-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_4676395-5021772

-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: +)Couldn't classify 111242, 111363
Couldn't classify 111605, 111749
Sorry, prediction CodingQuarry_transcript_37299-T1 fails validation.
(ATG)	 TC	108125-108142	GT	AGG
(GCA)	 AG	109161-109256	GT	TGG
(GCC)	 AG	109374-109503	GT	AGG
(AGG)	 AG	109591-109716	GT	TGG
(ATG)	 AG	110042-110155	GT	GGG
(ATT)	 AG	110338-110487	GT	GGG
(AGG)	 AG	110964-111047	GT	TGG
(GGG)	 AG	111242-111363	CT	CAC
(TCC)	 TT	111605-111749	GT	AGG
(AGA)	 AG	111857-111983	GT	GGG
(CAT)	 AG	112096-112232	GT	AGG
(CTG)	 AG	112507-112639	GT	GGG
(GTT)	 AG	112917-113062	GT	GGG
(GGC)	 AG	113176-113302	GT	GGG
(CTT)	 AG	113596-113876	GT	CGG
(GTG)	 AG	114061-114125	AA	AAA
-recovered CodingQuarry_transcript_37299-T1, initial, 108125, 108142
add_exon() Sorry, CodingQuarry_transcript_37299-T1 110042-110155-initial-1 is invalid.
-recovered CodingQuarry_transcript_37299-T1, initial, 110042, 110155
-recovered CodingQuarry_transcript_37299-T1, terminal, 114061, 114125
-recovered CodingQuarry_transcript_37299-T1, internal, 109161, 109256
-recovered CodingQuarry_transcript_37299-T1, internal, 109374, 109503
-recovered CodingQuarry_transcript_37299-T1, internal, 109591, 109716
-recovered CodingQuarry_transcript_37299-T1, internal, 110042, 110155
-recovered CodingQuarry_transcript_37299-T1, internal, 110338, 110487
-recovered CodingQuarry_transcript_37299-T1, internal, 110964, 111047
-recovered CodingQuarry_transcript_37299-T1, internal, 111857, 111983
-recovered CodingQuarry_transcript_37299-T1, internal, 112096, 112232
-recovered CodingQuarry_transcript_37299-T1, internal, 112507, 112639
-recovered CodingQuarry_transcript_37299-T1, internal, 112917, 113062
-recovered CodingQuarry_transcript_37299-T1, internal, 113176, 113302
-recovered CodingQuarry_transcript_37299-T1, internal, 113596, 113876
Valid prediction for HiQ_model.g34942.t1
Valid prediction for GlimmerHMM_glimmerT_52465-T1
Valid prediction for GlimmerHMM_glimmerT_52449-T1
Valid prediction for HiQ_model.g34948.t1
Valid prediction for pasa_asmbl_32205.p1
Valid prediction for GlimmerHMM_glimmerT_52468-T1
Valid prediction for snap_scaffold_24-snap.1011-T1
Valid prediction for snap_scaffold_24-snap.1010-T1
Valid prediction for snap_scaffold_24-snap.1000-T1
Valid prediction for snap_scaffold_24-snap.983-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34951.t1
Valid prediction for GlimmerHMM_glimmerT_52462-T1
Valid prediction for GlimmerHMM_glimmerT_52451-T1
Valid prediction for snap_scaffold_24-snap.1007-T1
Valid prediction for snap_scaffold_24-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_52454-T1
Valid prediction for GlimmerHMM_glimmerT_52444-T1
Valid prediction for snap_scaffold_24-snap.985-T1
Valid prediction for snap_scaffold_24-snap.1014-T1
Valid prediction for Augustus_model.g34950.t1
Couldn't classify 159239, 159269
Sorry, prediction pasa_asmbl_32206.p1 fails validation.
(AAC)	 CC	159239-159269	GT	AGG
(AGT)	 AG	159385-159458	GT	AGG
(ACC)	 AG	160077-160290	GT	AGG
(GCG)	 AG	160439-160561	GT	AGG
(GGT)	 AG	160790-160920	GT	CCG
(ATA)	 AG	161606-161686	TT	GAT
-recovered pasa_asmbl_32206.p1, terminal, 161606, 161686
-recovered pasa_asmbl_32206.p1, internal, 159385, 159458
-recovered pasa_asmbl_32206.p1, internal, 160077, 160290
-recovered pasa_asmbl_32206.p1, internal, 160439, 160561
-recovered pasa_asmbl_32206.p1, internal, 160790, 160920
Valid prediction for snap_scaffold_24-snap.987-T1
Valid prediction for snap_scaffold_24-snap.986-T1
Valid prediction for snap_scaffold_24-snap.1001-T1
Valid prediction for GlimmerHMM_glimmerT_52461-T1
Valid prediction for GlimmerHMM_glimmerT_52445-T1
Valid prediction for GlimmerHMM_glimmerT_52464-T1
Valid prediction for snap_scaffold_24-snap.1009-T1
Valid prediction for GlimmerHMM_glimmerT_52452-T1
Valid prediction for GlimmerHMM_glimmerT_52467-T1
Valid prediction for Augustus_model.g34943.t1
Valid prediction for Augustus_model.g34940.t1
Valid prediction for snap_scaffold_24-snap.1004-T1
Valid prediction for Augustus_model.g34949.t1
Valid prediction for GlimmerHMM_glimmerT_52456-T1
Valid prediction for GlimmerHMM_glimmerT_52455-T1
Valid prediction for snap_scaffold_24-snap.1006-T1
Valid prediction for snap_scaffold_24-snap.988-T1
Valid prediction for CodingQuarry_transcript_37302-T1
Valid prediction for GlimmerHMM_glimmerT_52460-T1
Valid prediction for GlimmerHMM_glimmerT_52446-T1
Valid prediction for Augustus_model.g34941.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_52466-T1
Valid prediction for GlimmerHMM_glimmerT_52459-T1
Valid prediction for snap_scaffold_24-snap.995-T1
Valid prediction for snap_scaffold_24-snap.1012-T1
Valid prediction for HiQ_model.g34945.t1
Valid prediction for CodingQuarry_transcript_37300-T1
Valid prediction for snap_scaffold_24-snap.1008-T1
Valid prediction for Augustus_model.g34936.t1
Valid prediction for GlimmerHMM_glimmerT_52439-T1
Valid prediction for GlimmerHMM_glimmerT_52450-T1
Valid prediction for Augustus_model.g34944.t1
Valid prediction for GlimmerHMM_glimmerT_52448-T1
Valid prediction for GlimmerHMM_glimmerT_52453-T1
Valid prediction for Augustus_model.g34946.t1
Valid prediction for snap_scaffold_24-snap.1002-T1
Valid prediction for snap_scaffold_24-snap.981-T1
Valid prediction for snap_scaffold_24-snap.979-T1
Valid prediction for snap_scaffold_24-snap.990-T1
Valid prediction for HiQ_model.g34947.t1
Valid prediction for snap_scaffold_24-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_52438-T1
Valid prediction for Augustus_model.g34939.t1
Valid prediction for snap_scaffold_24-snap.992-T1
Valid prediction for snap_scaffold_24-snap.997-T1
Valid prediction for snap_scaffold_24-snap.975-T1
Valid prediction for snap_scaffold_24-snap.1005-T1
Valid prediction for CodingQuarry_transcript_37301-T1
Valid prediction for snap_scaffold_24-snap.994-T1
Valid prediction for GlimmerHMM_glimmerT_52458-T1
Couldn't classify 198489, 198524
Sorry, prediction pasa_asmbl_32879.p2 fails validation.
(ATG)	 CA	196305-196335	GT	AGG
(ACG)	 AG	196464-196621	GT	TGG
(ATC)	 AG	196850-196948	GT	CTG
(GGA)	 AG	198489-198524	GT	ATG
-recovered pasa_asmbl_32879.p2, initial, 196305, 196335
-recovered pasa_asmbl_32879.p2, internal, 196464, 196621
-recovered pasa_asmbl_32879.p2, internal, 196850, 196948
-recovered pasa_asmbl_32879.p2, internal, 198489, 198524
Valid prediction for snap_scaffold_24-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_52463-T1
Valid prediction for GlimmerHMM_glimmerT_52440-T1
Valid prediction for snap_scaffold_24-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_52443-T1
Valid prediction for pasa_asmbl_32875.p1
Valid prediction for snap_scaffold_24-snap.998-T1
Valid prediction for snap_scaffold_24-snap.977-T1
Valid prediction for snap_scaffold_24-snap.989-T1
Valid prediction for Augustus_model.g34937.t1
Valid prediction for snap_scaffold_24-snap.1003-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.996-T1
Valid prediction for Augustus_model.g34938.t1
Valid prediction for snap_scaffold_24-snap.991-T1
Couldn't classify 194671, 194796
Sorry, prediction pasa_asmbl_32880.p1 fails validation.
(ATG)	 AC	193572-193646	GT	AGG
(TAT)	 AG	193812-193937	GT	AGG
(AAG)	 AG	194025-194195	GT	ATG
(GAT)	 AG	194671-194796	GT	CGG
-recovered pasa_asmbl_32880.p1, initial, 193572, 193646
-recovered pasa_asmbl_32880.p1, internal, 193812, 193937
-recovered pasa_asmbl_32880.p1, internal, 194025, 194195
-recovered pasa_asmbl_32880.p1, internal, 194671, 194796
Valid prediction for GlimmerHMM_glimmerT_52442-T1
Valid prediction for GlimmerHMM_glimmerT_52447-T1
Valid prediction for GlimmerHMM_glimmerT_52457-T1
Valid prediction for GlimmerHMM_glimmerT_52441-T1
Valid prediction for snap_scaffold_24-snap.978-T1
Valid prediction for GlimmerHMM_glimmerT_52437-T1
Valid prediction for snap_scaffold_24-snap.984-T1
Valid prediction for snap_scaffold_24-snap.982-T1
Valid prediction for snap_scaffold_24-snap.980-T1

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

-building trellis in range 1 - 345378
-exon list size: 311


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.7    
8.0    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.3    
15.7    
16.0    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.4    
20.8    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.3    
23.6    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.4    
36.7    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.5    
41.9    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.1    
58.5    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.3    
63.6    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.4    
76.7    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.2    
79.6    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.0    
84.3    
84.7    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.0    
92.3    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 30 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 328507 - 345378
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 334317 - 345378
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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