-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_3670221-3888450

-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.740-T1
Valid prediction for GeneMark_model.20223_t
Valid prediction for snap_scaffold_5-snap.732-T1
Valid prediction for snap_scaffold_5-snap.733-T1
Valid prediction for GeneMark_model.20203_t
Valid prediction for GeneMark_model.20202_t
Valid prediction for GlimmerHMM_glimmerT_11983-T1
Couldn't classify 173525, 173677
Sorry, prediction pasa_asmbl_43911.p1 fails validation.
(TTT)	 TG	173525-173677	GT	AGG
(TTC)	 AG	174209-174343	GT	AAG
(GTC)	 AG	174511-174642	CC	GAC
-recovered pasa_asmbl_43911.p1, terminal, 174511, 174642
-recovered pasa_asmbl_43911.p1, internal, 174209, 174343
Valid prediction for snap_scaffold_5-snap.735-T1
Valid prediction for Augustus_model.g7877.t1
Couldn't classify 119538, 119599
Couldn't classify 119945, 120293
Sorry, prediction pasa_asmbl_43907.p1 fails validation.
(CTA)	 CG	119538-119599	GT	AGG
(TGC)	 AG	119945-120293	CC	CGC
Valid prediction for snap_scaffold_5-snap.726-T1
Valid prediction for GeneMark_model.20224_t
Valid prediction for snap_scaffold_5-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_11992-T1
Valid prediction for snap_scaffold_5-snap.752-T1
Valid prediction for snap_scaffold_5-snap.737-T1
Couldn't classify 193463, 193705
Couldn't classify 194454, 194729
Sorry, prediction pasa_asmbl_43916.p1 fails validation.
(GGA)	 TG	193463-193705	GT	CGG
(TGT)	 AG	193897-194076	GT	ATG
(AAT)	 AG	194454-194729	GT	ATG
-recovered pasa_asmbl_43916.p1, internal, 193897, 194076
-recovered pasa_asmbl_43916.p1, internal, 194454, 194729
Valid prediction for GeneMark_model.20214_t
Valid prediction for GeneMark_model.20229_t
Valid prediction for snap_scaffold_5-snap.751-T1
Valid prediction for pasa_asmbl_43915.p1
Valid prediction for GeneMark_model.20226_t
Valid prediction for snap_scaffold_5-snap.728-T1
Valid prediction for HiQ_model.g7880.t1
Valid prediction for GeneMark_model.20205_t
Valid prediction for Augustus_model.g7887.t1
Valid prediction for Augustus_model.g7886.t1
Couldn't classify 101229, 101366
Sorry, prediction pasa_asmbl_43902.p1 fails validation.
(GCG)	 TA	101229-101366	GT	AAG
(GAG)	 AG	101811-101981	GT	TGG
(ATA)	 AG	102635-102718	GT	CGG
(GCC)	 AG	103913-104105	GT	GGG
(TGG)	 AG	104604-104740	GT	ATG
(TCT)	 AG	105268-105438	AG	AGA
-recovered pasa_asmbl_43902.p1, terminal, 105268, 105438
-recovered pasa_asmbl_43902.p1, internal, 101811, 101981
-recovered pasa_asmbl_43902.p1, internal, 102635, 102718
-recovered pasa_asmbl_43902.p1, internal, 103913, 104105
-recovered pasa_asmbl_43902.p1, internal, 104604, 104740
Valid prediction for GlimmerHMM_glimmerT_11987-T1
Couldn't classify 194787, 195143
Sorry, prediction pasa_asmbl_43917.p1 fails validation.
(GAG)	 GG	194787-195143	CT	GAC
Valid prediction for snap_scaffold_5-snap.750-T1
Valid prediction for CodingQuarry_transcript_51887-T1
Valid prediction for snap_scaffold_5-snap.765-T1
Valid prediction for HiQ_model.g7889.t1
Valid prediction for snap_scaffold_5-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_11988-T1
Valid prediction for GeneMark_model.20194_t
Valid prediction for GlimmerHMM_glimmerT_11984-T1
Valid prediction for GlimmerHMM_glimmerT_11995-T1
Valid prediction for GlimmerHMM_glimmerT_11976-T1
Valid prediction for GlimmerHMM_glimmerT_11994-T1
Valid prediction for pasa_asmbl_43906.p1
Valid prediction for snap_scaffold_5-snap.742-T1
Valid prediction for snap_scaffold_5-snap.727-T1
Valid prediction for Augustus_model.g7873.t1
Valid prediction for GlimmerHMM_glimmerT_11985-T1
Valid prediction for snap_scaffold_5-snap.730-T1
Valid prediction for Augustus_model.g7888.t1
Valid prediction for CodingQuarry_transcript_51885-T1
Valid prediction for GeneMark_model.20228_t
Valid prediction for GeneMark_model.20208_t
Valid prediction for snap_scaffold_5-snap.753-T1
Valid prediction for Augustus_model.g7891.t1
Valid prediction for GeneMark_model.20218_t
Valid prediction for Augustus_model.g7876.t1
Valid prediction for snap_scaffold_5-snap.761-T1
Valid prediction for pasa_asmbl_43912.p1
Valid prediction for GeneMark_model.20199_t
Valid prediction for snap_scaffold_5-snap.731-T1
Valid prediction for GeneMark_model.20213_t
Valid prediction for GlimmerHMM_glimmerT_11978-T1
Valid prediction for GeneMark_model.20206_t
Valid prediction for GlimmerHMM_glimmerT_11981-T1
Valid prediction for snap_scaffold_5-snap.759-T1
Valid prediction for GeneMark_model.20230_t
Valid prediction for GeneMark_model.20232_t
Valid prediction for GlimmerHMM_glimmerT_11993-T1
Valid prediction for snap_scaffold_5-snap.762-T1
Valid prediction for snap_scaffold_5-snap.763-T1
Valid prediction for GeneMark_model.20190_t
Valid prediction for snap_scaffold_5-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_11996-T1
Valid prediction for snap_scaffold_5-snap.756-T1
Valid prediction for snap_scaffold_5-snap.767-T1
Valid prediction for snap_scaffold_5-snap.736-T1
Valid prediction for Augustus_model.g7879.t1
Valid prediction for Augustus_model.g7884.t1
Valid prediction for Augustus_model.g7882.t1
Valid prediction for snap_scaffold_5-snap.741-T1
Valid prediction for Augustus_model.g7890.t1
Valid prediction for GlimmerHMM_glimmerT_11979-T1
Valid prediction for CodingQuarry_transcript_51886-T1
Valid prediction for GeneMark_model.20209_t
Valid prediction for GlimmerHMM_glimmerT_11989-T1
Valid prediction for GeneMark_model.20220_t
Valid prediction for Augustus_model.g7883.t1
Valid prediction for snap_scaffold_5-snap.760-T1
Valid prediction for GeneMark_model.20197_t
Valid prediction for HiQ_model.g7878.t1
Valid prediction for GeneMark_model.20211_t
Valid prediction for snap_scaffold_5-snap.766-T1
Couldn't classify 189269, 189976
Sorry, prediction pasa_asmbl_43914.p1 fails validation.
(TCT)	 CA	189269-189976	AA	TGA
Valid prediction for snap_scaffold_5-snap.746-T1
Valid prediction for snap_scaffold_5-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_11991-T1
Valid prediction for GeneMark_model.20212_t
Valid prediction for GeneMark_model.20216_t
Valid prediction for Augustus_model.g7874.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_11986-T1
Valid prediction for GeneMark_model.20207_t
Valid prediction for snap_scaffold_5-snap.745-T1
Valid prediction for Augustus_model.g7885.t1
Valid prediction for GeneMark_model.20225_t
Valid prediction for GlimmerHMM_glimmerT_11982-T1
Valid prediction for snap_scaffold_5-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_11980-T1
Valid prediction for snap_scaffold_5-snap.749-T1
Valid prediction for GeneMark_model.20222_t
Valid prediction for snap_scaffold_5-snap.747-T1
Valid prediction for GeneMark_model.20201_t
Valid prediction for GeneMark_model.20193_t
Valid prediction for GeneMark_model.20217_t
Valid prediction for GeneMark_model.20215_t
Valid prediction for GeneMark_model.20210_t
Valid prediction for snap_scaffold_5-snap.755-T1
Valid prediction for GeneMark_model.20191_t
Valid prediction for GlimmerHMM_glimmerT_11977-T1
Valid prediction for GeneMark_model.20227_t
Valid prediction for GeneMark_model.20204_t
Valid prediction for Augustus_model.g7875.t1
Valid prediction for GeneMark_model.20192_t
Couldn't classify 200897, 201208
Sorry, prediction pasa_asmbl_43900.p3 fails validation.
(TGT)	 GT	200897-201208	AA	GAA
Valid prediction for GeneMark_model.20221_t
Valid prediction for snap_scaffold_5-snap.729-T1
Valid prediction for snap_scaffold_5-snap.739-T1
Valid prediction for snap_scaffold_5-snap.754-T1
Valid prediction for GeneMark_model.20196_t
Valid prediction for GeneMark_model.20200_t
Valid prediction for GeneMark_model.20231_t
Valid prediction for snap_scaffold_5-snap.748-T1
Valid prediction for GeneMark_model.20195_t
Valid prediction for GeneMark_model.20198_t
Valid prediction for snap_scaffold_5-snap.738-T1
Valid prediction for Augustus_model.g7881.t1
Valid prediction for GlimmerHMM_glimmerT_11990-T1
Valid prediction for snap_scaffold_5-snap.734-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20672, rend_intergenic: 12449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60987, rend_intergenic: 57547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75619, rend_intergenic: 68401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100782, rend_intergenic: 98714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105438, rend_intergenic: 101727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153450, rend_intergenic: 145690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155478, rend_intergenic: 154668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218230
-exon list size: 586


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.6    
2.7    
2.9    
3.1    
3.2    
3.4    
3.6    
3.7    
3.9    
4.1    
4.3    
4.4    
4.6    
4.8    
4.9    
5.1    
5.3    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.6    
6.8    
7.0    
7.1    
7.3    
7.5    
7.7    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.1    
11.2    
11.4    
11.6    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.1    
15.3    
15.5    
15.6    
15.8    
16.0    
16.2    
16.3    
16.5    
16.7    
16.8    
17.0    
17.2    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.3    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.4    
22.6    
22.8    
23.0    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 20672, rend_intergenic: 12449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60987, rend_intergenic: 57547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75619, rend_intergenic: 68401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100782, rend_intergenic: 98714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105438, rend_intergenic: 101727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153450, rend_intergenic: 145690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155478, rend_intergenic: 154668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200522 - 218230
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 200522 - 215162
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 200522 - 214121
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 200522 - 212332
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 201544 - 212332
-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
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 201595 - 212332
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 201595 - 212140
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 201595 - 211765
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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