-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_11085670-11341036

-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_6-snap.2394-T1
Valid prediction for snap_scaffold_6-snap.2395-T1
Valid prediction for Augustus_model.g10618.t1
Valid prediction for snap_scaffold_6-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_15855-T1
Valid prediction for GeneMark_model.26663_t
Valid prediction for Augustus_model.g10619.t1
Valid prediction for snap_scaffold_6-snap.2409-T1
Valid prediction for GeneMark_model.26667_t
Valid prediction for GlimmerHMM_glimmerT_15838-T1
Valid prediction for GeneMark_model.26672_t
Valid prediction for GeneMark_model.26673_t
Valid prediction for snap_scaffold_6-snap.2411-T1
Valid prediction for snap_scaffold_6-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_15853-T1
Valid prediction for snap_scaffold_6-snap.2385-T1
Valid prediction for Augustus_model.g10620.t1
Valid prediction for GeneMark_model.26643_t
Valid prediction for snap_scaffold_6-snap.2388-T1
Valid prediction for GeneMark_model.26659_t
Valid prediction for GeneMark_model.26671_t
Valid prediction for GeneMark_model.26649_t
Valid prediction for snap_scaffold_6-snap.2380-T1
Valid prediction for GeneMark_model.26646_t
Valid prediction for snap_scaffold_6-snap.2405-T1
Valid prediction for GlimmerHMM_glimmerT_15845-T1
Valid prediction for GeneMark_model.26658_t
Valid prediction for snap_scaffold_6-snap.2371-T1
Valid prediction for GeneMark_model.26644_t
Valid prediction for HiQ_model.g10614.t1
Valid prediction for GeneMark_model.26651_t
Valid prediction for GlimmerHMM_glimmerT_15856-T1
Valid prediction for GeneMark_model.26656_t
Valid prediction for GeneMark_model.26657_t
Valid prediction for GeneMark_model.26653_t
Valid prediction for GeneMark_model.26640_t
Valid prediction for GlimmerHMM_glimmerT_15854-T1
Valid prediction for snap_scaffold_6-snap.2410-T1
Valid prediction for snap_scaffold_6-snap.2372-T1
Valid prediction for snap_scaffold_6-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_15840-T1
Valid prediction for GeneMark_model.26635_t
Valid prediction for snap_scaffold_6-snap.2400-T1
Valid prediction for snap_scaffold_6-snap.2402-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 GeneMark_model.26647_t
Valid prediction for snap_scaffold_6-snap.2392-T1
Valid prediction for GeneMark_model.26668_t
Valid prediction for GeneMark_model.26638_t
Valid prediction for GlimmerHMM_glimmerT_15837-T1
Valid prediction for GeneMark_model.26636_t
Valid prediction for GeneMark_model.26652_t
Valid prediction for CodingQuarry_transcript_55075-T1
Valid prediction for GlimmerHMM_glimmerT_15850-T1
Valid prediction for snap_scaffold_6-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_15842-T1
Valid prediction for snap_scaffold_6-snap.2398-T1
Valid prediction for Augustus_model.g10615.t1
Valid prediction for GlimmerHMM_glimmerT_15836-T1
Couldn't classify 36734, 37093
Sorry, prediction pasa_asmbl_48687.p1 fails validation.
(ATC)	 TC	36734-37093	TG	GAT
Valid prediction for snap_scaffold_6-snap.2384-T1
Valid prediction for snap_scaffold_6-snap.2397-T1
Valid prediction for Augustus_model.g10605.t1
Couldn't classify 223887, 223983
Sorry, prediction pasa_asmbl_48678.p1 fails validation.
(AGT)	 AG	223887-223983	GT	GGG
(AGG)	 AG	224068-224187	GT	AGG
(GTC)	 AG	224678-224796	GT	AGG
(GAC)	 AG	225040-225171	GT	TGG
(GAT)	 AG	225541-225651	GT	AGG
(GTG)	 AG	225795-225908	GT	TCG
(GAT)	 AG	226012-226096	GT	AAG
(GGG)	 AG	226280-226397	GT	AGG
(GGC)	 AG	226809-226942	GT	AGG
(CGG)	 AG	227187-227338	GT	CTG
(CCC)	 AG	227672-227820	GT	GAG
(GTT)	 AG	227974-228115	GT	ATG
(GGC)	 AG	228283-228381	GT	AGG
(GAA)	 AG	228568-228732	GT	AGG
(TCC)	 AG	229173-229325	GT	AGG
(GTT)	 AG	229709-229774	CC	AAC
add_exon() Sorry, pasa_asmbl_48678.p1 224068-224187-terminal-1 is invalid.
-recovered pasa_asmbl_48678.p1, terminal, 224068, 224187
-recovered pasa_asmbl_48678.p1, terminal, 229709, 229774
-recovered pasa_asmbl_48678.p1, internal, 223887, 223983
-recovered pasa_asmbl_48678.p1, internal, 224068, 224187
-recovered pasa_asmbl_48678.p1, internal, 224678, 224796
-recovered pasa_asmbl_48678.p1, internal, 225040, 225171
-recovered pasa_asmbl_48678.p1, internal, 225541, 225651
-recovered pasa_asmbl_48678.p1, internal, 225795, 225908
-recovered pasa_asmbl_48678.p1, internal, 226012, 226096
-recovered pasa_asmbl_48678.p1, internal, 226280, 226397
-recovered pasa_asmbl_48678.p1, internal, 226809, 226942
-recovered pasa_asmbl_48678.p1, internal, 227187, 227338
-recovered pasa_asmbl_48678.p1, internal, 227672, 227820
-recovered pasa_asmbl_48678.p1, internal, 227974, 228115
-recovered pasa_asmbl_48678.p1, internal, 228283, 228381
-recovered pasa_asmbl_48678.p1, internal, 228568, 228732
-recovered pasa_asmbl_48678.p1, internal, 229173, 229325
Valid prediction for snap_scaffold_6-snap.2386-T1
Couldn't classify 214840, 219411
Sorry, prediction pasa_asmbl_48680.p1 fails validation.
(GAA)	 AA	214840-219411	AA	AGA
Valid prediction for GeneMark_model.26639_t
Valid prediction for snap_scaffold_6-snap.2403-T1
Valid prediction for snap_scaffold_6-snap.2376-T1
Valid prediction for Augustus_model.g10601.t1
Valid prediction for Augustus_model.g10617.t1
Valid prediction for GeneMark_model.26666_t
Valid prediction for Augustus_model.g10612.t1
Valid prediction for snap_scaffold_6-snap.2377-T1
Valid prediction for snap_scaffold_6-snap.2379-T1
Valid prediction for Augustus_model.g10610.t1
Valid prediction for GeneMark_model.26645_t
Valid prediction for GeneMark_model.26665_t
Valid prediction for snap_scaffold_6-snap.2389-T1
Valid prediction for Augustus_model.g10613.t1
Valid prediction for Augustus_model.g10608.t1
Valid prediction for Augustus_model.g10616.t1
Valid prediction for GlimmerHMM_glimmerT_15834-T1
Valid prediction for snap_scaffold_6-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_15831-T1
Couldn't classify 223101, 223109
Sorry, prediction pasa_asmbl_48679.p1 fails validation.
(ATG)	 GT	222223-222663	GT	CTG
(TTG)	 AG	223101-223109	CC	ATC
-recovered pasa_asmbl_48679.p1, initial, 222223, 222663
Valid prediction for GlimmerHMM_glimmerT_15844-T1
Valid prediction for snap_scaffold_6-snap.2381-T1
Valid prediction for snap_scaffold_6-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_15839-T1
Couldn't classify 206861, 206942
Couldn't classify 209290, 209349
Sorry, prediction pasa_asmbl_48682.p1 fails validation.
(TTT)	 AC	206861-206942	GT	AGG
(TCC)	 AG	208136-208335	GT	CTG
(ACC)	 AG	208679-208826	GT	TGG
(ACG)	 AG	209059-209186	GT	AGG
(GAC)	 AG	209290-209349	CG	AGC
-recovered pasa_asmbl_48682.p1, internal, 208136, 208335
-recovered pasa_asmbl_48682.p1, internal, 208679, 208826
-recovered pasa_asmbl_48682.p1, internal, 209059, 209186
Valid prediction for GeneMark_model.26655_t
Valid prediction for Augustus_model.g10606.t1
Valid prediction for Augustus_model.g10611.t1
Valid prediction for snap_scaffold_6-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_15848-T1
Valid prediction for snap_scaffold_6-snap.2373-T1
Valid prediction for Augustus_model.g10603.t1
Valid prediction for snap_scaffold_6-snap.2370-T1
Valid prediction for GeneMark_model.26664_t
Valid prediction for snap_scaffold_6-snap.2396-T1
Valid prediction for snap_scaffold_6-snap.2375-T1
Valid prediction for GeneMark_model.26648_t
Valid prediction for GlimmerHMM_glimmerT_15841-T1
Valid prediction for GeneMark_model.26642_t
Valid prediction for Augustus_model.g10604.t1
Valid prediction for Augustus_model.g10609.t1
Valid prediction for snap_scaffold_6-snap.2404-T1
Valid prediction for snap_scaffold_6-snap.2408-T1
Valid prediction for GeneMark_model.26661_t
Valid prediction for Augustus_model.g10602.t1
Valid prediction for snap_scaffold_6-snap.2378-T1
Valid prediction for CodingQuarry_transcript_55076-T1
Valid prediction for GlimmerHMM_glimmerT_15852-T1
Valid prediction for snap_scaffold_6-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_15833-T1
Couldn't classify 72135, 72289
Couldn't classify 76445, 76525
Sorry, prediction pasa_asmbl_49389.p1 fails validation.
(GAG)	 AG	72135-72289	GT	CGG
(GAA)	 AG	72786-72915	GT	AGG
(GCC)	 AG	73264-73356	GT	GGG
(GAC)	 AG	73534-73593	GT	AGG
(GTG)	 AG	76445-76525	TA	GGT
-recovered pasa_asmbl_49389.p1, internal, 72135, 72289
-recovered pasa_asmbl_49389.p1, internal, 72786, 72915
-recovered pasa_asmbl_49389.p1, internal, 73264, 73356
-recovered pasa_asmbl_49389.p1, internal, 73534, 73593
Valid prediction for GlimmerHMM_glimmerT_15835-T1
Valid prediction for GeneMark_model.26634_t
Valid prediction for GlimmerHMM_glimmerT_15849-T1
Valid prediction for GlimmerHMM_glimmerT_15843-T1
Valid prediction for snap_scaffold_6-snap.2401-T1
Valid prediction for GeneMark_model.26660_t
Valid prediction for GeneMark_model.26662_t
Valid prediction for GlimmerHMM_glimmerT_15832-T1
Valid prediction for GeneMark_model.26650_t
Valid prediction for GlimmerHMM_glimmerT_15847-T1
Valid prediction for GlimmerHMM_glimmerT_15846-T1
Valid prediction for snap_scaffold_6-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_15857-T1
Valid prediction for CodingQuarry_transcript_55074-T1
Valid prediction for Augustus_model.g10600.t1
Valid prediction for GeneMark_model.26669_t
Valid prediction for snap_scaffold_6-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_15851-T1
Valid prediction for GeneMark_model.26637_t
Valid prediction for GeneMark_model.26641_t
Valid prediction for snap_scaffold_6-snap.2406-T1
Valid prediction for Augustus_model.g10607.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13443, rend_intergenic: 10638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16158, rend_intergenic: 15437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73270, rend_intergenic: 70525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89870, rend_intergenic: 86485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92399, rend_intergenic: 89910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115059, rend_intergenic: 111584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150096, rend_intergenic: 133446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159454, rend_intergenic: 154050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 255367
-exon list size: 562


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.2    
1.4    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.7    
2.8    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.1    
4.3    
4.4    
4.6    
4.8    
5.0    
5.1    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.6    
6.7    
6.9    
7.1    
7.3    
7.4    
7.6    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.9    
9.0    
9.2    
9.4    
9.6    
9.8    
9.9    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.1    
15.2    
15.4    
15.6    
15.8    
16.0    
16.1    
16.3    
16.5    
16.7    
16.8    
17.0    
17.2    
17.4    
17.6    
17.7    
17.9    
18.1    
18.3    
18.4    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.5    
24.6    
24.8    
25.0    
25.2    
25.4    
25.5    
25.7    
25.9    
26.1    
26.2    
26.4    
26.6    
26.8    
27.0    
27.1    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
30.0    
30.1    
30.3    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.1    
40.2    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.4    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
46.5    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 13443, rend_intergenic: 10638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16158, rend_intergenic: 15437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73270, rend_intergenic: 70525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89870, rend_intergenic: 86485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92399, rend_intergenic: 89910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115059, rend_intergenic: 111584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150096, rend_intergenic: 133446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159454, rend_intergenic: 154050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 242926 - 255367
-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