-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_11418252-11719422

-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.g12205.t1
Couldn't classify 216197, 216571
Sorry, prediction pasa_asmbl_50177.p1 fails validation.
(CAT)	 GG	216197-216571	AG	GGA
Couldn't classify 241073, 241119
Couldn't classify 241738, 241848
Sorry, prediction pasa_asmbl_50182.p1 fails validation.
(GAG)	 CA	241073-241119	GT	GGG
(AAG)	 AG	241281-241428	GT	AGG
(GTA)	 AG	241738-241848	GA	AGG
-recovered pasa_asmbl_50182.p1, internal, 241281, 241428
Valid prediction for GlimmerHMM_glimmerT_18154-T1
Valid prediction for snap_scaffold_7-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_18146-T1
Valid prediction for GlimmerHMM_glimmerT_18150-T1
Valid prediction for Augustus_model.g12206.t1
Valid prediction for GlimmerHMM_glimmerT_18145-T1
Valid prediction for snap_scaffold_7-snap.2183-T1
Valid prediction for Augustus_model.g12204.t1
Valid prediction for snap_scaffold_7-snap.2197-T1
Valid prediction for snap_scaffold_7-snap.2195-T1
Couldn't classify 215555, 215920
Sorry, prediction pasa_asmbl_50176.p1 fails validation.
(GGC)	 AG	215555-215920	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_18163-T1
Valid prediction for Augustus_model.g12214.t1
Valid prediction for Augustus_model.g12215.t1
Couldn't classify 233174, 233186
Couldn't classify 234550, 234618
Sorry, prediction pasa_asmbl_50179.p1 fails validation.
(ATC)	 AC	233174-233186	GT	AGG
(CCT)	 AG	233388-233459	GT	AGG
(GAT)	 AG	233698-233759	GT	AGG
(GCC)	 AG	233928-234086	GT	AGG
(ACC)	 AG	234386-234463	GT	AGG
(CCA)	 AG	234550-234618	CC	AAC
add_exon() Sorry, pasa_asmbl_50179.p1 233388-233459-terminal-1 is invalid.
-recovered pasa_asmbl_50179.p1, terminal, 233388, 233459
-recovered pasa_asmbl_50179.p1, internal, 233388, 233459
-recovered pasa_asmbl_50179.p1, internal, 233698, 233759
-recovered pasa_asmbl_50179.p1, internal, 233928, 234086
-recovered pasa_asmbl_50179.p1, internal, 234386, 234463
Valid prediction for snap_scaffold_7-snap.2190-T1
Valid prediction for snap_scaffold_7-snap.2213-T1
Valid prediction for snap_scaffold_7-snap.2192-T1
Valid prediction for snap_scaffold_7-snap.2211-T1
Valid prediction for snap_scaffold_7-snap.2196-T1
Valid prediction for snap_scaffold_7-snap.2217-T1
Valid prediction for Augustus_model.g12213.t1
Valid prediction for Augustus_model.g12199.t1
Valid prediction for GlimmerHMM_glimmerT_18157-T1
Valid prediction for GlimmerHMM_glimmerT_18148-T1
Valid prediction for Augustus_model.g12212.t1
Valid prediction for Augustus_model.g12208.t1
Valid prediction for GlimmerHMM_glimmerT_18156-T1
Valid prediction for snap_scaffold_7-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_18140-T1
Valid prediction for GlimmerHMM_glimmerT_18158-T1
Valid prediction for Augustus_model.g12203.t1
Valid prediction for Augustus_model.g12207.t1
Valid prediction for GlimmerHMM_glimmerT_18152-T1
Valid prediction for snap_scaffold_7-snap.2207-T1
Couldn't classify 242976, 243044
Sorry, prediction pasa_asmbl_50184.p1 fails validation.
(TCC)	 AA	242976-243044	GT	CGG
(GCT)	 AG	243246-243305	GT	AGG
(GTC)	 AG	243666-243823	GT	AGG
(GAC)	 AG	244502-244733	CT	GAC
-recovered pasa_asmbl_50184.p1, terminal, 244502, 244733
-recovered pasa_asmbl_50184.p1, internal, 243246, 243305
-recovered pasa_asmbl_50184.p1, internal, 243666, 243823
Couldn't classify 237945, 238014
Couldn't classify 240183, 240230
Sorry, prediction pasa_asmbl_50181.p1 fails validation.
(AGA)	 GC	237945-238014	GT	AGG
(GTC)	 AG	238808-239172	GT	AGG
(GAG)	 AG	240183-240230	CG	CCC
-recovered pasa_asmbl_50181.p1, internal, 238808, 239172
Valid prediction for GlimmerHMM_glimmerT_18155-T1
Valid prediction for snap_scaffold_7-snap.2209-T1
Valid prediction for Augustus_model.g12211.t1
Couldn't classify 234924, 234982
Couldn't classify 235076, 235439
Sorry, prediction pasa_asmbl_50180.p1 fails validation.
(CTG)	 TC	234924-234982	GT	GGG
(AAC)	 AG	235076-235439	GC	CTG
-recovered pasa_asmbl_50180.p1, internal, 235076, 235439
Valid prediction for GlimmerHMM_glimmerT_18161-T1
Valid prediction for snap_scaffold_7-snap.2204-T1
Valid prediction for Augustus_model.g12210.t1
Valid prediction for snap_scaffold_7-snap.2200-T1
Valid prediction for Augustus_model.g12209.t1
Valid prediction for snap_scaffold_7-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_18159-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_18141-T1
Valid prediction for Augustus_model.g12216.t1
Valid prediction for snap_scaffold_7-snap.2198-T1
Valid prediction for snap_scaffold_7-snap.2193-T1
Valid prediction for snap_scaffold_7-snap.2202-T1
Valid prediction for snap_scaffold_7-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_18153-T1
Valid prediction for snap_scaffold_7-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_18151-T1
Valid prediction for snap_scaffold_7-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_18162-T1
Valid prediction for snap_scaffold_7-snap.2184-T1
Valid prediction for snap_scaffold_7-snap.2205-T1
Valid prediction for snap_scaffold_7-snap.2203-T1
Valid prediction for GlimmerHMM_glimmerT_18143-T1
Valid prediction for Augustus_model.g12202.t1
Valid prediction for GlimmerHMM_glimmerT_18144-T1
Valid prediction for snap_scaffold_7-snap.2188-T1
Valid prediction for snap_scaffold_7-snap.2216-T1
Valid prediction for Augustus_model.g12200.t1
Valid prediction for snap_scaffold_7-snap.2187-T1
Valid prediction for Augustus_model.g12201.t1
Valid prediction for snap_scaffold_7-snap.2214-T1
Valid prediction for snap_scaffold_7-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_18149-T1
Valid prediction for GlimmerHMM_glimmerT_18160-T1
Valid prediction for GlimmerHMM_glimmerT_18142-T1
Valid prediction for snap_scaffold_7-snap.2189-T1
Valid prediction for snap_scaffold_7-snap.2194-T1
Valid prediction for GlimmerHMM_glimmerT_18147-T1
Valid prediction for snap_scaffold_7-snap.2206-T1
Valid prediction for snap_scaffold_7-snap.2185-T1
Valid prediction for snap_scaffold_7-snap.2212-T1
Valid prediction for snap_scaffold_7-snap.2210-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30039, rend_intergenic: 29878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62414, rend_intergenic: 57497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156070, rend_intergenic: 149447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176423, rend_intergenic: 168877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178144, rend_intergenic: 177201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186062, rend_intergenic: 184344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216592, rend_intergenic: 212180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260471, rend_intergenic: 258414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 301171
-exon list size: 355


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.6    
3.9    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 30039, rend_intergenic: 29878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62414, rend_intergenic: 57497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156070, rend_intergenic: 149447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176423, rend_intergenic: 168877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178144, rend_intergenic: 177201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186062, rend_intergenic: 184344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216592, rend_intergenic: 212180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260471, rend_intergenic: 258414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19709
-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 1 - 11615
-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

-building DP trellis

-building trellis in range 267043 - 301171
-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 2 predictions from path traversal
GOT 5prime partial gene.
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 272712 - 301171
-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

-building DP trellis

-building trellis in range 277438 - 301171
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 284225 - 301171
-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