-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_5735211-5928894

-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_9642-T1
Valid prediction for GlimmerHMM_glimmerT_9640-T1
Valid prediction for GlimmerHMM_glimmerT_9633-T1
Valid prediction for GlimmerHMM_glimmerT_9635-T1
Valid prediction for GeneMark_model.15743_t
Valid prediction for HiQ_model.g6291.t1
Valid prediction for Augustus_model.g6298.t1
Valid prediction for GlimmerHMM_glimmerT_9643-T1
Valid prediction for GeneMark_model.15729_t
Valid prediction for GeneMark_model.15744_t
Valid prediction for GeneMark_model.15726_t
Valid prediction for Augustus_model.g6284.t1
Valid prediction for pasa_asmbl_42703.p1
Valid prediction for GeneMark_model.15747_t
Valid prediction for GeneMark_model.15739_t
Valid prediction for snap_scaffold_4-snap.1270-T1
Valid prediction for snap_scaffold_4-snap.1268-T1
Valid prediction for snap_scaffold_4-snap.1271-T1
Valid prediction for snap_scaffold_4-snap.1269-T1
Valid prediction for GeneMark_model.15734_t
Valid prediction for GlimmerHMM_glimmerT_9627-T1
Couldn't classify 185896, 186201
Sorry, prediction pasa_asmbl_41390.p1 fails validation.
(CAC)	 TC	185896-186201	AC	ACA
Valid prediction for snap_scaffold_4-snap.1282-T1
Valid prediction for snap_scaffold_4-snap.1257-T1
Valid prediction for snap_scaffold_4-snap.1262-T1
Valid prediction for GeneMark_model.15723_t
Valid prediction for GlimmerHMM_glimmerT_9638-T1
Valid prediction for GeneMark_model.15732_t
Valid prediction for snap_scaffold_4-snap.1272-T1
Valid prediction for Augustus_model.g6287.t1
Valid prediction for GlimmerHMM_glimmerT_9624-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_48906-T1
Valid prediction for Augustus_model.g6293.t1
Valid prediction for snap_scaffold_4-snap.1274-T1
Valid prediction for CodingQuarry_transcript_48905-T1
Valid prediction for Augustus_model.g6283.t1
Valid prediction for snap_scaffold_4-snap.1276-T1
Valid prediction for Augustus_model.g6294.t1
Valid prediction for GlimmerHMM_glimmerT_9637-T1
Valid prediction for Augustus_model.g6280.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: -)Couldn't classify 34122, 34244
Couldn't classify 40521, 40539
Sorry, prediction pasa_asmbl_41388.p1 fails validation.
(TTT)	 AC	34122-34244	GT	AGG
(GCG)	 AG	36167-36253	GT	AGG
(CTG)	 AG	36359-36425	GT	ACG
(TTG)	 AG	38167-38312	GT	AGG
(ACT)	 AG	38391-38569	GT	AGG
(TTT)	 AG	40521-40539	GA	GGG
-recovered pasa_asmbl_41388.p1, internal, 36167, 36253
-recovered pasa_asmbl_41388.p1, internal, 36359, 36425
-recovered pasa_asmbl_41388.p1, internal, 38167, 38312
-recovered pasa_asmbl_41388.p1, internal, 38391, 38569
Valid prediction for snap_scaffold_4-snap.1258-T1
Valid prediction for snap_scaffold_4-snap.1281-T1
Valid prediction for Augustus_model.g6299.t1
Valid prediction for GeneMark_model.15746_t
Valid prediction for GlimmerHMM_glimmerT_9641-T1
Couldn't classify 153422, 153580
Sorry, prediction pasa_asmbl_41377.p1 fails validation.
(GAA)	 AG	153422-153580	GT	AGG
(GCA)	 AG	153713-153775	GT	AGG
(GGC)	 AG	154227-154385	GT	TGG
(AAA)	 AG	154466-154636	AC	AAA
-recovered pasa_asmbl_41377.p1, terminal, 154466, 154636
-recovered pasa_asmbl_41377.p1, internal, 153422, 153580
-recovered pasa_asmbl_41377.p1, internal, 153713, 153775
-recovered pasa_asmbl_41377.p1, internal, 154227, 154385
Valid prediction for snap_scaffold_4-snap.1259-T1
Valid prediction for GeneMark_model.15733_t
Valid prediction for GeneMark_model.15740_t
Valid prediction for snap_scaffold_4-snap.1267-T1
Valid prediction for snap_scaffold_4-snap.1255-T1
Valid prediction for GeneMark_model.15727_t
Valid prediction for snap_scaffold_4-snap.1265-T1
Valid prediction for GlimmerHMM_glimmerT_9631-T1
Valid prediction for Augustus_model.g6296.t1
Valid prediction for snap_scaffold_4-snap.1273-T1
Valid prediction for GlimmerHMM_glimmerT_9626-T1
Valid prediction for GlimmerHMM_glimmerT_9625-T1
Valid prediction for Augustus_model.g6290.t1
Valid prediction for GeneMark_model.15736_t
Valid prediction for HiQ_model.g6278.t1
Valid prediction for CodingQuarry_transcript_48908-T1
Valid prediction for snap_scaffold_4-snap.1277-T1
Valid prediction for snap_scaffold_4-snap.1261-T1
Valid prediction for GlimmerHMM_glimmerT_9634-T1
Valid prediction for CodingQuarry_transcript_48904-T1
Valid prediction for snap_scaffold_4-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_9628-T1
Valid prediction for Augustus_model.g6279.t1
Valid prediction for snap_scaffold_4-snap.1264-T1
Valid prediction for snap_scaffold_4-snap.1280-T1
Valid prediction for snap_scaffold_4-snap.1284-T1
Valid prediction for HiQ_model.g6282.t1
Valid prediction for GlimmerHMM_glimmerT_9623-T1
Valid prediction for Augustus_model.g6289.t1
Valid prediction for Augustus_model.g6288.t1
Couldn't classify 153422, 153580
Sorry, prediction GeneMark_model.15728_t fails validation.
(GAA)	 AG	153422-153580	GT	AGG
(AAA)	 AG	154466-154636	AC	AAA
-recovered GeneMark_model.15728_t, terminal, 154466, 154636
-recovered GeneMark_model.15728_t, internal, 153422, 153580
Valid prediction for snap_scaffold_4-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_9632-T1
Couldn't classify 4246, 4416
Couldn't classify 5835, 5951
Sorry, prediction pasa_asmbl_41391.p1 fails validation.
(TCC)	 GG	4246-4416	GT	AGG
(CTT)	 AG	5274-5456	GT	AGG
(ATT)	 AG	5835-5951	GG	ATG
-recovered pasa_asmbl_41391.p1, internal, 5274, 5456
Valid prediction for GlimmerHMM_glimmerT_9629-T1
Valid prediction for pasa_asmbl_41374.p1
Valid prediction for GeneMark_model.15724_t
Valid prediction for CodingQuarry_transcript_48907-T1
Valid prediction for snap_scaffold_4-snap.1263-T1
Valid prediction for GlimmerHMM_glimmerT_9644-T1
Valid prediction for snap_scaffold_4-snap.1278-T1
Valid prediction for Augustus_model.g6292.t1
Valid prediction for GlimmerHMM_glimmerT_9639-T1
Valid prediction for Augustus_model.g6286.t1
Valid prediction for pasa_asmbl_41384.p1
Valid prediction for GeneMark_model.15741_t
Valid prediction for CodingQuarry_transcript_48903-T1
Valid prediction for GeneMark_model.15725_t
Valid prediction for GeneMark_model.15738_t
Valid prediction for Augustus_model.g6281.t1
Valid prediction for Augustus_model.g6297.t1
Couldn't classify 19854, 19993
Sorry, prediction pasa_asmbl_41389.p1 fails validation.
(CAC)	 TC	19854-19993	GT	TGG
(GGA)	 AG	20623-20711	GT	ATG
(TGG)	 AG	20916-21058	CT	AAC
-recovered pasa_asmbl_41389.p1, terminal, 20916, 21058
-recovered pasa_asmbl_41389.p1, internal, 20623, 20711
Valid prediction for GeneMark_model.15742_t
Valid prediction for GlimmerHMM_glimmerT_9622-T1
Valid prediction for snap_scaffold_4-snap.1283-T1
Valid prediction for snap_scaffold_4-snap.1266-T1
Valid prediction for snap_scaffold_4-snap.1275-T1
Valid prediction for CodingQuarry_transcript_48902-T1
Valid prediction for GeneMark_model.15731_t
Valid prediction for snap_scaffold_4-snap.1260-T1
Valid prediction for Augustus_model.g6285.t1
Valid prediction for GeneMark_model.15735_t
Valid prediction for Augustus_model.g6295.t1
Valid prediction for GlimmerHMM_glimmerT_9630-T1
Valid prediction for GlimmerHMM_glimmerT_9636-T1

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

-building trellis in range 1 - 193684
-exon list size: 291


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.4    
4.8    
5.1    
5.5    
5.8    
6.1    
6.5    
6.8    
7.2    
7.5    
7.8    
8.2    
8.5    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
11.9    
12.3    
12.6    
13.0    
13.3    
13.7    
14.0    
14.3    
14.7    
15.0    
15.4    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
25.9    
26.3    
26.6    
27.0    
27.3    
27.6    
28.0    
28.3    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.1    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.8    
36.2    
36.5    
36.9    
37.2    
37.5    
37.9    
38.2    
38.6    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.6    
42.0    
42.3    
42.7    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.7    
46.1    
46.4    
46.8    
47.1    
47.4    
47.8    
48.1    
48.5    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.5    
51.9    
52.2    
52.6    
52.9    
53.2    
53.6    
53.9    
54.3    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.3    
57.7    
58.0    
58.4    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.4    
61.8    
62.1    
62.5    
62.8    
63.1    
63.5    
63.8    
64.2    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
68.9    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.7    
72.0    
72.4    
72.7    
73.0    
73.4    
73.7    
74.1    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.6    
85.0    
85.3    
85.7    
86.0    
86.3    
86.7    
87.0    
87.4    
87.7    
88.1    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.5    
91.8    
92.2    
92.5    
92.8    
93.2    
93.5    
93.9    
94.2    
94.5    
94.9    
95.2    
95.6    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 24 predictions from path traversal

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