-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_7327499-7645089

-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 Augustus_model.g17122.t1
Valid prediction for GlimmerHMM_glimmerT_25490-T1
Valid prediction for GeneMark_model.43572_t
Valid prediction for snap_scaffold_10-snap.1512-T1
Valid prediction for GeneMark_model.43574_t
Valid prediction for Augustus_model.g17112.t1
Valid prediction for snap_scaffold_10-snap.1516-T1
Valid prediction for GeneMark_model.43573_t
Valid prediction for GeneMark_model.43575_t
Couldn't classify 158428, 158781
Sorry, prediction pasa_asmbl_4557.p1 fails validation.
(GCC)	 GA	158428-158781	GA	AGG
Couldn't classify 170154, 170277
Sorry, prediction pasa_asmbl_4559.p1 fails validation.
(TGC)	 AC	170154-170277	GT	AGG
(GTG)	 AG	170512-170643	GT	TGG
(ACG)	 AG	171098-171255	GT	AGG
(ATC)	 AG	172199-172673	GT	AGG
(GCT)	 AG	172821-172974	GT	CGG
(ATG)	 AG	173524-173634	GT	AGG
(GTG)	 AG	173782-174425	GT	CGG
(CTA)	 AG	174547-174684	GT	TGG
(AGT)	 AG	176737-176772	GT	AGG
(GCT)	 AG	177614-178269	CA	GAC
add_exon() Sorry, pasa_asmbl_4559.p1 173524-173634-initial-1 is invalid.
-recovered pasa_asmbl_4559.p1, initial, 173524, 173634
-recovered pasa_asmbl_4559.p1, terminal, 177614, 178269
-recovered pasa_asmbl_4559.p1, internal, 170512, 170643
-recovered pasa_asmbl_4559.p1, internal, 171098, 171255
-recovered pasa_asmbl_4559.p1, internal, 172199, 172673
-recovered pasa_asmbl_4559.p1, internal, 172821, 172974
-recovered pasa_asmbl_4559.p1, internal, 173524, 173634
-recovered pasa_asmbl_4559.p1, internal, 173782, 174425
-recovered pasa_asmbl_4559.p1, internal, 174547, 174684
-recovered pasa_asmbl_4559.p1, internal, 176737, 176772
Valid prediction for GeneMark_model.43550_t
Valid prediction for GlimmerHMM_glimmerT_25493-T1
Valid prediction for GlimmerHMM_glimmerT_25488-T1
Valid prediction for snap_scaffold_10-snap.1522-T1
Valid prediction for snap_scaffold_10-snap.1509-T1
Valid prediction for snap_scaffold_10-snap.1524-T1
Valid prediction for GlimmerHMM_glimmerT_25478-T1
Valid prediction for GeneMark_model.43549_t
Valid prediction for snap_scaffold_10-snap.1513-T1
Valid prediction for GlimmerHMM_glimmerT_25487-T1
Valid prediction for snap_scaffold_10-snap.1517-T1
Valid prediction for Augustus_model.g17113.t1
Valid prediction for snap_scaffold_10-snap.1523-T1
Valid prediction for snap_scaffold_10-snap.1514-T1
Valid prediction for Augustus_model.g17114.t1
Couldn't classify 164533, 164841
Sorry, prediction pasa_asmbl_5130.p1 fails validation.
(CTG)	 TC	164533-164841	GA	GGG
Valid prediction for Augustus_model.g17117.t1
Valid prediction for GeneMark_model.43558_t
Valid prediction for snap_scaffold_10-snap.1506-T1
Couldn't classify 167705, 167812
Couldn't classify 169255, 169566
Sorry, prediction pasa_asmbl_4558.p1 fails validation.
(GTG)	 TG	167705-167812	GT	AGG
(GTA)	 AG	169255-169566	AC	TGA
Valid prediction for snap_scaffold_10-snap.1508-T1
Valid prediction for GeneMark_model.43560_t
Valid prediction for GlimmerHMM_glimmerT_25497-T1
Valid prediction for snap_scaffold_10-snap.1507-T1
Valid prediction for GeneMark_model.43556_t
Valid prediction for Augustus_model.g17121.t1
Valid prediction for GeneMark_model.43562_t
Valid prediction for snap_scaffold_10-snap.1510-T1
Valid prediction for Augustus_model.g17116.t1
Valid prediction for GeneMark_model.43552_t
Valid prediction for GeneMark_model.43578_t
Valid prediction for GlimmerHMM_glimmerT_25489-T1
Valid prediction for snap_scaffold_10-snap.1511-T1
Valid prediction for GeneMark_model.43564_t
Valid prediction for GlimmerHMM_glimmerT_25483-T1
Valid prediction for GeneMark_model.43553_t
Valid prediction for snap_scaffold_10-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_25485-T1
Valid prediction for GlimmerHMM_glimmerT_25491-T1
Valid prediction for GeneMark_model.43569_t
Valid prediction for GeneMark_model.43566_t
Valid prediction for GlimmerHMM_glimmerT_25484-T1
Valid prediction for GeneMark_model.43567_t
Valid prediction for GeneMark_model.43555_t
Valid prediction for GlimmerHMM_glimmerT_25486-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_25482-T1
Valid prediction for pasa_asmbl_3460.p2
Valid prediction for GlimmerHMM_glimmerT_25479-T1
Valid prediction for GeneMark_model.43561_t
Valid prediction for GeneMark_model.43582_t
Valid prediction for GeneMark_model.43571_t
Valid prediction for snap_scaffold_10-snap.1504-T1
Valid prediction for Augustus_model.g17120.t1
Couldn't classify 35424, 36131
Sorry, prediction pasa_asmbl_3463.p1 fails validation.
(AAA)	 GG	35424-36131	AT	AGA
Valid prediction for GeneMark_model.43577_t
Valid prediction for GlimmerHMM_glimmerT_25492-T1
Couldn't classify 34426, 34653
Couldn't classify 35049, 35147
Sorry, prediction pasa_asmbl_3464.p1 fails validation.
(CTG)	 CT	34426-34653	GT	AGG
(AGC)	 AG	35049-35147	AA	ACA
Valid prediction for GeneMark_model.43581_t
Valid prediction for GlimmerHMM_glimmerT_25495-T1
Valid prediction for GlimmerHMM_glimmerT_25494-T1
Valid prediction for GeneMark_model.43580_t
Valid prediction for Augustus_model.g17118.t1
Valid prediction for GeneMark_model.43579_t
Valid prediction for snap_scaffold_10-snap.1518-T1
Valid prediction for GeneMark_model.43568_t
Valid prediction for GlimmerHMM_glimmerT_25496-T1
Valid prediction for GeneMark_model.43563_t
Valid prediction for GeneMark_model.43548_t
Valid prediction for GeneMark_model.43583_t
Valid prediction for GeneMark_model.43557_t
Valid prediction for CodingQuarry_transcript_5454-T1
Valid prediction for snap_scaffold_10-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_25480-T1
Valid prediction for GeneMark_model.43565_t
Valid prediction for GeneMark_model.43559_t
Valid prediction for Augustus_model.g17115.t1
Valid prediction for GlimmerHMM_glimmerT_25481-T1
Valid prediction for HiQ_model.g17119.t1
Valid prediction for snap_scaffold_10-snap.1521-T1
Valid prediction for snap_scaffold_10-snap.1515-T1
Valid prediction for snap_scaffold_10-snap.1519-T1
Valid prediction for GeneMark_model.43576_t
Valid prediction for snap_scaffold_10-snap.1520-T1
Valid prediction for GeneMark_model.43551_t
Valid prediction for GeneMark_model.43554_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 178269, rend_intergenic: 166096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236145, rend_intergenic: 229170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 317591
-exon list size: 386


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 178269, rend_intergenic: 166096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236145, rend_intergenic: 229170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 60186
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 - 11632
-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

-building DP trellis

-building trellis in range 1 - 10747
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 11641 - 60186
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 11641 - 33796
-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 11641 - 33724
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 11641 - 24759
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 33813 - 60186
-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
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 33813 - 60053
-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 41590 - 60053
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 41590 - 55829
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 44982 - 55829
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 45698 - 55829

-building DP trellis

-building trellis in range 304347 - 317591
-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 304534 - 317591
-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

-building DP trellis

-building trellis in range 304848 - 317591
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 305701 - 317591
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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