-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_5240294-5548238

-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.g34135.t1
Valid prediction for GlimmerHMM_glimmerT_51020-T1
Valid prediction for snap_scaffold_23-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_51023-T1
Valid prediction for Augustus_model.g34114.t1
Valid prediction for snap_scaffold_23-snap.948-T1
Valid prediction for Augustus_model.g34124.t1
Valid prediction for GlimmerHMM_glimmerT_51006-T1
Valid prediction for snap_scaffold_23-snap.947-T1
Couldn't classify 104686, 104837
Couldn't classify 105142, 105269
Sorry, prediction CodingQuarry_transcript_35657-T1 fails validation.
(ATG)	 AC	104190-104242	GT	AGG
(TCG)	 AG	104686-104837	AT	TGA
(TTT)	 AC	105142-105269	GT	ATG
(GCA)	 AG	105378-105476	GT	AGG
(GTT)	 AG	106529-106681	GT	GGG
(AAT)	 AG	106783-106895	GT	AGG
(ACC)	 AG	107177-107281	GT	TGG
(GGC)	 AG	107532-107658	GT	AGG
(AAT)	 AG	108460-108549	GT	AGG
(AAA)	 AG	110014-110065	GT	AGG
(TCC)	 AG	110434-110570	AA	GAA
-recovered CodingQuarry_transcript_35657-T1, initial, 104190, 104242
-recovered CodingQuarry_transcript_35657-T1, terminal, 110434, 110570
-recovered CodingQuarry_transcript_35657-T1, internal, 105378, 105476
-recovered CodingQuarry_transcript_35657-T1, internal, 106529, 106681
-recovered CodingQuarry_transcript_35657-T1, internal, 106783, 106895
-recovered CodingQuarry_transcript_35657-T1, internal, 107177, 107281
-recovered CodingQuarry_transcript_35657-T1, internal, 107532, 107658
-recovered CodingQuarry_transcript_35657-T1, internal, 108460, 108549
-recovered CodingQuarry_transcript_35657-T1, internal, 110014, 110065
Valid prediction for GlimmerHMM_glimmerT_51007-T1
Valid prediction for GlimmerHMM_glimmerT_51035-T1
Valid prediction for snap_scaffold_23-snap.977-T1
Valid prediction for snap_scaffold_23-snap.979-T1
Valid prediction for Augustus_model.g34110.t1
Valid prediction for HiQ_model.g34122.t1
Valid prediction for snap_scaffold_23-snap.976-T1
Couldn't classify 52090, 52382
Sorry, prediction pasa_asmbl_31553.p1 fails validation.
(TGC)	 GA	52090-52382	GT	GGG
(GTA)	 AG	54105-54384	AG	AAA
-recovered pasa_asmbl_31553.p1, terminal, 54105, 54384
Valid prediction for GlimmerHMM_glimmerT_51028-T1
Valid prediction for snap_scaffold_23-snap.949-T1
Valid prediction for snap_scaffold_23-snap.971-T1
Valid prediction for snap_scaffold_23-snap.953-T1
Valid prediction for Augustus_model.g34117.t1
Valid prediction for snap_scaffold_23-snap.975-T1
Valid prediction for Augustus_model.g34119.t1
Valid prediction for snap_scaffold_23-snap.965-T1
Valid prediction for GlimmerHMM_glimmerT_51031-T1
Valid prediction for Augustus_model.g34130.t1
Valid prediction for Augustus_model.g34123.t1
Valid prediction for snap_scaffold_23-snap.986-T1
Valid prediction for CodingQuarry_transcript_35654-T1
Valid prediction for snap_scaffold_23-snap.959-T1
Valid prediction for HiQ_model.g34116.t1
Valid prediction for GlimmerHMM_glimmerT_51016-T1
Valid prediction for snap_scaffold_23-snap.980-T1
Valid prediction for snap_scaffold_23-snap.960-T1
Valid prediction for Augustus_model.g34111.t1
Valid prediction for Augustus_model.g34113.t1
Valid prediction for snap_scaffold_23-snap.957-T1
Valid prediction for snap_scaffold_23-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_51034-T1
Valid prediction for GlimmerHMM_glimmerT_51024-T1
Couldn't classify 78322, 78512
Couldn't classify 78916, 78944
Sorry, prediction pasa_asmbl_31564.p1 fails validation.
(GCC)	 AG	78322-78512	GT	TGG
(GCT)	 AG	78675-78775	GT	TGG
(GGC)	 AG	78916-78944	TA	GCT
-recovered pasa_asmbl_31564.p1, internal, 78322, 78512
-recovered pasa_asmbl_31564.p1, internal, 78675, 78775
Valid prediction for snap_scaffold_23-snap.982-T1
Valid prediction for GlimmerHMM_glimmerT_51015-T1
Valid prediction for HiQ_model.g34121.t1
Valid prediction for snap_scaffold_23-snap.974-T1
Valid prediction for snap_scaffold_23-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_51011-T1
Valid prediction for Augustus_model.g34139.t1
Valid prediction for CodingQuarry_transcript_35655-T1
Valid prediction for Augustus_model.g34133.t1
Couldn't classify 104686, 104837
Couldn't classify 105142, 105269
Sorry, prediction pasa_asmbl_31567.p1 fails validation.
(ATG)	 AC	104190-104242	GT	AGG
(TCG)	 AG	104686-104837	AT	TGA
(TTT)	 AC	105142-105269	GT	ATG
(GCA)	 AG	105378-105476	GT	AGG
(GTT)	 AG	106529-106681	GT	GGG
(AAT)	 AG	106783-106895	GT	AGG
(ACC)	 AG	107177-107281	GT	TGG
(GGC)	 AG	107532-107658	GT	AGG
(AAT)	 AG	108460-108549	GT	AGG
(AAA)	 AG	110014-110065	GT	AGG
(TCC)	 AG	110434-110570	AA	GAA
-recovered pasa_asmbl_31567.p1, initial, 104190, 104242
-recovered pasa_asmbl_31567.p1, terminal, 110434, 110570
-recovered pasa_asmbl_31567.p1, internal, 105378, 105476
-recovered pasa_asmbl_31567.p1, internal, 106529, 106681
-recovered pasa_asmbl_31567.p1, internal, 106783, 106895
-recovered pasa_asmbl_31567.p1, internal, 107177, 107281
-recovered pasa_asmbl_31567.p1, internal, 107532, 107658
-recovered pasa_asmbl_31567.p1, internal, 108460, 108549
-recovered pasa_asmbl_31567.p1, internal, 110014, 110065
Valid prediction for GlimmerHMM_glimmerT_51012-T1
Valid prediction for snap_scaffold_23-snap.987-T1
Valid prediction for pasa_asmbl_31559.p1
Valid prediction for snap_scaffold_23-snap.958-T1
Valid prediction for snap_scaffold_23-snap.951-T1
Couldn't classify 288683, 288739
Couldn't classify 289523, 289582
Sorry, prediction pasa_asmbl_31570.p1 fails validation.
(GGT)	 CA	288683-288739	GT	AGG
(CCT)	 AG	289031-289195	GT	GTG
(GTG)	 AG	289334-289447	GT	AGG
(GAC)	 AG	289523-289582	CG	AGC
-recovered pasa_asmbl_31570.p1, internal, 289031, 289195
-recovered pasa_asmbl_31570.p1, internal, 289334, 289447
Valid prediction for GlimmerHMM_glimmerT_51010-T1
Valid prediction for snap_scaffold_23-snap.961-T1
Valid prediction for GlimmerHMM_glimmerT_51018-T1
Valid prediction for snap_scaffold_23-snap.956-T1
Valid prediction for snap_scaffold_23-snap.969-T1
Valid prediction for HiQ_model.g34118.t1
Valid prediction for pasa_asmbl_31565.p1
Valid prediction for GlimmerHMM_glimmerT_51008-T1
Valid prediction for snap_scaffold_23-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_51003-T1
Valid prediction for Augustus_model.g34138.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_51014-T1
Valid prediction for snap_scaffold_23-snap.952-T1
Valid prediction for GlimmerHMM_glimmerT_51013-T1
Valid prediction for snap_scaffold_23-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_51025-T1
Valid prediction for GlimmerHMM_glimmerT_51032-T1
Valid prediction for snap_scaffold_23-snap.970-T1
Valid prediction for GlimmerHMM_glimmerT_51022-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g34127.t1
Valid prediction for snap_scaffold_23-snap.972-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34137.t1
Valid prediction for Augustus_model.g34128.t1
Valid prediction for Augustus_model.g34131.t1
Valid prediction for GlimmerHMM_glimmerT_51027-T1
Valid prediction for GlimmerHMM_glimmerT_51017-T1
Valid prediction for CodingQuarry_transcript_35656-T1
Valid prediction for GlimmerHMM_glimmerT_51036-T1
Valid prediction for Augustus_model.g34134.t1
Valid prediction for GlimmerHMM_glimmerT_51026-T1
Valid prediction for Augustus_model.g34132.t1
Valid prediction for snap_scaffold_23-snap.967-T1
Valid prediction for Augustus_model.g34115.t1
Valid prediction for snap_scaffold_23-snap.981-T1
Valid prediction for snap_scaffold_23-snap.984-T1
Valid prediction for pasa_asmbl_30906.p1
Valid prediction for GlimmerHMM_glimmerT_51019-T1
Valid prediction for snap_scaffold_23-snap.978-T1
Valid prediction for pasa_asmbl_30916.p1
Valid prediction for GlimmerHMM_glimmerT_51009-T1
Valid prediction for Augustus_model.g34126.t1
Valid prediction for Augustus_model.g34125.t1
Valid prediction for GlimmerHMM_glimmerT_51005-T1
Valid prediction for GlimmerHMM_glimmerT_51021-T1
Valid prediction for GlimmerHMM_glimmerT_51004-T1
Valid prediction for Augustus_model.g34129.t1
Valid prediction for GlimmerHMM_glimmerT_51033-T1
Valid prediction for GlimmerHMM_glimmerT_51030-T1
Valid prediction for snap_scaffold_23-snap.954-T1
Valid prediction for snap_scaffold_23-snap.950-T1
Valid prediction for snap_scaffold_23-snap.968-T1
Valid prediction for snap_scaffold_23-snap.962-T1
Valid prediction for snap_scaffold_23-snap.985-T1
Valid prediction for snap_scaffold_23-snap.966-T1
Valid prediction for Augustus_model.g34112.t1
Valid prediction for GlimmerHMM_glimmerT_51029-T1
Valid prediction for HiQ_model.g34120.t1
Valid prediction for Augustus_model.g34136.t1

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

-building trellis in range 1 - 307945
-exon list size: 328


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 39 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support