-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_10210618-10567992

-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_5-snap.1925-T1
Valid prediction for snap_scaffold_5-snap.1918-T1
Valid prediction for Augustus_model.g8284.t1
Valid prediction for Augustus_model.g8274.t1
Valid prediction for snap_scaffold_5-snap.1953-T1
Valid prediction for GlimmerHMM_glimmerT_12537-T1
Valid prediction for pasa_asmbl_45670.p1
Valid prediction for HiQ_model.g8298.t1
Valid prediction for GlimmerHMM_glimmerT_12546-T1
Valid prediction for GlimmerHMM_glimmerT_12534-T1
Valid prediction for pasa_asmbl_45675.p1
Valid prediction for snap_scaffold_5-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_12545-T1
Valid prediction for pasa_asmbl_45667.p1
Valid prediction for snap_scaffold_5-snap.1924-T1
Valid prediction for snap_scaffold_5-snap.1948-T1
Valid prediction for snap_scaffold_5-snap.1934-T1
Valid prediction for CodingQuarry_transcript_52224-T1
Valid prediction for snap_scaffold_5-snap.1947-T1
Valid prediction for pasa_asmbl_45669.p1
Valid prediction for pasa_asmbl_45681.p1
Valid prediction for pasa_asmbl_45679.p1
Valid prediction for GlimmerHMM_glimmerT_12557-T1
Valid prediction for CodingQuarry_transcript_52215-T1
Valid prediction for CodingQuarry_transcript_52210-T1
Valid prediction for CodingQuarry_transcript_52223-T1
Valid prediction for Augustus_model.g8295.t1
Valid prediction for GlimmerHMM_glimmerT_12559-T1
Valid prediction for Augustus_model.g8275.t1
Valid prediction for HiQ_model.g8271.t1
Valid prediction for snap_scaffold_5-snap.1929-T1
Valid prediction for snap_scaffold_5-snap.1937-T1
Valid prediction for Augustus_model.g8268.t1
Valid prediction for GlimmerHMM_glimmerT_12532-T1
Valid prediction for Augustus_model.g8286.t1
Valid prediction for HiQ_model.g8282.t1
Valid prediction for snap_scaffold_5-snap.1949-T1
Valid prediction for snap_scaffold_5-snap.1935-T1
Couldn't classify 67401, 67709
Sorry, prediction pasa_asmbl_45668.p1 fails validation.
(CAC)	 CC	67401-67709	CC	CCC
Valid prediction for Augustus_model.g8299.t1
Valid prediction for GlimmerHMM_glimmerT_12544-T1
Valid prediction for snap_scaffold_5-snap.1923-T1
Valid prediction for snap_scaffold_5-snap.1930-T1
Valid prediction for GlimmerHMM_glimmerT_12541-T1
Valid prediction for Augustus_model.g8281.t1
Valid prediction for GlimmerHMM_glimmerT_12549-T1
Valid prediction for HiQ_model.g8280.t1
Valid prediction for GlimmerHMM_glimmerT_12553-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_12547-T1
Valid prediction for pasa_asmbl_44331.p1
Valid prediction for CodingQuarry_transcript_52217-T1
Valid prediction for pasa_asmbl_44329.p1
Valid prediction for snap_scaffold_5-snap.1916-T1
Valid prediction for pasa_asmbl_44353.p1
Valid prediction for pasa_asmbl_44359.p1
Valid prediction for CodingQuarry_transcript_52214-T1
Valid prediction for GlimmerHMM_glimmerT_12533-T1
Valid prediction for Augustus_model.g8279.t1
Couldn't classify 205413, 205432
Sorry, prediction pasa_asmbl_44347.p1 fails validation.
(CAG)	 TT	205413-205432	GT	AGG
(GTT)	 AG	205550-205682	GT	AGG
(ATG)	 AG	205820-205924	GT	AGG
(AAA)	 AG	206058-206108	GT	GGG
(GAA)	 AG	206347-206397	GT	AGG
(CAG)	 AG	207100-207141	AA	GAA
-recovered pasa_asmbl_44347.p1, initial, 205820, 205924
-recovered pasa_asmbl_44347.p1, terminal, 207100, 207141
-recovered pasa_asmbl_44347.p1, internal, 205550, 205682
-recovered pasa_asmbl_44347.p1, internal, 205820, 205924
-recovered pasa_asmbl_44347.p1, internal, 206058, 206108
-recovered pasa_asmbl_44347.p1, internal, 206347, 206397
Valid prediction for Augustus_model.g8273.t1
Valid prediction for HiQ_model.g8272.t1
Valid prediction for Augustus_model.g8287.t1
Valid prediction for GlimmerHMM_glimmerT_12552-T1
Valid prediction for HiQ_model.g8297.t1
Valid prediction for CodingQuarry_transcript_52213-T1
Valid prediction for snap_scaffold_5-snap.1940-T1
Valid prediction for GlimmerHMM_glimmerT_12539-T1
Valid prediction for snap_scaffold_5-snap.1931-T1
Valid prediction for snap_scaffold_5-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_12555-T1
Valid prediction for snap_scaffold_5-snap.1917-T1
Valid prediction for HiQ_model.g8290.t1
Valid prediction for CodingQuarry_transcript_52219-T1
Couldn't classify 270483, 270619
Sorry, prediction pasa_asmbl_44341.p1 fails validation.
(TGG)	 TG	270483-270619	GT	AAG
(ACA)	 AG	270823-270910	GT	AGG
(TTA)	 AG	271000-271077	GT	CAG
(GTG)	 AG	271266-271470	GT	AGG
(ATA)	 AG	271583-271659	GT	AGG
(GCA)	 AG	271784-271885	GT	AGG
(AAT)	 AG	272006-272133	GT	GGG
(GTC)	 AG	272271-272316	GT	AGG
(GCT)	 AG	272474-272625	GT	ACG
(TGT)	 AG	272733-272895	CC	GAC
-recovered pasa_asmbl_44341.p1, terminal, 272733, 272895
-recovered pasa_asmbl_44341.p1, internal, 270823, 270910
-recovered pasa_asmbl_44341.p1, internal, 271000, 271077
-recovered pasa_asmbl_44341.p1, internal, 271266, 271470
-recovered pasa_asmbl_44341.p1, internal, 271583, 271659
-recovered pasa_asmbl_44341.p1, internal, 271784, 271885
-recovered pasa_asmbl_44341.p1, internal, 272006, 272133
-recovered pasa_asmbl_44341.p1, internal, 272271, 272316
-recovered pasa_asmbl_44341.p1, internal, 272474, 272625
Valid prediction for snap_scaffold_5-snap.1919-T1
Valid prediction for snap_scaffold_5-snap.1915-T1
Couldn't classify 181755, 181879
Couldn't classify 182975, 183121
Sorry, prediction CodingQuarry_transcript_52220-T1 fails validation.
(ATG)	 AG	175164-175209	GT	AGG
(CTG)	 AG	176746-176868	GT	AGG
(GGA)	 AG	176974-177113	GT	AGG
(ATG)	 AG	177230-177329	GT	GGG
(TCG)	 AG	177450-177491	GT	CTG
(CAT)	 AG	177660-177702	GT	AGG
(AGC)	 AG	177820-178006	GT	AGG
(TAT)	 AG	178171-178284	GT	AGG
(GAT)	 AG	178557-178719	GT	GAG
(TTC)	 AG	178865-179137	GT	AGG
(CTG)	 AG	179239-179646	GT	AGG
(AAC)	 AG	179790-179891	GT	TGG
(GCC)	 AG	180794-180922	GT	TGG
(GCC)	 AG	181755-181879	AT	TGA
(ACC)	 TC	182975-183121	CT	GAC
-recovered CodingQuarry_transcript_52220-T1, initial, 175164, 175209
-recovered CodingQuarry_transcript_52220-T1, initial, 177230, 177329
-recovered CodingQuarry_transcript_52220-T1, internal, 175164, 175209
-recovered CodingQuarry_transcript_52220-T1, internal, 176746, 176868
-recovered CodingQuarry_transcript_52220-T1, internal, 176974, 177113
-recovered CodingQuarry_transcript_52220-T1, internal, 177230, 177329
-recovered CodingQuarry_transcript_52220-T1, internal, 177450, 177491
-recovered CodingQuarry_transcript_52220-T1, internal, 177660, 177702
-recovered CodingQuarry_transcript_52220-T1, internal, 177820, 178006
-recovered CodingQuarry_transcript_52220-T1, internal, 178171, 178284
-recovered CodingQuarry_transcript_52220-T1, internal, 178557, 178719
-recovered CodingQuarry_transcript_52220-T1, internal, 178865, 179137
-recovered CodingQuarry_transcript_52220-T1, internal, 179239, 179646
-recovered CodingQuarry_transcript_52220-T1, internal, 179790, 179891
-recovered CodingQuarry_transcript_52220-T1, internal, 180794, 180922
Valid prediction for snap_scaffold_5-snap.1936-T1
Valid prediction for CodingQuarry_transcript_52208-T1
Valid prediction for Augustus_model.g8292.t1
Valid prediction for snap_scaffold_5-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_12535-T1
Valid prediction for GlimmerHMM_glimmerT_12538-T1
Valid prediction for snap_scaffold_5-snap.1928-T1
Valid prediction for snap_scaffold_5-snap.1945-T1
Valid prediction for GlimmerHMM_glimmerT_12548-T1
Valid prediction for snap_scaffold_5-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_12543-T1
Valid prediction for CodingQuarry_transcript_52218-T1
Valid prediction for GlimmerHMM_glimmerT_12542-T1
Valid prediction for Augustus_model.g8293.t1
Valid prediction for pasa_asmbl_44350.p1
Valid prediction for CodingQuarry_transcript_52209-T1
Valid prediction for GlimmerHMM_glimmerT_12554-T1
Valid prediction for GlimmerHMM_glimmerT_12540-T1
Valid prediction for snap_scaffold_5-snap.1932-T1
Valid prediction for HiQ_model.g8288.t1
Valid prediction for snap_scaffold_5-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_12550-T1
Valid prediction for Augustus_model.g8283.t1
Valid prediction for pasa_asmbl_44366.p1
Valid prediction for Augustus_model.g8269.t1
Valid prediction for snap_scaffold_5-snap.1927-T1
Valid prediction for snap_scaffold_5-snap.1942-T1
Valid prediction for snap_scaffold_5-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_12556-T1
Valid prediction for Augustus_model.g8278.t1
Valid prediction for GlimmerHMM_glimmerT_12551-T1
Valid prediction for snap_scaffold_5-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_12536-T1
Valid prediction for CodingQuarry_transcript_52222-T1
Valid prediction for pasa_asmbl_44335.p1
Couldn't classify 125043, 125179
Couldn't classify 127328, 127413
Sorry, prediction pasa_asmbl_44987.p1 fails validation.
(GGA)	 CA	125043-125179	GT	AGG
(ACG)	 AG	126890-127044	GT	AGG
(GAT)	 AG	127328-127413	TG	AGT
-recovered pasa_asmbl_44987.p1, internal, 126890, 127044
Valid prediction for snap_scaffold_5-snap.1943-T1
Valid prediction for snap_scaffold_5-snap.1938-T1
Valid prediction for HiQ_model.g8289.t1
Valid prediction for Augustus_model.g8277.t1
Valid prediction for snap_scaffold_5-snap.1950-T1
Valid prediction for snap_scaffold_5-snap.1946-T1
Valid prediction for snap_scaffold_5-snap.1922-T1
Valid prediction for Augustus_model.g8285.t1
Valid prediction for CodingQuarry_transcript_52216-T1
Valid prediction for CodingQuarry_transcript_52211-T1
Valid prediction for HiQ_model.g8270.t1
Valid prediction for snap_scaffold_5-snap.1939-T1
Valid prediction for HiQ_model.g8276.t1
Valid prediction for HiQ_model.g8296.t1
Valid prediction for GlimmerHMM_glimmerT_12558-T1
Valid prediction for Augustus_model.g8291.t1
Valid prediction for CodingQuarry_transcript_52221-T1
Valid prediction for snap_scaffold_5-snap.1951-T1
Valid prediction for pasa_asmbl_44351.p2
Valid prediction for Augustus_model.g8294.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 150996, rend_intergenic: 148634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 357375
-exon list size: 429


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
6.5    
6.7    
7.0    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 150996, rend_intergenic: 148634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21062
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 1 - 18576
-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 5836 - 18576
-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