-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_2278663-2485669

-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 GlimmerHMM_glimmerT_50249-T1
Valid prediction for GeneMark_model.86977_t
Valid prediction for GlimmerHMM_glimmerT_50265-T1
Valid prediction for GeneMark_model.86958_t
Valid prediction for GeneMark_model.86981_t
Valid prediction for snap_scaffold_22-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_50257-T1
Valid prediction for GlimmerHMM_glimmerT_50244-T1
Valid prediction for snap_scaffold_22-snap.403-T1
Couldn't classify 96047, 96133
Sorry, prediction pasa_asmbl_29717.p1 fails validation.
(ATG)	 AG	91743-91758	GT	GGG
(ATA)	 AG	93067-93233	GT	AGG
(GGA)	 AG	95325-95483	GT	AGG
(GGC)	 AG	96047-96133	GG	GGG
-recovered pasa_asmbl_29717.p1, initial, 91743, 91758
-recovered pasa_asmbl_29717.p1, internal, 91743, 91758
-recovered pasa_asmbl_29717.p1, internal, 93067, 93233
-recovered pasa_asmbl_29717.p1, internal, 95325, 95483
Valid prediction for snap_scaffold_22-snap.401-T1
Valid prediction for GeneMark_model.86971_t
Valid prediction for GeneMark_model.86957_t
Valid prediction for GeneMark_model.86972_t
Valid prediction for GlimmerHMM_glimmerT_50263-T1
Valid prediction for snap_scaffold_22-snap.399-T1
Valid prediction for GeneMark_model.86976_t
Valid prediction for GlimmerHMM_glimmerT_50258-T1
Valid prediction for GlimmerHMM_glimmerT_50264-T1
Valid prediction for GeneMark_model.86974_t
Valid prediction for snap_scaffold_22-snap.400-T1
Valid prediction for snap_scaffold_22-snap.408-T1
Valid prediction for GeneMark_model.86966_t
Valid prediction for GlimmerHMM_glimmerT_50250-T1
Valid prediction for GeneMark_model.86962_t
Couldn't classify 96739, 96822
Couldn't classify 99267, 99314
Sorry, prediction pasa_asmbl_29231.p1 fails validation.
(AGG)	 CC	96739-96822	GT	CTG
(GCG)	 AG	97425-97553	GT	AGG
(GAT)	 AG	98505-98690	GT	AGG
(GGC)	 AG	99267-99314	AA	AGA
-recovered pasa_asmbl_29231.p1, internal, 97425, 97553
-recovered pasa_asmbl_29231.p1, internal, 98505, 98690
Couldn't classify 100941, 100968
Sorry, prediction pasa_asmbl_29232.p1 fails validation.
(GAG)	 TG	100941-100968	GT	AGG
(AAG)	 AG	101595-101669	GT	CGG
(GAG)	 AG	101911-101990	GT	TTG
(GTG)	 AG	102191-102337	GT	AGG
(GTC)	 AG	102636-102806	GT	AGG
(ATA)	 AG	103544-103741	GT	AGG
(GAC)	 AG	104502-104711	GT	CAG
(ATT)	 AG	106202-106363	GT	AGG
(GGA)	 AG	108122-108233	GT	TGG
(GGA)	 AG	108620-108818	GT	GGG
(ATC)	 AG	109453-109494	GT	GTG
(CAT)	 AG	111072-111167	GT	AGG
(GAG)	 AG	111413-111514	GT	AAG
(AGT)	 AG	111782-111959	GT	AGG
(GTG)	 AG	112740-112850	GT	GAG
(TCA)	 AG	114754-114816	GT	AGG
(ATC)	 AG	115935-116103	GT	GAG
(AGA)	 AG	117496-117692	GT	AGG
(ATC)	 AG	117897-117988	GT	AGG
(GAA)	 AG	118596-118671	GT	AGG
(GTG)	 AG	119817-119909	GT	AGG
(GAT)	 AG	120026-120100	GT	CGG
(GTC)	 AG	120240-120423	GT	CAG
(GTT)	 AG	120720-120865	GT	TGG
(GGT)	 AG	122712-122795	GT	AGG
(GTG)	 AG	123613-123806	GT	AGG
(GAG)	 AG	125018-125165	GT	AGG
(TGC)	 AG	125384-125470	GT	AGG
(ATG)	 AG	125696-125792	GT	CTG
(CAC)	 AG	125878-125918	GT	AGG
(GGT)	 AG	126007-126129	GT	AGG
(ATA)	 AG	126992-127096	GT	AGG
(GTG)	 AG	127323-127432	GT	GGG
(CCC)	 AG	127878-128001	GT	AGG
(GGG)	 AG	128444-128590	AC	AGA
-recovered pasa_asmbl_29232.p1, initial, 125696, 125792
-recovered pasa_asmbl_29232.p1, terminal, 128444, 128590
-recovered pasa_asmbl_29232.p1, internal, 101595, 101669
-recovered pasa_asmbl_29232.p1, internal, 101911, 101990
-recovered pasa_asmbl_29232.p1, internal, 102191, 102337
-recovered pasa_asmbl_29232.p1, internal, 102636, 102806
-recovered pasa_asmbl_29232.p1, internal, 103544, 103741
-recovered pasa_asmbl_29232.p1, internal, 104502, 104711
-recovered pasa_asmbl_29232.p1, internal, 106202, 106363
-recovered pasa_asmbl_29232.p1, internal, 108122, 108233
-recovered pasa_asmbl_29232.p1, internal, 108620, 108818
-recovered pasa_asmbl_29232.p1, internal, 109453, 109494
-recovered pasa_asmbl_29232.p1, internal, 111072, 111167
-recovered pasa_asmbl_29232.p1, internal, 111413, 111514
-recovered pasa_asmbl_29232.p1, internal, 111782, 111959
-recovered pasa_asmbl_29232.p1, internal, 112740, 112850
-recovered pasa_asmbl_29232.p1, internal, 114754, 114816
-recovered pasa_asmbl_29232.p1, internal, 115935, 116103
-recovered pasa_asmbl_29232.p1, internal, 117496, 117692
-recovered pasa_asmbl_29232.p1, internal, 117897, 117988
-recovered pasa_asmbl_29232.p1, internal, 118596, 118671
-recovered pasa_asmbl_29232.p1, internal, 119817, 119909
-recovered pasa_asmbl_29232.p1, internal, 120026, 120100
-recovered pasa_asmbl_29232.p1, internal, 120240, 120423
-recovered pasa_asmbl_29232.p1, internal, 120720, 120865
-recovered pasa_asmbl_29232.p1, internal, 122712, 122795
-recovered pasa_asmbl_29232.p1, internal, 123613, 123806
-recovered pasa_asmbl_29232.p1, internal, 125018, 125165
-recovered pasa_asmbl_29232.p1, internal, 125384, 125470
-recovered pasa_asmbl_29232.p1, internal, 125696, 125792
-recovered pasa_asmbl_29232.p1, internal, 125878, 125918
-recovered pasa_asmbl_29232.p1, internal, 126007, 126129
-recovered pasa_asmbl_29232.p1, internal, 126992, 127096
-recovered pasa_asmbl_29232.p1, internal, 127323, 127432
-recovered pasa_asmbl_29232.p1, internal, 127878, 128001
Valid prediction for Augustus_model.g33715.t1
Valid prediction for snap_scaffold_22-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_50252-T1
Valid prediction for snap_scaffold_22-snap.405-T1
Valid prediction for snap_scaffold_22-snap.390-T1
Valid prediction for snap_scaffold_22-snap.398-T1
Valid prediction for snap_scaffold_22-snap.387-T1
Valid prediction for CodingQuarry_transcript_34054-T1
Valid prediction for snap_scaffold_22-snap.385-T1
Valid prediction for snap_scaffold_22-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_50260-T1
Valid prediction for GlimmerHMM_glimmerT_50248-T1
Valid prediction for GeneMark_model.86968_t
Valid prediction for GeneMark_model.86965_t
Valid prediction for snap_scaffold_22-snap.389-T1
Valid prediction for snap_scaffold_22-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_50256-T1
Valid prediction for Augustus_model.g33712.t1
Valid prediction for pasa_asmbl_29238.p1

-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_22-snap.394-T1
Valid prediction for snap_scaffold_22-snap.406-T1
Valid prediction for GeneMark_model.86970_t
Valid prediction for GlimmerHMM_glimmerT_50255-T1
Valid prediction for snap_scaffold_22-snap.411-T1
Valid prediction for GeneMark_model.86960_t
Valid prediction for snap_scaffold_22-snap.388-T1
Valid prediction for Augustus_model.g33711.t1
Valid prediction for snap_scaffold_22-snap.396-T1
Valid prediction for GeneMark_model.86964_t
Valid prediction for GeneMark_model.86961_t
Valid prediction for GeneMark_model.86963_t
Valid prediction for GeneMark_model.86967_t
Valid prediction for GlimmerHMM_glimmerT_50266-T1
Valid prediction for snap_scaffold_22-snap.410-T1
Valid prediction for snap_scaffold_22-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_50254-T1
Couldn't classify 53668, 53725
Sorry, prediction pasa_asmbl_29919.p1 fails validation.
(TTC)	 CC	53668-53725	GT	GGG
(GCT)	 AG	53994-54173	GT	GGG
(ATT)	 AG	54442-54588	GT	ATG
(CTC)	 AG	54946-55130	GA	AAG
-recovered pasa_asmbl_29919.p1, terminal, 54946, 55130
-recovered pasa_asmbl_29919.p1, internal, 53994, 54173
-recovered pasa_asmbl_29919.p1, internal, 54442, 54588
Valid prediction for GlimmerHMM_glimmerT_50247-T1
Valid prediction for snap_scaffold_22-snap.409-T1
Valid prediction for Augustus_model.g33713.t1
Valid prediction for snap_scaffold_22-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_50261-T1
Valid prediction for HiQ_model.g33716.t1
Valid prediction for snap_scaffold_22-snap.382-T1
Valid prediction for pasa_asmbl_29918.p1
Valid prediction for GlimmerHMM_glimmerT_50245-T1
Valid prediction for CodingQuarry_transcript_34056-T1
Valid prediction for CodingQuarry_transcript_34055-T1
Valid prediction for snap_scaffold_22-snap.395-T1
Valid prediction for GeneMark_model.86980_t
Valid prediction for GeneMark_model.86979_t
Valid prediction for snap_scaffold_22-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_50253-T1
Valid prediction for GlimmerHMM_glimmerT_50246-T1
Valid prediction for GeneMark_model.86975_t
Valid prediction for Augustus_model.g33717.t1
Valid prediction for snap_scaffold_22-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_50259-T1
Valid prediction for GlimmerHMM_glimmerT_50251-T1
Valid prediction for GeneMark_model.86969_t
Valid prediction for Augustus_model.g33710.t1
Valid prediction for GeneMark_model.86956_t
Valid prediction for GeneMark_model.86973_t
Valid prediction for Augustus_model.g33714.t1
Valid prediction for snap_scaffold_22-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_50262-T1
Valid prediction for GeneMark_model.86959_t
Valid prediction for snap_scaffold_22-snap.391-T1
Valid prediction for snap_scaffold_22-snap.384-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30161, rend_intergenic: 27225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 66365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125176, rend_intergenic: 122010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207007
-exon list size: 421


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.4    
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5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.5    
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10.2    
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10.6    
10.9    
11.1    
11.3    
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    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.3    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
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    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.3    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 30161, rend_intergenic: 27225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 66365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125176, rend_intergenic: 122010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 191757 - 207007
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 195430 - 207007
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

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