-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_11139137-11394550

-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.g31147.t1
Valid prediction for snap_scaffold_20-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_46816-T1
Valid prediction for Augustus_model.g31131.t1
Valid prediction for snap_scaffold_20-snap.2365-T1
Valid prediction for snap_scaffold_20-snap.2354-T1
Couldn't classify 151478, 151600
Couldn't classify 154014, 154045
Sorry, prediction pasa_asmbl_27189.p1 fails validation.
(GGA)	 CA	151478-151600	GT	AGG
(GCC)	 AG	152003-152110	GT	TGG
(AAT)	 AG	152790-152990	GT	AGG
(GTT)	 AG	153828-153924	GT	TGG
(GTG)	 AG	154014-154045	AG	ACA
-recovered pasa_asmbl_27189.p1, internal, 152003, 152110
-recovered pasa_asmbl_27189.p1, internal, 152790, 152990
-recovered pasa_asmbl_27189.p1, internal, 153828, 153924
Valid prediction for GlimmerHMM_glimmerT_46820-T1
Valid prediction for GlimmerHMM_glimmerT_46828-T1
Valid prediction for snap_scaffold_20-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_46811-T1
Valid prediction for snap_scaffold_20-snap.2362-T1
Valid prediction for GlimmerHMM_glimmerT_46819-T1
Valid prediction for GlimmerHMM_glimmerT_46805-T1
Valid prediction for GlimmerHMM_glimmerT_46807-T1
Valid prediction for snap_scaffold_20-snap.2373-T1
Valid prediction for snap_scaffold_20-snap.2364-T1
Valid prediction for snap_scaffold_20-snap.2363-T1
Valid prediction for snap_scaffold_20-snap.2374-T1
Valid prediction for snap_scaffold_20-snap.2357-T1
Valid prediction for snap_scaffold_20-snap.2370-T1
Valid prediction for snap_scaffold_20-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_46824-T1
Valid prediction for Augustus_model.g31137.t1
Valid prediction for Augustus_model.g31148.t1
Valid prediction for snap_scaffold_20-snap.2358-T1
Valid prediction for Augustus_model.g31146.t1
Valid prediction for snap_scaffold_20-snap.2352-T1
Valid prediction for snap_scaffold_20-snap.2350-T1
Valid prediction for Augustus_model.g31151.t1
Valid prediction for GlimmerHMM_glimmerT_46832-T1
Valid prediction for GlimmerHMM_glimmerT_46818-T1
Valid prediction for HiQ_model.g31121.t1
Valid prediction for snap_scaffold_20-snap.2351-T1
Valid prediction for GlimmerHMM_glimmerT_46814-T1
Valid prediction for Augustus_model.g31143.t1
Couldn't classify 251698, 251725
Couldn't classify 252235, 252387
Sorry, prediction pasa_asmbl_27040.p1 fails validation.
(GCC)	 AA	251698-251725	GT	CAG
(AGT)	 AG	251908-252107	GT	AGG
(GAT)	 AG	252235-252387	GT	CTG
-recovered pasa_asmbl_27040.p1, internal, 251908, 252107
-recovered pasa_asmbl_27040.p1, internal, 252235, 252387
Valid prediction for snap_scaffold_20-snap.2367-T1
Valid prediction for Augustus_model.g31133.t1
Valid prediction for GlimmerHMM_glimmerT_46837-T1
Valid prediction for GlimmerHMM_glimmerT_46834-T1
Valid prediction for HiQ_model.g31138.t1
Valid prediction for Augustus_model.g31145.t1
Valid prediction for snap_scaffold_20-snap.2353-T1
Valid prediction for GlimmerHMM_glimmerT_46822-T1
Valid prediction for Augustus_model.g31149.t1
Valid prediction for Augustus_model.g31125.t1
Valid prediction for Augustus_model.g31142.t1
Valid prediction for pasa_asmbl_27015.p1
Couldn't classify 199641, 199775
Couldn't classify 202277, 202495
Sorry, prediction pasa_asmbl_27150.p1 fails validation.
(ATT)	 AG	199641-199775	GT	TGG
(TCA)	 AG	202277-202495	GG	AAG
-recovered pasa_asmbl_27150.p1, internal, 199641, 199775
Valid prediction for GlimmerHMM_glimmerT_46835-T1
Valid prediction for Augustus_model.g31136.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_46829-T1
Valid prediction for GlimmerHMM_glimmerT_46817-T1
Valid prediction for Augustus_model.g31127.t1
Valid prediction for snap_scaffold_20-snap.2375-T1
Valid prediction for Augustus_model.g31150.t1
Valid prediction for Augustus_model.g31123.t1
Valid prediction for snap_scaffold_20-snap.2343-T1
Valid prediction for Augustus_model.g31124.t1
Valid prediction for GlimmerHMM_glimmerT_46808-T1
Valid prediction for snap_scaffold_20-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_46810-T1
Valid prediction for GlimmerHMM_glimmerT_46836-T1
Valid prediction for snap_scaffold_20-snap.2372-T1
Valid prediction for Augustus_model.g31144.t1
Couldn't classify 218621, 218708
Couldn't classify 222768, 222795
Sorry, prediction pasa_asmbl_26146.p1 fails validation.
(ACA)	 CA	218621-218708	GT	AGG
(TGA)	 AG	219506-219670	GT	AAG
(ATA)	 AG	220898-221011	GT	CAG
(ACA)	 AG	221340-221453	GT	AAG
(GGG)	 AG	221748-221861	GT	CGG
(GCA)	 AG	222126-222242	GT	GAG
(ATT)	 AG	222389-222416	GT	TGG
(CTA)	 AG	222768-222795	GA	GGG
-recovered pasa_asmbl_26146.p1, internal, 219506, 219670
-recovered pasa_asmbl_26146.p1, internal, 220898, 221011
-recovered pasa_asmbl_26146.p1, internal, 221340, 221453
-recovered pasa_asmbl_26146.p1, internal, 221748, 221861
-recovered pasa_asmbl_26146.p1, internal, 222126, 222242
-recovered pasa_asmbl_26146.p1, internal, 222389, 222416
Valid prediction for Augustus_model.g31134.t1
Valid prediction for snap_scaffold_20-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_46815-T1
Valid prediction for GlimmerHMM_glimmerT_46823-T1
Valid prediction for GlimmerHMM_glimmerT_46806-T1
Valid prediction for Augustus_model.g31140.t1
Valid prediction for GlimmerHMM_glimmerT_46826-T1
Valid prediction for snap_scaffold_20-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_46821-T1
Valid prediction for Augustus_model.g31126.t1
Valid prediction for snap_scaffold_20-snap.2342-T1
Valid prediction for Augustus_model.g31132.t1
Valid prediction for GlimmerHMM_glimmerT_46827-T1
Valid prediction for Augustus_model.g31129.t1
Valid prediction for snap_scaffold_20-snap.2340-T1
Valid prediction for snap_scaffold_20-snap.2359-T1
Valid prediction for GlimmerHMM_glimmerT_46831-T1
Valid prediction for Augustus_model.g31135.t1
Valid prediction for GlimmerHMM_glimmerT_46833-T1
Valid prediction for snap_scaffold_20-snap.2360-T1
Valid prediction for Augustus_model.g31141.t1
Valid prediction for snap_scaffold_20-snap.2349-T1
Valid prediction for GlimmerHMM_glimmerT_46830-T1
Valid prediction for GlimmerHMM_glimmerT_46813-T1
Valid prediction for Augustus_model.g31130.t1
Valid prediction for snap_scaffold_20-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_46825-T1
Valid prediction for snap_scaffold_20-snap.2355-T1
Couldn't classify 210394, 210481
Couldn't classify 212075, 212115
Sorry, prediction pasa_asmbl_26150.p1 fails validation.
(CGG)	 CT	210394-210481	GT	TGG
(CAA)	 AG	211244-211304	GT	AAG
(GTG)	 AG	211744-211874	GT	AGG
(ATC)	 AG	212075-212115	GG	GGG
-recovered pasa_asmbl_26150.p1, internal, 211244, 211304
-recovered pasa_asmbl_26150.p1, internal, 211744, 211874
Valid prediction for GlimmerHMM_glimmerT_46809-T1
Valid prediction for snap_scaffold_20-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_46812-T1
Couldn't classify 215198, 215312
Couldn't classify 217703, 217720
Sorry, prediction pasa_asmbl_26148.p1 fails validation.
(GCG)	 TA	215198-215312	GT	CAG
(ATG)	 AG	215506-215619	GT	CGG
(ATG)	 AG	216446-216559	GT	AAG
(ATG)	 AG	217262-217308	GT	AGG
(GAC)	 AG	217703-217720	AA	ACA
add_exon() Sorry, pasa_asmbl_26148.p1 215506-215619-initial-1 is invalid.
-recovered pasa_asmbl_26148.p1, initial, 215506, 215619
add_exon() Sorry, pasa_asmbl_26148.p1 216446-216559-initial-1 is invalid.
-recovered pasa_asmbl_26148.p1, initial, 216446, 216559
-recovered pasa_asmbl_26148.p1, initial, 217262, 217308
-recovered pasa_asmbl_26148.p1, internal, 215506, 215619
-recovered pasa_asmbl_26148.p1, internal, 216446, 216559
-recovered pasa_asmbl_26148.p1, internal, 217262, 217308
Valid prediction for Augustus_model.g31139.t1
Valid prediction for snap_scaffold_20-snap.2344-T1
Valid prediction for Augustus_model.g31128.t1
Valid prediction for snap_scaffold_20-snap.2347-T1
Valid prediction for snap_scaffold_20-snap.2345-T1
Couldn't classify 229617, 229715
Sorry, prediction pasa_asmbl_26145.p1 fails validation.
(TGG)	 GC	229617-229715	GT	AAG
(GGC)	 AG	229958-230089	GT	TCG
(TCA)	 AG	230265-230415	GT	CGG
(ATT)	 AG	230645-231162	CA	AGC
-recovered pasa_asmbl_26145.p1, terminal, 230645, 231162
-recovered pasa_asmbl_26145.p1, internal, 229958, 230089
-recovered pasa_asmbl_26145.p1, internal, 230265, 230415
Valid prediction for Augustus_model.g31122.t1
Valid prediction for snap_scaffold_20-snap.2348-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 255414
-exon list size: 314


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 39 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support