-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_1-163909

-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_22-snap.42-T1
Valid prediction for GlimmerHMM_glimmerT_49964-T1
Valid prediction for GlimmerHMM_glimmerT_49989-T1
Valid prediction for pasa_asmbl_29091.p1
Valid prediction for HiQ_model.g33499.t1
Valid prediction for snap_scaffold_22-snap.29-T1
Valid prediction for Augustus_model.g33514.t1
Valid prediction for snap_scaffold_22-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_49980-T1
Valid prediction for GeneMark_model.86607_t
Valid prediction for Augustus_model.g33510.t1
Valid prediction for GlimmerHMM_glimmerT_49994-T1
Valid prediction for snap_scaffold_22-snap.2-T1
Valid prediction for Augustus_model.g33528.t1
Valid prediction for snap_scaffold_22-snap.26-T1
Couldn't classify 156842, 156982
Couldn't classify 158062, 158213
Sorry, prediction pasa_asmbl_29824.p1 fails validation.
(CAG)	 AT	156842-156982	GT	AGG
(CTC)	 AG	157621-157738	GT	GTG
(GGG)	 AG	158062-158213	AG	AGA
-recovered pasa_asmbl_29824.p1, internal, 157621, 157738
Valid prediction for GlimmerHMM_glimmerT_49965-T1
Valid prediction for GeneMark_model.86623_t
Valid prediction for snap_scaffold_22-snap.7-T1
Valid prediction for CodingQuarry_transcript_33996-T1
Couldn't classify 18815, 19244
Sorry, prediction pasa_asmbl_29089.p1 fails validation.
(TGC)	 CC	18815-19244	GT	CGG
(TGA)	 AG	19465-19662	GT	AGG
(GGA)	 AG	19931-20184	AG	AGA
-recovered pasa_asmbl_29089.p1, terminal, 19931, 20184
-recovered pasa_asmbl_29089.p1, internal, 19465, 19662
Valid prediction for Augustus_model.g33527.t1
Couldn't classify 30427, 30439
Sorry, prediction pasa_asmbl_29095.p1 fails validation.
(TAT)	 AT	30427-30439	GT	AGG
(AAC)	 AG	30528-30636	GT	ACG
(CAT)	 AG	30783-30917	GT	AGG
(GGC)	 AG	31040-31358	GC	GAG
-recovered pasa_asmbl_29095.p1, terminal, 31040, 31358
-recovered pasa_asmbl_29095.p1, internal, 30528, 30636
-recovered pasa_asmbl_29095.p1, internal, 30783, 30917
-recovered pasa_asmbl_29095.p1, internal, 31040, 31358
Valid prediction for GlimmerHMM_glimmerT_49996-T1
Valid prediction for GeneMark_model.86614_t
Valid prediction for GlimmerHMM_glimmerT_49992-T1
Valid prediction for GeneMark_model.86593_t
Valid prediction for GeneMark_model.86605_t
Valid prediction for Augustus_model.g33505.t1
Valid prediction for snap_scaffold_22-snap.3-T1
Valid prediction for snap_scaffold_22-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_49959-T1
Valid prediction for GlimmerHMM_glimmerT_49972-T1
Valid prediction for Augustus_model.g33517.t1
Valid prediction for snap_scaffold_22-snap.20-T1
Valid prediction for snap_scaffold_22-snap.23-T1
Valid prediction for HiQ_model.g33503.t1
Valid prediction for Augustus_model.g33501.t1
Valid prediction for GeneMark_model.86625_t
Valid prediction for GeneMark_model.86621_t
Valid prediction for Augustus_model.g33512.t1
Couldn't classify 140040, 140215
Couldn't classify 140499, 140670
Sorry, prediction pasa_asmbl_29102.p1 fails validation.
(GTA)	 AG	140040-140215	GT	GGG
(GTA)	 AG	140499-140670	AG	AGA
-recovered pasa_asmbl_29102.p1, internal, 140040, 140215
Valid prediction for Augustus_model.g33520.t1
Valid prediction for CodingQuarry_transcript_33995-T1
Valid prediction for GlimmerHMM_glimmerT_49960-T1
Valid prediction for snap_scaffold_22-snap.9-T1
Valid prediction for Augustus_model.g33522.t1
Valid prediction for GlimmerHMM_glimmerT_49968-T1
Valid prediction for snap_scaffold_22-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_49975-T1
Valid prediction for GeneMark_model.86592_t
Valid prediction for Augustus_model.g33529.t1
Valid prediction for GeneMark_model.86591_t
Valid prediction for snap_scaffold_22-snap.10-T1
Valid prediction for snap_scaffold_22-snap.41-T1
Valid prediction for Augustus_model.g33506.t1
Valid prediction for GlimmerHMM_glimmerT_49974-T1
Valid prediction for snap_scaffold_22-snap.8-T1
Valid prediction for snap_scaffold_22-snap.4-T1
Valid prediction for Augustus_model.g33530.t1
Valid prediction for snap_scaffold_22-snap.28-T1
Valid prediction for GeneMark_model.86622_t
Valid prediction for HiQ_model.g33519.t1
Valid prediction for GlimmerHMM_glimmerT_49961-T1
Valid prediction for HiQ_model.g33500.t1
Valid prediction for GeneMark_model.86608_t
Valid prediction for GeneMark_model.86624_t
Valid prediction for snap_scaffold_22-snap.11-T1
Valid prediction for snap_scaffold_22-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_49981-T1
Valid prediction for GeneMark_model.86620_t
Valid prediction for snap_scaffold_22-snap.24-T1
Valid prediction for snap_scaffold_22-snap.46-T1
Couldn't classify 100748, 100863
Couldn't classify 107658, 107783
Sorry, prediction pasa_asmbl_29097.p1 fails validation.
(GGT)	 TG	100748-100863	GT	TTG
(ATC)	 AG	101595-101695	GT	TGG
(TGA)	 AG	102325-102543	GT	AGG
(GGT)	 AG	103267-103412	GT	AGG
(CTT)	 AG	103971-104009	GT	AGG
(GTT)	 AG	104443-104573	GT	AGG
(TTA)	 AG	104676-104808	GT	AGG
(GAG)	 AG	107658-107783	AC	CCA
-recovered pasa_asmbl_29097.p1, internal, 101595, 101695
-recovered pasa_asmbl_29097.p1, internal, 102325, 102543
-recovered pasa_asmbl_29097.p1, internal, 103267, 103412
-recovered pasa_asmbl_29097.p1, internal, 103971, 104009
-recovered pasa_asmbl_29097.p1, internal, 104443, 104573
-recovered pasa_asmbl_29097.p1, internal, 104676, 104808
Valid prediction for snap_scaffold_22-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_49966-T1
Couldn't classify 16966, 17013
Couldn't classify 17113, 17361
Sorry, prediction pasa_asmbl_29085.p1 fails validation.
(GAG)	 AG	16966-17013	GT	TGG
(GAG)	 AG	17113-17361	AA	CCA
-recovered pasa_asmbl_29085.p1, internal, 16966, 17013
Valid prediction for GlimmerHMM_glimmerT_49993-T1
Couldn't classify 131723, 132787
Couldn't classify 136686, 136741
Sorry, prediction pasa_asmbl_29101.p1 fails validation.
(GGC)	 GT	131723-132787	GT	AGG
(GAT)	 AG	135549-135741	GT	ATG
(ATC)	 AG	136686-136741	TT	GGT
-recovered pasa_asmbl_29101.p1, internal, 135549, 135741
Valid prediction for Augustus_model.g33523.t1
Valid prediction for pasa_asmbl_29082.p1
Valid prediction for GeneMark_model.86599_t
Valid prediction for Augustus_model.g33504.t1
Couldn't classify 84027, 84278
Couldn't classify 84491, 84559
Sorry, prediction pasa_asmbl_29763.p1 fails validation.
(GTT)	 GG	84027-84278	GT	TGG
(TGG)	 AG	84491-84559	GG	CTG
Valid prediction for GlimmerHMM_glimmerT_49963-T1
Valid prediction for GeneMark_model.86596_t
Valid prediction for GlimmerHMM_glimmerT_49988-T1
Valid prediction for snap_scaffold_22-snap.31-T1
Valid prediction for Augustus_model.g33507.t1
Couldn't classify 12450, 12605
Couldn't classify 13685, 13726
Sorry, prediction pasa_asmbl_29083.p1 fails validation.
(GCA)	 CC	12450-12605	GT	ATG
(CGG)	 AG	13205-13516	GT	AGG
(GAG)	 AG	13685-13726	AC	GGA
-recovered pasa_asmbl_29083.p1, internal, 13205, 13516
Valid prediction for GlimmerHMM_glimmerT_49983-T1
Valid prediction for snap_scaffold_22-snap.19-T1
Valid prediction for GeneMark_model.86598_t
Valid prediction for snap_scaffold_22-snap.32-T1
Valid prediction for GlimmerHMM_glimmerT_49991-T1
Valid prediction for GeneMark_model.86600_t
Valid prediction for snap_scaffold_22-snap.22-T1
Valid prediction for GeneMark_model.86617_t
Couldn't classify 110357, 110740
Sorry, prediction pasa_asmbl_29098.p1 fails validation.
(AGT)	 CA	110357-110740	CA	TGC
Valid prediction for GlimmerHMM_glimmerT_49984-T1
Valid prediction for snap_scaffold_22-snap.40-T1
Valid prediction for GeneMark_model.86597_t
Valid prediction for GlimmerHMM_glimmerT_49967-T1
Valid prediction for snap_scaffold_22-snap.18-T1
Couldn't classify 115538, 115666
Sorry, prediction pasa_asmbl_29099.p1 fails validation.
(GTT)	 AG	115538-115666	GT	AGG
(GCT)	 AG	117679-117823	GT	AGG
(CAC)	 AG	118118-118213	GT	AGG
(GGG)	 AG	118291-118424	AG	AAA
-recovered pasa_asmbl_29099.p1, terminal, 118291, 118424
-recovered pasa_asmbl_29099.p1, internal, 115538, 115666
-recovered pasa_asmbl_29099.p1, internal, 117679, 117823
-recovered pasa_asmbl_29099.p1, internal, 118118, 118213
Valid prediction for Augustus_model.g33525.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.86601_t
Valid prediction for snap_scaffold_22-snap.38-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g33516.t1
Valid prediction for GeneMark_model.86606_t
Valid prediction for GeneMark_model.86612_t
Valid prediction for GeneMark_model.86616_t
Valid prediction for snap_scaffold_22-snap.17-T1
Valid prediction for snap_scaffold_22-snap.16-T1
Valid prediction for snap_scaffold_22-snap.13-T1
Valid prediction for GeneMark_model.86615_t
Valid prediction for snap_scaffold_22-snap.44-T1
Valid prediction for GlimmerHMM_glimmerT_49990-T1
Valid prediction for GeneMark_model.86602_t
Valid prediction for Augustus_model.g33524.t1
Valid prediction for GeneMark_model.86613_t
Valid prediction for GlimmerHMM_glimmerT_49970-T1
Valid prediction for Augustus_model.g33513.t1
Valid prediction for GlimmerHMM_glimmerT_49979-T1
Valid prediction for GlimmerHMM_glimmerT_49986-T1
Valid prediction for snap_scaffold_22-snap.39-T1
Valid prediction for GeneMark_model.86610_t
Valid prediction for snap_scaffold_22-snap.5-T1
Valid prediction for snap_scaffold_22-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_49971-T1
Valid prediction for Augustus_model.g33511.t1
Valid prediction for GlimmerHMM_glimmerT_49987-T1
Valid prediction for snap_scaffold_22-snap.25-T1
Valid prediction for snap_scaffold_22-snap.36-T1
Valid prediction for snap_scaffold_22-snap.45-T1
Valid prediction for Augustus_model.g33515.t1
Valid prediction for GlimmerHMM_glimmerT_49977-T1
Valid prediction for GlimmerHMM_glimmerT_49995-T1
Valid prediction for GlimmerHMM_glimmerT_49976-T1
Valid prediction for GlimmerHMM_glimmerT_49969-T1
Valid prediction for snap_scaffold_22-snap.35-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.33-T1
Valid prediction for Augustus_model.g33526.t1
Valid prediction for Augustus_model.g33508.t1
Valid prediction for Augustus_model.g33521.t1
Valid prediction for GlimmerHMM_glimmerT_49962-T1
Valid prediction for GeneMark_model.86609_t
Valid prediction for snap_scaffold_22-snap.21-T1
Valid prediction for Augustus_model.g33502.t1
Valid prediction for GlimmerHMM_glimmerT_49982-T1
Valid prediction for Augustus_model.g33509.t1
Valid prediction for GeneMark_model.86594_t
Valid prediction for GeneMark_model.86611_t
Valid prediction for GeneMark_model.86603_t
Valid prediction for GlimmerHMM_glimmerT_49978-T1
Valid prediction for Augustus_model.g33518.t1
Valid prediction for GlimmerHMM_glimmerT_49985-T1
Valid prediction for snap_scaffold_22-snap.14-T1
Valid prediction for GeneMark_model.86604_t
Valid prediction for GlimmerHMM_glimmerT_49973-T1
Valid prediction for snap_scaffold_22-snap.37-T1
Valid prediction for snap_scaffold_22-snap.15-T1
Valid prediction for snap_scaffold_22-snap.34-T1
Valid prediction for GeneMark_model.86618_t

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

-building trellis in range 1 - 163909
-exon list size: 470


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support