid prediction for snap_scaffold_4-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_9855-T1
Valid prediction for snap_scaffold_4-snap.1877-T1
Valid prediction for snap_scaffold_4-snap.1904-T1
Valid prediction for GlimmerHMM_glimmerT_9860-T1
Valid prediction for snap_scaffold_4-snap.1889-T1
Couldn't classify 86719, 86878
Couldn't classify 89597, 89718
Sorry, prediction pasa_asmbl_41599.p1 fails validation.
(GGT)	 CA	86719-86878	GT	TGG
(TCA)	 AG	87000-87154	GT	AGG
(GGT)	 AG	87266-87394	GT	GAG
(CTG)	 AG	87543-87737	GT	AGG
(GAA)	 AG	88765-88894	GT	AGG
(GAG)	 AG	89258-89431	GT	CGG
(CCC)	 AG	89597-89718	AG	GCA
-recovered pasa_asmbl_41599.p1, internal, 87000, 87154
-recovered pasa_asmbl_41599.p1, internal, 87266, 87394
-recovered pasa_asmbl_41599.p1, internal, 87543, 87737
-recovered pasa_asmbl_41599.p1, internal, 88765, 88894
-recovered pasa_asmbl_41599.p1, internal, 89258, 89431
Valid prediction for snap_scaffold_4-snap.1899-T1
Valid prediction for snap_scaffold_4-snap.1903-T1
Valid prediction for snap_scaffold_4-snap.1873-T1
Valid prediction for HiQ_model.g6408.t1
Valid prediction for GlimmerHMM_glimmerT_9861-T1
Valid prediction for snap_scaffold_4-snap.1875-T1
Valid prediction for snap_scaffold_4-snap.1884-T1
Valid prediction for snap_scaffold_4-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_9853-T1
Valid prediction for snap_scaffold_4-snap.1898-T1
Valid prediction for snap_scaffold_4-snap.1896-T1
Valid prediction for snap_scaffold_4-snap.1879-T1
Valid prediction for CodingQuarry_transcript_49096-T1
Valid prediction for snap_scaffold_4-snap.1878-T1
Couldn't classify 48980, 49087
Couldn't classify 52317, 52481
Sorry, prediction pasa_asmbl_41594.p1 fails validation.
(ACC)	 GA	48980-49087	GT	AGG
(CCA)	 AG	51474-51542	GT	AGG
(ACC)	 AG	52317-52481	AG	CCA
-recovered pasa_asmbl_41594.p1, internal, 51474, 51542
Valid prediction for Augustus_model.g6409.t1
Valid prediction for Augustus_model.g6405.t1
Valid prediction for CodingQuarry_transcript_49095-T1
Valid prediction for GlimmerHMM_glimmerT_9854-T1
Valid prediction for Augustus_model.g6412.t1
Valid prediction for Augustus_model.g6406.t1
Valid prediction for snap_scaffold_4-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_9859-T1
Valid prediction for GlimmerHMM_glimmerT_9862-T1
Valid prediction for snap_scaffold_4-snap.1871-T1
Valid prediction for pasa_asmbl_41598.p1
Valid prediction for CodingQuarry_transcript_49097-T1
Valid prediction for GlimmerHMM_glimmerT_9850-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_4-snap.1894-T1
Valid prediction for Augustus_model.g6410.t1
Valid prediction for snap_scaffold_4-snap.1885-T1
Valid prediction for snap_scaffold_4-snap.1887-T1
Valid prediction for GlimmerHMM_glimmerT_9856-T1
Valid prediction for GlimmerHMM_glimmerT_9847-T1
Valid prediction for GlimmerHMM_glimmerT_9857-T1
Valid prediction for GlimmerHMM_glimmerT_9866-T1
Valid prediction for CodingQuarry_transcript_49094-T1
Valid prediction for CodingQuarry_transcript_49093-T1
Valid prediction for GlimmerHMM_glimmerT_9849-T1
Valid prediction for Augustus_model.g6411.t1
Valid prediction for snap_scaffold_4-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_9846-T1
Valid prediction for pasa_asmbl_42796.p1
Valid prediction for snap_scaffold_4-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_9863-T1
Valid prediction for GlimmerHMM_glimmerT_9858-T1
Valid prediction for snap_scaffold_4-snap.1891-T1
Valid prediction for Augustus_model.g6414.t1
Valid prediction for snap_scaffold_4-snap.1892-T1
Valid prediction for HiQ_model.g6403.t1
Valid prediction for snap_scaffold_4-snap.1886-T1
Valid prediction for snap_scaffold_4-snap.1883-T1
Valid prediction for snap_scaffold_4-snap.1905-T1
Valid prediction for snap_scaffold_4-snap.1869-T1
Valid prediction for snap_scaffold_4-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_9848-T1
Valid prediction for GlimmerHMM_glimmerT_9865-T1
Valid prediction for Augustus_model.g6402.t1
Valid prediction for pasa_asmbl_42797.p1
Valid prediction for snap_scaffold_4-snap.1867-T1
Valid prediction for snap_scaffold_4-snap.1895-T1
Valid prediction for snap_scaffold_4-snap.1874-T1
Valid prediction for snap_scaffold_4-snap.1868-T1
Valid prediction for snap_scaffold_4-snap.1888-T1
Valid prediction for snap_scaffold_4-snap.1890-T1
Valid prediction for snap_scaffold_4-snap.1900-T1
Valid prediction for Augustus_model.g6404.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22179, rend_intergenic: 18368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37039, rend_intergenic: 32673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70274, rend_intergenic: 66177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81059, rend_intergenic: 76667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89742, rend_intergenic: 86734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111181, rend_intergenic: 106263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173624
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
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2.0    
2.3    
2.6    
2.9    
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3.8    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 22179, rend_intergenic: 18368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37039, rend_intergenic: 32673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70274, rend_intergenic: 66177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81059, rend_intergenic: 76667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89742, rend_intergenic: 86734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111181, rend_intergenic: 106263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 161820 - 173624
-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 161920 - 173624
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support