-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_3551674-3677552

-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_25-snap.730-T1
Valid prediction for snap_scaffold_25-snap.731-T1
Valid prediction for CodingQuarry_transcript_38681-T1
Valid prediction for CodingQuarry_transcript_38678-T1
Valid prediction for GlimmerHMM_glimmerT_53880-T1
Valid prediction for snap_scaffold_25-snap.738-T1
Valid prediction for pasa_asmbl_33430.p1
Valid prediction for pasa_asmbl_33436.p1
Valid prediction for Augustus_model.g35755.t1
Valid prediction for GlimmerHMM_glimmerT_53877-T1
Valid prediction for GlimmerHMM_glimmerT_53882-T1
Valid prediction for GlimmerHMM_glimmerT_53873-T1
Couldn't classify 33527, 33712
Sorry, prediction pasa_asmbl_33431.p1 fails validation.
(TCC)	 AG	33527-33712	GT	AGG
(AAC)	 AG	33856-33947	GT	AGG
(CAG)	 AG	34243-34368	GT	AGG
(CTC)	 AG	36694-36789	GT	GAG
(GTT)	 AG	36895-36997	GT	TGG
(AAA)	 AG	38110-38217	TG	AAT
add_exon() Sorry, pasa_asmbl_33431.p1 36694-36789-terminal-1 is invalid.
-recovered pasa_asmbl_33431.p1, terminal, 36694, 36789
-recovered pasa_asmbl_33431.p1, terminal, 38110, 38217
-recovered pasa_asmbl_33431.p1, internal, 33527, 33712
-recovered pasa_asmbl_33431.p1, internal, 33856, 33947
-recovered pasa_asmbl_33431.p1, internal, 34243, 34368
-recovered pasa_asmbl_33431.p1, internal, 36694, 36789
-recovered pasa_asmbl_33431.p1, internal, 36895, 36997
Valid prediction for Augustus_model.g35759.t1
Valid prediction for GlimmerHMM_glimmerT_53885-T1
Valid prediction for snap_scaffold_25-snap.743-T1
Valid prediction for CodingQuarry_transcript_38679-T1
Valid prediction for GlimmerHMM_glimmerT_53872-T1
Valid prediction for snap_scaffold_25-snap.740-T1
Valid prediction for Augustus_model.g35749.t1
Valid prediction for CodingQuarry_transcript_38673-T1
Valid prediction for snap_scaffold_25-snap.727-T1
Valid prediction for snap_scaffold_25-snap.721-T1
Valid prediction for pasa_asmbl_33435.p1
Valid prediction for CodingQuarry_transcript_38677-T1
Valid prediction for GlimmerHMM_glimmerT_53876-T1
Valid prediction for Augustus_model.g35752.t1
Valid prediction for GlimmerHMM_glimmerT_53874-T1
Valid prediction for snap_scaffold_25-snap.741-T1
Couldn't classify 105660, 105714
Sorry, prediction pasa_asmbl_33444.p1 fails validation.
(ATC)	 TC	105660-105714	GT	AGG
(ATG)	 AG	105862-105987	GT	GGG
(ACG)	 AG	106401-106523	GT	AGG
(ACG)	 AG	106627-106749	GT	TGG
(ATG)	 AG	107064-107186	GT	TGG
(ATG)	 AG	107878-108000	GT	CGG
(ATA)	 AG	108290-108412	GT	CAG
(ATG)	 AG	109083-109208	GT	GGG
(ACG)	 AG	109426-109554	GT	GCG
(CCA)	 AG	109657-109749	GT	AGG
(CTA)	 AG	109955-110050	GT	AGG
(CCG)	 AG	110166-110261	GT	CCG
(CCC)	 AG	110377-110472	GT	AGG
(AAC)	 AG	110555-110656	GT	AGG
(CGA)	 AG	110758-110863	GT	CTG
(AAC)	 AG	111194-111310	GT	AGG
(GAT)	 AG	111449-111527	AC	GAA
add_exon() Sorry, pasa_asmbl_33444.p1 105862-105987-initial-1 is invalid.
-recovered pasa_asmbl_33444.p1, initial, 105862, 105987
add_exon() Sorry, pasa_asmbl_33444.p1 107064-107186-initial-1 is invalid.
-recovered pasa_asmbl_33444.p1, initial, 107064, 107186
-recovered pasa_asmbl_33444.p1, initial, 107878, 108000
add_exon() Sorry, pasa_asmbl_33444.p1 109083-109208-initial-1 is invalid.
-recovered pasa_asmbl_33444.p1, initial, 109083, 109208
-recovered pasa_asmbl_33444.p1, terminal, 110377, 110472
-recovered pasa_asmbl_33444.p1, terminal, 111449, 111527
-recovered pasa_asmbl_33444.p1, internal, 105862, 105987
-recovered pasa_asmbl_33444.p1, internal, 106401, 106523
-recovered pasa_asmbl_33444.p1, internal, 106627, 106749
-recovered pasa_asmbl_33444.p1, internal, 107064, 107186
-recovered pasa_asmbl_33444.p1, internal, 107878, 108000
-recovered pasa_asmbl_33444.p1, internal, 108290, 108412
-recovered pasa_asmbl_33444.p1, internal, 109083, 109208
-recovered pasa_asmbl_33444.p1, internal, 109426, 109554
-recovered pasa_asmbl_33444.p1, internal, 109657, 109749
-recovered pasa_asmbl_33444.p1, internal, 109955, 110050
-recovered pasa_asmbl_33444.p1, internal, 110166, 110261
-recovered pasa_asmbl_33444.p1, internal, 110377, 110472
-recovered pasa_asmbl_33444.p1, internal, 110555, 110656
-recovered pasa_asmbl_33444.p1, internal, 110758, 110863
-recovered pasa_asmbl_33444.p1, internal, 111194, 111310
Valid prediction for Augustus_model.g35758.t1
Valid prediction for CodingQuarry_transcript_38680-T1
Valid prediction for pasa_asmbl_33445.p1
Valid prediction for GlimmerHMM_glimmerT_53887-T1
Valid prediction for HiQ_model.g35757.t1
Valid prediction for snap_scaffold_25-snap.737-T1
Valid prediction for snap_scaffold_25-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_53889-T1
Valid prediction for GlimmerHMM_glimmerT_53884-T1
Valid prediction for snap_scaffold_25-snap.722-T1
Valid prediction for snap_scaffold_25-snap.720-T1
Valid prediction for snap_scaffold_25-snap.745-T1
Valid prediction for snap_scaffold_25-snap.724-T1
Valid prediction for snap_scaffold_25-snap.742-T1
Valid prediction for Augustus_model.g35750.t1
Valid prediction for snap_scaffold_25-snap.732-T1
Valid prediction for GlimmerHMM_glimmerT_53886-T1
Valid prediction for HiQ_model.g35762.t1
Valid prediction for snap_scaffold_25-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_53871-T1
Valid prediction for Augustus_model.g35760.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 Augustus_model.g35761.t1
Valid prediction for snap_scaffold_25-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_53883-T1
Valid prediction for HiQ_model.g35754.t1
Valid prediction for GlimmerHMM_glimmerT_53888-T1
Valid prediction for GlimmerHMM_glimmerT_53879-T1
Valid prediction for Augustus_model.g35756.t1
Valid prediction for GlimmerHMM_glimmerT_53890-T1
Valid prediction for snap_scaffold_25-snap.739-T1
Valid prediction for snap_scaffold_25-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_53881-T1
Valid prediction for GlimmerHMM_glimmerT_53875-T1
Valid prediction for pasa_asmbl_34569.p1
Valid prediction for GlimmerHMM_glimmerT_53878-T1
Valid prediction for Augustus_model.g35753.t1
Valid prediction for snap_scaffold_25-snap.744-T1
Valid prediction for CodingQuarry_transcript_38675-T1
Valid prediction for CodingQuarry_transcript_38676-T1
Couldn't classify 72369, 72495
Couldn't classify 72696, 72871
Sorry, prediction pasa_asmbl_34139.p1 fails validation.
(ACC)	 CC	72369-72495	GT	AGG
(GTG)	 AG	72696-72871	GG	AAG
Couldn't classify 6336, 6482
Couldn't classify 7090, 7184
Sorry, prediction pasa_asmbl_34144.p1 fails validation.
(CTT)	 TT	6336-6482	GT	AGG
(CTA)	 AG	6764-6926	GT	GGG
(GTG)	 AG	7090-7184	TC	AGT
-recovered pasa_asmbl_34144.p1, internal, 6764, 6926
Valid prediction for snap_scaffold_25-snap.734-T1
Valid prediction for snap_scaffold_25-snap.726-T1
Couldn't classify 122060, 122307
Sorry, prediction pasa_asmbl_34137.p2 fails validation.
(ATG)	 AA	121166-121223	GT	GTG
(ACT)	 AG	122060-122307	GT	TGG
-recovered pasa_asmbl_34137.p2, initial, 121166, 121223
-recovered pasa_asmbl_34137.p2, internal, 122060, 122307
Valid prediction for snap_scaffold_25-snap.733-T1
Valid prediction for snap_scaffold_25-snap.725-T1
Valid prediction for Augustus_model.g35751.t1
Valid prediction for snap_scaffold_25-snap.735-T1
Valid prediction for snap_scaffold_25-snap.736-T1
Valid prediction for snap_scaffold_25-snap.746-T1
Valid prediction for pasa_asmbl_34141.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12379, rend_intergenic: 5435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28837, rend_intergenic: 25171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33318, rend_intergenic: 29473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34372, rend_intergenic: 33538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49553, rend_intergenic: 47300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111527, rend_intergenic: 106605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 125879
-exon list size: 283


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.2    
10.5    
10.9    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.3    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.4    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.7    
28.1    
28.4    
28.8    
29.1    
29.5    
29.8    
30.2    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.2    
38.6    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.9    
44.2    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.8    
56.1    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.4    
61.8    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.8    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.6    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.7    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.1    
89.5    
89.8    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 12379, rend_intergenic: 5435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28837, rend_intergenic: 25171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33318, rend_intergenic: 29473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34372, rend_intergenic: 33538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49553, rend_intergenic: 47300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111527, rend_intergenic: 106605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support