-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_5422460-5661318

-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 GeneMark_model.25438_t
Valid prediction for CodingQuarry_transcript_54906-T1
Valid prediction for GeneMark_model.25429_t
Valid prediction for CodingQuarry_transcript_54910-T1
Valid prediction for GlimmerHMM_glimmerT_15032-T1
Valid prediction for snap_scaffold_6-snap.1281-T1
Valid prediction for Augustus_model.g9999.t1
Valid prediction for GlimmerHMM_glimmerT_15036-T1
Valid prediction for snap_scaffold_6-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_15034-T1
Couldn't classify 233248, 233366
Couldn't classify 234312, 234329
Sorry, prediction pasa_asmbl_46908.p1 fails validation.
(CAG)	 CC	233248-233366	GT	CAG
(AGG)	 AG	233574-233703	GT	AGG
(GCC)	 AG	233800-233979	GT	AAG
(AGA)	 AG	234077-234226	GT	AGG
(GGG)	 AG	234312-234329	AC	TGA
-recovered pasa_asmbl_46908.p1, internal, 233574, 233703
-recovered pasa_asmbl_46908.p1, internal, 233800, 233979
-recovered pasa_asmbl_46908.p1, internal, 234077, 234226
Valid prediction for Augustus_model.g9995.t1
Valid prediction for snap_scaffold_6-snap.1277-T1
Valid prediction for Augustus_model.g10011.t1
Valid prediction for GlimmerHMM_glimmerT_15016-T1
Valid prediction for GeneMark_model.25425_t
Valid prediction for snap_scaffold_6-snap.1279-T1
Valid prediction for snap_scaffold_6-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_15021-T1
Couldn't classify 88532, 88654
Sorry, prediction pasa_asmbl_46898.p1 fails validation.
(GTG)	 GA	88532-88654	GT	AGG
(CAA)	 AG	88906-89055	GT	AGG
(ATG)	 AG	89167-89259	TT	AGT
-recovered pasa_asmbl_46898.p1, terminal, 89167, 89259
-recovered pasa_asmbl_46898.p1, internal, 88906, 89055
Valid prediction for GlimmerHMM_glimmerT_15009-T1
Valid prediction for snap_scaffold_6-snap.1282-T1
Valid prediction for snap_scaffold_6-snap.1299-T1
Couldn't classify 229509, 229630
Sorry, prediction pasa_asmbl_46906.p2 fails validation.
(ATG)	 AG	228854-228908	GT	AGG
(GAC)	 AG	229123-229407	GT	AGG
(TCC)	 AG	229509-229630	AT	ACA
-recovered pasa_asmbl_46906.p2, initial, 228854, 228908
-recovered pasa_asmbl_46906.p2, internal, 228854, 228908
-recovered pasa_asmbl_46906.p2, internal, 229123, 229407
Valid prediction for Augustus_model.g10002.t1
Valid prediction for HiQ_model.g9998.t1
Valid prediction for GlimmerHMM_glimmerT_15015-T1
Valid prediction for GlimmerHMM_glimmerT_15037-T1
Valid prediction for GeneMark_model.25423_t
Valid prediction for GlimmerHMM_glimmerT_15025-T1
Valid prediction for GlimmerHMM_glimmerT_15033-T1
Valid prediction for pasa_asmbl_46886.p1
Valid prediction for pasa_asmbl_46897.p1
Valid prediction for Augustus_model.g10005.t1
Valid prediction for snap_scaffold_6-snap.1291-T1
Valid prediction for GeneMark_model.25420_t
Valid prediction for CodingQuarry_transcript_54905-T1
Valid prediction for snap_scaffold_6-snap.1284-T1
Valid prediction for Augustus_model.g10000.t1
Valid prediction for snap_scaffold_6-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_15027-T1
Valid prediction for GlimmerHMM_glimmerT_15017-T1
Valid prediction for snap_scaffold_6-snap.1295-T1
Valid prediction for GlimmerHMM_glimmerT_15029-T1
Valid prediction for GeneMark_model.25422_t
Couldn't classify 234615, 234701
Couldn't classify 236079, 236191
Sorry, prediction pasa_asmbl_46909.p1 fails validation.
(GAC)	 CA	234615-234701	GT	TGG
(GAT)	 AG	234869-235036	GT	GGG
(TCC)	 AG	235121-235232	GT	AGG
(GGG)	 AG	235377-235535	GT	AGG
(CGT)	 AG	235640-235786	GT	GAG
(CGT)	 AG	235875-235973	GT	AGG
(ACA)	 AG	236079-236191	AT	GCA
-recovered pasa_asmbl_46909.p1, internal, 234869, 235036
-recovered pasa_asmbl_46909.p1, internal, 235121, 235232
-recovered pasa_asmbl_46909.p1, internal, 235377, 235535
-recovered pasa_asmbl_46909.p1, internal, 235640, 235786
-recovered pasa_asmbl_46909.p1, internal, 235875, 235973
Valid prediction for GeneMark_model.25435_t
Valid prediction for Augustus_model.g10001.t1
Valid prediction for snap_scaffold_6-snap.1280-T1
Couldn't classify 17794, 17862
Sorry, prediction pasa_asmbl_46892.p1 fails validation.
(GTC)	 CT	17794-17862	GT	AAG
(ACC)	 AG	18464-18604	GT	AGG
(GCT)	 AG	18833-18908	GT	AGG
(GCG)	 AG	19179-19308	GT	AGG
(AGA)	 AG	19562-19685	AT	AGA
-recovered pasa_asmbl_46892.p1, terminal, 19562, 19685
-recovered pasa_asmbl_46892.p1, internal, 18464, 18604
-recovered pasa_asmbl_46892.p1, internal, 18833, 18908
-recovered pasa_asmbl_46892.p1, internal, 19179, 19308
Valid prediction for pasa_asmbl_46896.p1
Valid prediction for GlimmerHMM_glimmerT_15023-T1
Valid prediction for snap_scaffold_6-snap.1301-T1
Valid prediction for snap_scaffold_6-snap.1283-T1
Valid prediction for Augustus_model.g10008.t1
Valid prediction for GeneMark_model.25439_t
Valid prediction for GeneMark_model.25433_t
Valid prediction for CodingQuarry_transcript_54908-T1
Valid prediction for GeneMark_model.25418_t
Valid prediction for GlimmerHMM_glimmerT_15010-T1
Valid prediction for GlimmerHMM_glimmerT_15012-T1
Valid prediction for HiQ_model.g9996.t1
Couldn't classify 231425, 231604
Couldn't classify 232627, 232712
Sorry, prediction pasa_asmbl_46907.p1 fails validation.
(CAG)	 CC	231425-231604	GT	AAG
(GAA)	 AG	231714-231822	GT	GAG
(ATC)	 AG	231921-232041	GT	TGG
(CCT)	 AG	232171-232248	GT	AAG
(CTT)	 AG	232373-232530	GT	TGG
(ATC)	 AG	232627-232712	CT	AGC
-recovered pasa_asmbl_46907.p1, internal, 231714, 231822
-recovered pasa_asmbl_46907.p1, internal, 231921, 232041
-recovered pasa_asmbl_46907.p1, internal, 232171, 232248
-recovered pasa_asmbl_46907.p1, internal, 232373, 232530
Valid prediction for GeneMark_model.25416_t

-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.25424_t
Valid prediction for GlimmerHMM_glimmerT_15019-T1
Valid prediction for HiQ_model.g9997.t1
Valid prediction for GlimmerHMM_glimmerT_15014-T1
Valid prediction for GeneMark_model.25431_t
Valid prediction for snap_scaffold_6-snap.1297-T1
Valid prediction for GeneMark_model.25428_t
Valid prediction for GeneMark_model.25426_t
Valid prediction for Augustus_model.g10004.t1
Valid prediction for GlimmerHMM_glimmerT_15013-T1
Valid prediction for GlimmerHMM_glimmerT_15035-T1
Valid prediction for snap_scaffold_6-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_15026-T1
Valid prediction for snap_scaffold_6-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_15024-T1
Valid prediction for GeneMark_model.25432_t
Valid prediction for GlimmerHMM_glimmerT_15028-T1
Valid prediction for Augustus_model.g10003.t1
Valid prediction for GeneMark_model.25436_t
Valid prediction for snap_scaffold_6-snap.1296-T1
Valid prediction for GeneMark_model.25430_t
Valid prediction for GlimmerHMM_glimmerT_15022-T1
Valid prediction for Augustus_model.g10010.t1
Valid prediction for HiQ_model.g10006.t1
Valid prediction for GlimmerHMM_glimmerT_15011-T1
Valid prediction for snap_scaffold_6-snap.1288-T1
Valid prediction for snap_scaffold_6-snap.1302-T1
Valid prediction for GeneMark_model.25419_t
Valid prediction for CodingQuarry_transcript_54911-T1
Valid prediction for pasa_asmbl_48367.p1
Valid prediction for GeneMark_model.25440_t
Valid prediction for GlimmerHMM_glimmerT_15018-T1
Valid prediction for snap_scaffold_6-snap.1290-T1
Valid prediction for pasa_asmbl_48363.p1
Valid prediction for Augustus_model.g10009.t1
Valid prediction for GlimmerHMM_glimmerT_15030-T1
Valid prediction for GeneMark_model.25437_t
Valid prediction for GeneMark_model.25417_t
Valid prediction for GlimmerHMM_glimmerT_15020-T1
Couldn't classify 147262, 147280
Sorry, prediction pasa_asmbl_48366.p1 fails validation.
(AAG)	 AC	147262-147280	GT	GAG
(GTG)	 AG	147427-147586	GT	AGG
(GGA)	 AG	147673-147818	GT	GGG
(AGA)	 AG	147918-148090	GA	GAG
-recovered pasa_asmbl_48366.p1, terminal, 147918, 148090
-recovered pasa_asmbl_48366.p1, internal, 147427, 147586
-recovered pasa_asmbl_48366.p1, internal, 147673, 147818
Valid prediction for HiQ_model.g10012.t1
Valid prediction for snap_scaffold_6-snap.1285-T1
Valid prediction for snap_scaffold_6-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_15031-T1
Valid prediction for snap_scaffold_6-snap.1298-T1
Valid prediction for CodingQuarry_transcript_54912-T1
Valid prediction for GeneMark_model.25421_t
Valid prediction for Augustus_model.g10007.t1
Valid prediction for snap_scaffold_6-snap.1289-T1
Valid prediction for snap_scaffold_6-snap.1292-T1
Valid prediction for GeneMark_model.25427_t
Valid prediction for GeneMark_model.25434_t
Valid prediction for CodingQuarry_transcript_54907-T1

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

-building trellis in range 1 - 238859
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal

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