-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_294642-637244

-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 GlimmerHMM_glimmerT_50374-T1
Valid prediction for snap_scaffold_23-snap.42-T1
Valid prediction for snap_scaffold_23-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_50348-T1
Valid prediction for snap_scaffold_23-snap.44-T1
Valid prediction for Augustus_model.g33612.t1
Valid prediction for GlimmerHMM_glimmerT_50367-T1
Valid prediction for snap_scaffold_23-snap.78-T1
Valid prediction for snap_scaffold_23-snap.81-T1
Valid prediction for snap_scaffold_23-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_50373-T1
Valid prediction for GlimmerHMM_glimmerT_50368-T1
Valid prediction for GlimmerHMM_glimmerT_50340-T1
Valid prediction for GlimmerHMM_glimmerT_50360-T1
Valid prediction for Augustus_model.g33616.t1
Valid prediction for Augustus_model.g33586.t1
Valid prediction for Augustus_model.g33603.t1
Valid prediction for Augustus_model.g33605.t1
Valid prediction for snap_scaffold_23-snap.58-T1
Valid prediction for snap_scaffold_23-snap.43-T1
Valid prediction for Augustus_model.g33607.t1
Valid prediction for GlimmerHMM_glimmerT_50359-T1
Valid prediction for Augustus_model.g33617.t1
Valid prediction for snap_scaffold_23-snap.80-T1
Valid prediction for Augustus_model.g33614.t1
Valid prediction for Augustus_model.g33585.t1
Valid prediction for GlimmerHMM_glimmerT_50351-T1
Valid prediction for Augustus_model.g33611.t1
Valid prediction for Augustus_model.g33595.t1
Valid prediction for Augustus_model.g33599.t1
Couldn't classify 294573, 294929
Sorry, prediction pasa_asmbl_31296.p1 fails validation.
(ATT)	 AT	294573-294929	GG	AGG
Valid prediction for snap_scaffold_23-snap.59-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g33587.t1
Valid prediction for GlimmerHMM_glimmerT_50344-T1
Valid prediction for Augustus_model.g33613.t1
Valid prediction for snap_scaffold_23-snap.73-T1
Valid prediction for Augustus_model.g33609.t1
Valid prediction for snap_scaffold_23-snap.45-T1
Valid prediction for Augustus_model.g33598.t1
Valid prediction for GlimmerHMM_glimmerT_50366-T1
Valid prediction for GlimmerHMM_glimmerT_50339-T1
Valid prediction for GlimmerHMM_glimmerT_50347-T1
Valid prediction for GlimmerHMM_glimmerT_50342-T1
Couldn't classify 292881, 293240
Sorry, prediction pasa_asmbl_31294.p1 fails validation.
(ATG)	 TC	292881-293240	CT	ACC
Valid prediction for GlimmerHMM_glimmerT_50346-T1
Valid prediction for snap_scaffold_23-snap.68-T1
Valid prediction for GlimmerHMM_glimmerT_50369-T1
Valid prediction for Augustus_model.g33591.t1
Valid prediction for GlimmerHMM_glimmerT_50365-T1
Valid prediction for GlimmerHMM_glimmerT_50355-T1
Valid prediction for snap_scaffold_23-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_50349-T1
Couldn't classify 293721, 294317
Sorry, prediction pasa_asmbl_31295.p1 fails validation.
(AAG)	 CT	293721-294317	GT	CTG
Valid prediction for GlimmerHMM_glimmerT_50338-T1
Valid prediction for Augustus_model.g33596.t1
Valid prediction for snap_scaffold_23-snap.67-T1
Valid prediction for snap_scaffold_23-snap.79-T1
Valid prediction for snap_scaffold_23-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_50363-T1
Valid prediction for GlimmerHMM_glimmerT_50372-T1
Valid prediction for snap_scaffold_23-snap.72-T1
Valid prediction for snap_scaffold_23-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_50350-T1
Valid prediction for Augustus_model.g33594.t1
Valid prediction for Augustus_model.g33608.t1
Valid prediction for GlimmerHMM_glimmerT_50354-T1
Valid prediction for snap_scaffold_23-snap.61-T1
Valid prediction for snap_scaffold_23-snap.56-T1
Valid prediction for Augustus_model.g33604.t1
Valid prediction for GlimmerHMM_glimmerT_50371-T1
Couldn't classify 178444, 178471
Couldn't classify 178787, 179073
Sorry, prediction pasa_asmbl_31956.p1 fails validation.
(TGG)	 CC	178444-178471	GT	AGG
(GTG)	 AG	178787-179073	TA	GCT
Valid prediction for snap_scaffold_23-snap.40-T1
Valid prediction for snap_scaffold_23-snap.74-T1
Valid prediction for snap_scaffold_23-snap.62-T1
Valid prediction for snap_scaffold_23-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_50341-T1
Valid prediction for GlimmerHMM_glimmerT_50356-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 snap_scaffold_23-snap.39-T1
Valid prediction for CodingQuarry_transcript_35537-T1
Valid prediction for HiQ_model.g33589.t1
Valid prediction for snap_scaffold_23-snap.48-T1
Valid prediction for CodingQuarry_transcript_35539-T1
Valid prediction for Augustus_model.g33590.t1
Valid prediction for snap_scaffold_23-snap.60-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.52-T1
Valid prediction for snap_scaffold_23-snap.70-T1
Valid prediction for CodingQuarry_transcript_35535-T1
Valid prediction for pasa_asmbl_30596.p1
Valid prediction for snap_scaffold_23-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_50370-T1
Valid prediction for Augustus_model.g33615.t1
Valid prediction for snap_scaffold_23-snap.64-T1
Valid prediction for Augustus_model.g33610.t1
Valid prediction for snap_scaffold_23-snap.47-T1
Couldn't classify 312601, 312633
Couldn't classify 316174, 316306
Sorry, prediction pasa_asmbl_30583.p1 fails validation.
(CTC)	 AA	312601-312633	GT	AGG
(CTG)	 AG	312727-312823	GT	AGG
(ATC)	 AG	313879-314070	GT	GGG
(GAG)	 AG	314275-314375	GT	AGG
(GGC)	 AG	314547-314676	GT	TGG
(GGG)	 AG	314757-314886	GT	AGG
(GTG)	 AG	315873-315968	GT	AAG
(GGA)	 AG	316174-316306	CT	AAC
-recovered pasa_asmbl_30583.p1, internal, 312727, 312823
-recovered pasa_asmbl_30583.p1, internal, 313879, 314070
-recovered pasa_asmbl_30583.p1, internal, 314275, 314375
-recovered pasa_asmbl_30583.p1, internal, 314547, 314676
-recovered pasa_asmbl_30583.p1, internal, 314757, 314886
-recovered pasa_asmbl_30583.p1, internal, 315873, 315968
Couldn't classify 299950, 300180
Couldn't classify 300852, 300968
Sorry, prediction pasa_asmbl_30587.p1 fails validation.
(TGC)	 TC	299950-300180	GT	AAG
(GTC)	 AG	300852-300968	GT	AGG
-recovered pasa_asmbl_30587.p1, internal, 300852, 300968
Valid prediction for GlimmerHMM_glimmerT_50362-T1
Valid prediction for CodingQuarry_transcript_35536-T1
Valid prediction for CodingQuarry_transcript_35538-T1
Valid prediction for GlimmerHMM_glimmerT_50343-T1
Valid prediction for CodingQuarry_transcript_35540-T1
Couldn't classify 289294, 289614
Sorry, prediction pasa_asmbl_30588.p1 fails validation.
(AAT)	 AC	289294-289614	AC	GAA
Valid prediction for snap_scaffold_23-snap.46-T1
Valid prediction for HiQ_model.g33593.t1
Valid prediction for CodingQuarry_transcript_35541-T1
Valid prediction for snap_scaffold_23-snap.84-T1
Valid prediction for Augustus_model.g33584.t1
Valid prediction for snap_scaffold_23-snap.85-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 327172, 327225
Couldn't classify 328833, 328960
Sorry, prediction pasa_asmbl_30580.p1 fails validation.
(ACA)	 CT	327172-327225	GT	GGG
(ACC)	 AG	328280-328372	GT	AGG
(GTG)	 AG	328493-328649	GT	AGG
(AGT)	 AG	328833-328960	GT	CAG
-recovered pasa_asmbl_30580.p1, internal, 328280, 328372
-recovered pasa_asmbl_30580.p1, internal, 328493, 328649
-recovered pasa_asmbl_30580.p1, internal, 328833, 328960
Valid prediction for GlimmerHMM_glimmerT_50361-T1
Valid prediction for Augustus_model.g33602.t1
Valid prediction for GlimmerHMM_glimmerT_50345-T1
Valid prediction for snap_scaffold_23-snap.54-T1
Valid prediction for snap_scaffold_23-snap.51-T1
Valid prediction for Augustus_model.g33600.t1
Valid prediction for Augustus_model.g33601.t1
Couldn't classify 323714, 323803
Sorry, prediction pasa_asmbl_30581.p1 fails validation.
(ATG)	 AG	316725-316829	GT	AGG
(GCA)	 AG	318960-319010	GT	TGG
(CTG)	 AG	319132-319240	GT	AGG
(GTT)	 AG	319376-319512	GT	CGG
(GCT)	 AG	319635-319768	GT	AGG
(GAT)	 AG	319896-319978	GT	TGG
(GGA)	 AG	320094-320164	GT	AGG
(GCC)	 AG	320263-320387	GT	ACG
(TTT)	 AG	323346-323427	GT	CAG
(GAC)	 AG	323511-323594	GT	AGG
(AGT)	 AG	323714-323803	GT	AGG
-recovered pasa_asmbl_30581.p1, initial, 316725, 316829
-recovered pasa_asmbl_30581.p1, internal, 316725, 316829
-recovered pasa_asmbl_30581.p1, internal, 318960, 319010
-recovered pasa_asmbl_30581.p1, internal, 319132, 319240
-recovered pasa_asmbl_30581.p1, internal, 319376, 319512
-recovered pasa_asmbl_30581.p1, internal, 319635, 319768
-recovered pasa_asmbl_30581.p1, internal, 319896, 319978
-recovered pasa_asmbl_30581.p1, internal, 320094, 320164
-recovered pasa_asmbl_30581.p1, internal, 320263, 320387
-recovered pasa_asmbl_30581.p1, internal, 323346, 323427
-recovered pasa_asmbl_30581.p1, internal, 323511, 323594
-recovered pasa_asmbl_30581.p1, internal, 323714, 323803
Valid prediction for snap_scaffold_23-snap.57-T1
Valid prediction for snap_scaffold_23-snap.69-T1
Valid prediction for snap_scaffold_23-snap.50-T1
Valid prediction for Augustus_model.g33606.t1
Valid prediction for GlimmerHMM_glimmerT_50375-T1
Valid prediction for GlimmerHMM_glimmerT_50352-T1
Valid prediction for snap_scaffold_23-snap.82-T1
Valid prediction for snap_scaffold_23-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_50358-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50357-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.86-T1
Valid prediction for snap_scaffold_23-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_50364-T1
Valid prediction for Augustus_model.g33588.t1
Valid prediction for snap_scaffold_23-snap.63-T1
Valid prediction for snap_scaffold_23-snap.66-T1
Valid prediction for snap_scaffold_23-snap.75-T1
Valid prediction for Augustus_model.g33592.t1
Valid prediction for Augustus_model.g33597.t1
Valid prediction for GlimmerHMM_glimmerT_50353-T1

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

-building trellis in range 1 - 342603
-exon list size: 411


building trellis

0.2    
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1.0    
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1.5    
1.7    
1.9    
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2.9    
3.1    
3.4    
3.6    
3.9    
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4.6    
4.8    
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5.8    
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6.3    
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7.0    
7.3    
7.5    
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8.2    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 50 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 44 predictions persist after filtering for low support