-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_11039419-11416873

-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_11-snap.2462-T1
Valid prediction for GeneMark_model.49175_t
Valid prediction for GlimmerHMM_glimmerT_28473-T1
Valid prediction for GeneMark_model.49168_t
Valid prediction for snap_scaffold_11-snap.2463-T1
Valid prediction for snap_scaffold_11-snap.2480-T1
Valid prediction for GeneMark_model.49161_t
Valid prediction for snap_scaffold_11-snap.2451-T1
Couldn't classify 282024, 282103
Sorry, prediction pasa_asmbl_5931.p1 fails validation.
(ATG)	 AC	277713-277740	GT	GAG
(GCC)	 AG	278509-278652	GT	CGG
(AGT)	 AG	280387-280526	GT	AGG
(ATT)	 AG	280983-281076	GT	TGG
(GTG)	 AG	281279-281440	GT	TGG
(AGG)	 AG	282024-282103	AA	TCA
-recovered pasa_asmbl_5931.p1, initial, 277713, 277740
-recovered pasa_asmbl_5931.p1, internal, 278509, 278652
-recovered pasa_asmbl_5931.p1, internal, 280387, 280526
-recovered pasa_asmbl_5931.p1, internal, 280983, 281076
-recovered pasa_asmbl_5931.p1, internal, 281279, 281440
Valid prediction for snap_scaffold_11-snap.2458-T1
Valid prediction for snap_scaffold_11-snap.2471-T1
Valid prediction for snap_scaffold_11-snap.2472-T1
Valid prediction for HiQ_model.g19006.t1
Valid prediction for Augustus_model.g19004.t1
Couldn't classify 13202, 13336
Couldn't classify 15843, 16006
Sorry, prediction pasa_asmbl_6313.p2 fails validation.
(AGC)	 TC	13202-13336	GT	AGG
(GTG)	 AG	14475-14538	GT	AGG
(AGT)	 AG	14771-14833	GT	AGG
(GTC)	 AG	15843-16006	GG	ACG
-recovered pasa_asmbl_6313.p2, internal, 14475, 14538
-recovered pasa_asmbl_6313.p2, internal, 14771, 14833
Valid prediction for Augustus_model.g19008.t1
Valid prediction for GlimmerHMM_glimmerT_28485-T1
Valid prediction for GeneMark_model.49155_t
Valid prediction for snap_scaffold_11-snap.2466-T1
Couldn't classify 300868, 300994
Sorry, prediction pasa_asmbl_5938.p1 fails validation.
(TGC)	 AT	300868-300994	GT	TGG
(GGA)	 AG	301161-301236	GT	AGG
(GAC)	 AG	301756-302146	GA	GAG
-recovered pasa_asmbl_5938.p1, terminal, 301756, 302146
-recovered pasa_asmbl_5938.p1, internal, 301161, 301236
Valid prediction for GlimmerHMM_glimmerT_28469-T1
Valid prediction for GeneMark_model.49179_t
Valid prediction for GeneMark_model.49154_t
Valid prediction for snap_scaffold_11-snap.2457-T1
Valid prediction for snap_scaffold_11-snap.2454-T1
Couldn't classify 288255, 288503
Couldn't classify 290474, 290601
Sorry, prediction pasa_asmbl_5934.p1 fails validation.
(AAC)	 AG	288255-288503	GT	AGG
(GTG)	 AG	289825-289960	GT	CGG
(GAA)	 AG	290474-290601	AA	GTA
-recovered pasa_asmbl_5934.p1, internal, 288255, 288503
-recovered pasa_asmbl_5934.p1, internal, 289825, 289960
Valid prediction for snap_scaffold_11-snap.2469-T1
Valid prediction for GeneMark_model.49182_t
Valid prediction for GeneMark_model.49162_t
Valid prediction for Augustus_model.g19013.t1
Valid prediction for CodingQuarry_transcript_8208-T1
Valid prediction for snap_scaffold_11-snap.2455-T1
Valid prediction for snap_scaffold_11-snap.2461-T1
Valid prediction for GeneMark_model.49174_t
Valid prediction for GlimmerHMM_glimmerT_28470-T1
Valid prediction for GlimmerHMM_glimmerT_28472-T1
Valid prediction for snap_scaffold_11-snap.2470-T1
Valid prediction for GeneMark_model.49177_t
Valid prediction for GeneMark_model.49181_t
Valid prediction for GeneMark_model.49159_t
Valid prediction for Augustus_model.g19009.t1
Valid prediction for GlimmerHMM_glimmerT_28475-T1
Valid prediction for GeneMark_model.49171_t
Valid prediction for pasa_asmbl_5929.p1
Valid prediction for GeneMark_model.49157_t
Valid prediction for snap_scaffold_11-snap.2468-T1
Couldn't classify 47608, 47689
Couldn't classify 51090, 51128
Sorry, prediction pasa_asmbl_5925.p1 fails validation.
(ATC)	 AG	47608-47689	GT	AGG
(AAC)	 AG	47870-48390	GT	AGG
(AAA)	 AG	51090-51128	AC	GGA
-recovered pasa_asmbl_5925.p1, internal, 47608, 47689
-recovered pasa_asmbl_5925.p1, internal, 47870, 48390
Valid prediction for Augustus_model.g19002.t1
Valid prediction for snap_scaffold_11-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_28481-T1
Valid prediction for snap_scaffold_11-snap.2460-T1
Valid prediction for Augustus_model.g19003.t1
Valid prediction for GlimmerHMM_glimmerT_28487-T1
Valid prediction for GeneMark_model.49158_t
Valid prediction for GeneMark_model.49172_t
Valid prediction for Augustus_model.g19012.t1
Valid prediction for GlimmerHMM_glimmerT_28477-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 Augustus_model.g19015.t1
Valid prediction for GlimmerHMM_glimmerT_28488-T1
Valid prediction for GlimmerHMM_glimmerT_28479-T1
Valid prediction for GeneMark_model.49183_t
Valid prediction for HiQ_model.g19001.t1
Couldn't classify 312181, 312645
Sorry, prediction pasa_asmbl_6998.p1 fails validation.
(ATG)	 GT	312181-312645	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_28486-T1
Valid prediction for GeneMark_model.49166_t
Valid prediction for snap_scaffold_11-snap.2478-T1
Valid prediction for GlimmerHMM_glimmerT_28482-T1
Valid prediction for GeneMark_model.49173_t
Valid prediction for snap_scaffold_11-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_28471-T1
Valid prediction for GlimmerHMM_glimmerT_28480-T1
Valid prediction for Augustus_model.g19011.t1
Valid prediction for GeneMark_model.49185_t
Valid prediction for GeneMark_model.49164_t
Valid prediction for Augustus_model.g19017.t1
Valid prediction for snap_scaffold_11-snap.2479-T1
Valid prediction for GlimmerHMM_glimmerT_28474-T1
Couldn't classify 312856, 312996
Sorry, prediction pasa_asmbl_6996.p1 fails validation.
(AGG)	 AG	312856-312996	GT	AGG
(GGT)	 AG	313130-313340	GT	GGG
(CTG)	 AG	313480-313608	GT	AGG
(GAG)	 AG	313770-313830	GT	AGG
(ACT)	 AG	313973-314112	GT	AGG
(TTT)	 AG	314316-314476	GT	TGG
(GTG)	 AG	314728-314797	GT	AGG
(ACT)	 AG	314892-315081	GT	AGG
(TTT)	 AG	315360-315465	GT	GGG
(AAG)	 AG	315761-316007	GT	AGG
(GGA)	 AG	316381-316476	GT	AGG
(AGG)	 AG	316609-316685	GT	GAG
(CCT)	 AG	316923-316992	GT	AGG
(GTC)	 AG	318447-318496	AA	AGA
-recovered pasa_asmbl_6996.p1, terminal, 318447, 318496
-recovered pasa_asmbl_6996.p1, internal, 312856, 312996
-recovered pasa_asmbl_6996.p1, internal, 313130, 313340
-recovered pasa_asmbl_6996.p1, internal, 313480, 313608
-recovered pasa_asmbl_6996.p1, internal, 313770, 313830
-recovered pasa_asmbl_6996.p1, internal, 313973, 314112
-recovered pasa_asmbl_6996.p1, internal, 314316, 314476
-recovered pasa_asmbl_6996.p1, internal, 314728, 314797
-recovered pasa_asmbl_6996.p1, internal, 314892, 315081
-recovered pasa_asmbl_6996.p1, internal, 315360, 315465
-recovered pasa_asmbl_6996.p1, internal, 315761, 316007
-recovered pasa_asmbl_6996.p1, internal, 316381, 316476
-recovered pasa_asmbl_6996.p1, internal, 316609, 316685
-recovered pasa_asmbl_6996.p1, internal, 316923, 316992
Valid prediction for HiQ_model.g19005.t1
Valid prediction for snap_scaffold_11-snap.2474-T1
Valid prediction for GeneMark_model.49163_t
Valid prediction for GlimmerHMM_glimmerT_28483-T1
Valid prediction for GlimmerHMM_glimmerT_28478-T1
Valid prediction for snap_scaffold_11-snap.2475-T1
Valid prediction for Augustus_model.g19014.t1
Valid prediction for snap_scaffold_11-snap.2453-T1
Valid prediction for snap_scaffold_11-snap.2456-T1
Valid prediction for snap_scaffold_11-snap.2477-T1
Valid prediction for GlimmerHMM_glimmerT_28468-T1
Valid prediction for snap_scaffold_11-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_28484-T1
Valid prediction for snap_scaffold_11-snap.2459-T1
Valid prediction for GeneMark_model.49165_t
Valid prediction for Augustus_model.g19016.t1
Valid prediction for GlimmerHMM_glimmerT_28476-T1
Valid prediction for snap_scaffold_11-snap.2467-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.49180_t
Valid prediction for Augustus_model.g19007.t1
Valid prediction for Augustus_model.g19010.t1
Valid prediction for GeneMark_model.49178_t
Valid prediction for GeneMark_model.49167_t
Valid prediction for snap_scaffold_11-snap.2465-T1
Valid prediction for snap_scaffold_11-snap.2473-T1
Valid prediction for GeneMark_model.49156_t
Valid prediction for snap_scaffold_11-snap.2449-T1
Valid prediction for GeneMark_model.49160_t
Valid prediction for GeneMark_model.49184_t
Valid prediction for snap_scaffold_11-snap.2452-T1
Valid prediction for GeneMark_model.49176_t
Valid prediction for GeneMark_model.49153_t
Couldn't classify 321843, 322154
Sorry, prediction pasa_asmbl_5928.p1 fails validation.
(ATG)	 AC	321843-322154	TT	TGT

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55439, rend_intergenic: 47453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 377455
-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: 55439, rend_intergenic: 47453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 357079 - 377455
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 357079 - 373296
-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 357524 - 373296
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 357524 - 372836
-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