-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_5826205-6126457

-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_9477-T1
Valid prediction for snap_scaffold_4-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_9453-T1
Valid prediction for GlimmerHMM_glimmerT_9454-T1
Valid prediction for Augustus_model.g6113.t1
Valid prediction for snap_scaffold_4-snap.1276-T1
Valid prediction for snap_scaffold_4-snap.1319-T1
Valid prediction for Augustus_model.g6137.t1
Valid prediction for GlimmerHMM_glimmerT_9451-T1
Valid prediction for snap_scaffold_4-snap.1320-T1
Valid prediction for Augustus_model.g6139.t1
Valid prediction for snap_scaffold_4-snap.1280-T1
Valid prediction for snap_scaffold_4-snap.1293-T1
Valid prediction for snap_scaffold_4-snap.1309-T1
Valid prediction for snap_scaffold_4-snap.1282-T1
Valid prediction for pasa_asmbl_41373.p1
Valid prediction for GlimmerHMM_glimmerT_9478-T1
Valid prediction for CodingQuarry_transcript_49010-T1
Valid prediction for GlimmerHMM_glimmerT_9448-T1
Valid prediction for snap_scaffold_4-snap.1297-T1
Valid prediction for snap_scaffold_4-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_9459-T1
Valid prediction for Augustus_model.g6120.t1
Valid prediction for snap_scaffold_4-snap.1286-T1
Valid prediction for CodingQuarry_transcript_49011-T1
Valid prediction for snap_scaffold_4-snap.1294-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9447-T1
Valid prediction for GlimmerHMM_glimmerT_9479-T1
Valid prediction for GlimmerHMM_glimmerT_9476-T1
Valid prediction for Augustus_model.g6122.t1
Valid prediction for GlimmerHMM_glimmerT_9474-T1
Valid prediction for Augustus_model.g6114.t1
Valid prediction for GlimmerHMM_glimmerT_9461-T1
Valid prediction for GlimmerHMM_glimmerT_9457-T1
Valid prediction for Augustus_model.g6140.t1
Valid prediction for HiQ_model.g6111.t1
Valid prediction for snap_scaffold_4-snap.1321-T1
Valid prediction for Augustus_model.g6118.t1
Valid prediction for GlimmerHMM_glimmerT_9456-T1
Valid prediction for snap_scaffold_4-snap.1295-T1
Couldn't classify 94902, 95207
Sorry, prediction pasa_asmbl_42649.p1 fails validation.
(CAC)	 TC	94902-95207	AC	ACA
Valid prediction for Augustus_model.g6141.t1
Valid prediction for snap_scaffold_4-snap.1289-T1
Valid prediction for snap_scaffold_4-snap.1275-T1
Valid prediction for snap_scaffold_4-snap.1316-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_4-snap.1311-T1
Valid prediction for Augustus_model.g6134.t1
Valid prediction for Augustus_model.g6123.t1
Valid prediction for snap_scaffold_4-snap.1298-T1
Valid prediction for Augustus_model.g6121.t1
Valid prediction for Augustus_model.g6127.t1
Valid prediction for snap_scaffold_4-snap.1283-T1
Valid prediction for snap_scaffold_4-snap.1284-T1
Valid prediction for snap_scaffold_4-snap.1305-T1
Valid prediction for snap_scaffold_4-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_9464-T1
Valid prediction for GlimmerHMM_glimmerT_9455-T1
Valid prediction for Augustus_model.g6133.t1
Valid prediction for GlimmerHMM_glimmerT_9473-T1
Valid prediction for GlimmerHMM_glimmerT_9470-T1
Valid prediction for snap_scaffold_4-snap.1314-T1
Valid prediction for snap_scaffold_4-snap.1281-T1
Valid prediction for Augustus_model.g6124.t1
Valid prediction for pasa_asmbl_42643.p1
Valid prediction for GlimmerHMM_glimmerT_9450-T1
Valid prediction for GlimmerHMM_glimmerT_9466-T1
Valid prediction for snap_scaffold_4-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_9469-T1
Valid prediction for CodingQuarry_transcript_49013-T1
Valid prediction for snap_scaffold_4-snap.1315-T1
Valid prediction for snap_scaffold_4-snap.1291-T1
Valid prediction for snap_scaffold_4-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_9458-T1
Valid prediction for Augustus_model.g6129.t1
Valid prediction for GlimmerHMM_glimmerT_9471-T1
Valid prediction for GlimmerHMM_glimmerT_9467-T1
Valid prediction for Augustus_model.g6138.t1
Valid prediction for snap_scaffold_4-snap.1299-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9480-T1
Valid prediction for snap_scaffold_4-snap.1296-T1
Valid prediction for Augustus_model.g6136.t1
Valid prediction for snap_scaffold_4-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_9452-T1
Valid prediction for snap_scaffold_4-snap.1310-T1
Valid prediction for GlimmerHMM_glimmerT_9460-T1
Valid prediction for GlimmerHMM_glimmerT_9475-T1
Valid prediction for Augustus_model.g6128.t1
Valid prediction for Augustus_model.g6115.t1
Valid prediction for Augustus_model.g6117.t1
Valid prediction for Augustus_model.g6135.t1
Valid prediction for snap_scaffold_4-snap.1301-T1
Valid prediction for snap_scaffold_4-snap.1317-T1
Valid prediction for Augustus_model.g6132.t1
Valid prediction for Augustus_model.g6119.t1
Valid prediction for Augustus_model.g6125.t1
Valid prediction for snap_scaffold_4-snap.1292-T1
Valid prediction for GlimmerHMM_glimmerT_9468-T1
Valid prediction for snap_scaffold_4-snap.1303-T1
Valid prediction for snap_scaffold_4-snap.1304-T1
Valid prediction for snap_scaffold_4-snap.1285-T1
Valid prediction for snap_scaffold_4-snap.1313-T1
Valid prediction for GlimmerHMM_glimmerT_9462-T1
Valid prediction for GlimmerHMM_glimmerT_9472-T1
Valid prediction for Augustus_model.g6130.t1
Valid prediction for snap_scaffold_4-snap.1307-T1
Couldn't classify 217417, 217556
Sorry, prediction pasa_asmbl_42648.p1 fails validation.
(CAC)	 TC	217417-217556	GT	TGG
(GGA)	 AG	218186-218274	GT	ATG
(TGG)	 AG	218479-218621	CT	AAC
-recovered pasa_asmbl_42648.p1, terminal, 218479, 218621
-recovered pasa_asmbl_42648.p1, internal, 218186, 218274
Valid prediction for snap_scaffold_4-snap.1302-T1
Valid prediction for GlimmerHMM_glimmerT_9449-T1
Valid prediction for GlimmerHMM_glimmerT_9465-T1
Valid prediction for snap_scaffold_4-snap.1308-T1
Valid prediction for GlimmerHMM_glimmerT_9446-T1
Valid prediction for GlimmerHMM_glimmerT_9463-T1
Valid prediction for snap_scaffold_4-snap.1318-T1
Couldn't classify 201809, 201979
Couldn't classify 203398, 203514
Sorry, prediction pasa_asmbl_42650.p1 fails validation.
(TCC)	 GG	201809-201979	GT	AGG
(CTT)	 AG	202837-203019	GT	AGG
(ATT)	 AG	203398-203514	GG	ATG
-recovered pasa_asmbl_42650.p1, internal, 202837, 203019
Valid prediction for snap_scaffold_4-snap.1300-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_49012-T1
Valid prediction for GlimmerHMM_glimmerT_9445-T1
Valid prediction for snap_scaffold_4-snap.1288-T1
Valid prediction for Augustus_model.g6131.t1
Valid prediction for Augustus_model.g6126.t1
Valid prediction for Augustus_model.g6112.t1
Couldn't classify 231685, 231807
Couldn't classify 238084, 238102
Sorry, prediction pasa_asmbl_42647.p1 fails validation.
(TTT)	 AC	231685-231807	GT	AGG
(GCG)	 AG	233730-233816	GT	AGG
(CTG)	 AG	233922-233988	GT	ACG
(TTG)	 AG	235730-235875	GT	AGG
(ACT)	 AG	235954-236132	GT	AGG
(TTT)	 AG	238084-238102	GA	GGG
-recovered pasa_asmbl_42647.p1, internal, 233730, 233816
-recovered pasa_asmbl_42647.p1, internal, 233922, 233988
-recovered pasa_asmbl_42647.p1, internal, 235730, 235875
-recovered pasa_asmbl_42647.p1, internal, 235954, 236132
Valid prediction for snap_scaffold_4-snap.1290-T1
Valid prediction for Augustus_model.g6116.t1

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

-building trellis in range 1 - 300253
-exon list size: 360


building trellis

0.3    
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11.9    
12.2    
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12.7    
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13.5    
13.8    
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14.4    
14.6    
14.9    
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16.0    
16.3    
16.6    
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17.1    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.1    
19.3    
19.6    
19.9    
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20.4    
20.7    
21.0    
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22.4    
22.7    
22.9    
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23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.1    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.1    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
51.9    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.9    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
80.9    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.3    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 43 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 286260 - 300253
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 286260 - 296814
-exon list size: 1


building trellis

33.3    
66.7    
-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