-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_5414607-5650641

-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_58802-T1
Valid prediction for GlimmerHMM_glimmerT_58807-T1
Valid prediction for CodingQuarry_transcript_43675-T1
Valid prediction for GlimmerHMM_glimmerT_58826-T1
Valid prediction for GlimmerHMM_glimmerT_58818-T1
Valid prediction for Augustus_model.g38971.t1
Valid prediction for HiQ_model.g38984.t1
Valid prediction for GlimmerHMM_glimmerT_58803-T1
Valid prediction for GlimmerHMM_glimmerT_58815-T1
Valid prediction for Augustus_model.g38978.t1
Valid prediction for GlimmerHMM_glimmerT_58809-T1
Valid prediction for snap_scaffold_28-snap.1248-T1
Valid prediction for Augustus_model.g38982.t1
Valid prediction for snap_scaffold_28-snap.1256-T1
Valid prediction for snap_scaffold_28-snap.1270-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_43676-T1
Valid prediction for pasa_asmbl_37592.p2
Valid prediction for snap_scaffold_28-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_58824-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1259-T1
Valid prediction for snap_scaffold_28-snap.1284-T1
Valid prediction for GlimmerHMM_glimmerT_58811-T1
Valid prediction for GlimmerHMM_glimmerT_58813-T1
Valid prediction for GlimmerHMM_glimmerT_58822-T1
Valid prediction for Augustus_model.g38981.t1
Valid prediction for snap_scaffold_28-snap.1276-T1
Valid prediction for snap_scaffold_28-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_58819-T1
Valid prediction for Augustus_model.g38987.t1
Valid prediction for snap_scaffold_28-snap.1267-T1
Valid prediction for Augustus_model.g38980.t1
Valid prediction for snap_scaffold_28-snap.1246-T1
Valid prediction for Augustus_model.g38975.t1
Valid prediction for snap_scaffold_28-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_58808-T1
Valid prediction for Augustus_model.g38992.t1
Couldn't classify 205975, 206958
Sorry, prediction pasa_asmbl_37598.p1 fails validation.
(GAG)	 GA	205975-206958	TG	AGT
Valid prediction for snap_scaffold_28-snap.1281-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1273-T1
Valid prediction for Augustus_model.g38970.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_28-snap.1260-T1
Valid prediction for snap_scaffold_28-snap.1255-T1
Valid prediction for snap_scaffold_28-snap.1257-T1
Valid prediction for snap_scaffold_28-snap.1263-T1
Valid prediction for Augustus_model.g38976.t1
Valid prediction for snap_scaffold_28-snap.1265-T1
Valid prediction for snap_scaffold_28-snap.1250-T1
Valid prediction for snap_scaffold_28-snap.1272-T1
Valid prediction for snap_scaffold_28-snap.1268-T1
Valid prediction for Augustus_model.g38979.t1
Valid prediction for snap_scaffold_28-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_58805-T1
Valid prediction for snap_scaffold_28-snap.1262-T1
Valid prediction for Augustus_model.g38983.t1
Valid prediction for pasa_asmbl_38307.p1
Valid prediction for Augustus_model.g38977.t1
Valid prediction for snap_scaffold_28-snap.1251-T1
Valid prediction for snap_scaffold_28-snap.1283-T1
Valid prediction for snap_scaffold_28-snap.1280-T1
Valid prediction for GlimmerHMM_glimmerT_58821-T1
Valid prediction for snap_scaffold_28-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_58825-T1
Valid prediction for GlimmerHMM_glimmerT_58823-T1
Valid prediction for snap_scaffold_28-snap.1269-T1
Valid prediction for GlimmerHMM_glimmerT_58820-T1
Valid prediction for snap_scaffold_28-snap.1266-T1
Valid prediction for snap_scaffold_28-snap.1261-T1
Valid prediction for HiQ_model.g38985.t1
Valid prediction for snap_scaffold_28-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_58804-T1
Couldn't classify 44825, 44997
Sorry, prediction pasa_asmbl_38297.p1 fails validation.
(ATG)	 TC	43902-44250	GT	GGG
(GGC)	 AG	44825-44997	GA	TGG
-recovered pasa_asmbl_38297.p1, initial, 43902, 44250
Couldn't classify 94116, 94439
Sorry, prediction pasa_asmbl_38292.p1 fails validation.
(GCT)	 AA	94116-94439	TA	AAT
Valid prediction for snap_scaffold_28-snap.1253-T1
Valid prediction for snap_scaffold_28-snap.1264-T1
Valid prediction for snap_scaffold_28-snap.1274-T1
Valid prediction for GlimmerHMM_glimmerT_58810-T1
Valid prediction for Augustus_model.g38986.t1
Valid prediction for CodingQuarry_transcript_43678-T1
Couldn't classify 56877, 57095
Sorry, prediction pasa_asmbl_38294.p1 fails validation.
(AGA)	 AC	56877-57095	GT	AGG
(CAA)	 AG	58184-58367	GT	AGG
(GGA)	 AG	59851-60002	GT	GGG
(CTG)	 AG	60225-60392	GT	AGG
(GAG)	 AG	62645-62810	GT	GAG
(CTG)	 AG	62993-63233	GT	AGG
(ACA)	 AG	63811-63926	GT	GGG
(GTA)	 AG	64347-64483	GT	AGG
(GTG)	 AG	64660-64771	GT	TGG
(GTG)	 AG	64868-64938	AT	AAA
-recovered pasa_asmbl_38294.p1, terminal, 64868, 64938
-recovered pasa_asmbl_38294.p1, internal, 58184, 58367
-recovered pasa_asmbl_38294.p1, internal, 59851, 60002
-recovered pasa_asmbl_38294.p1, internal, 60225, 60392
-recovered pasa_asmbl_38294.p1, internal, 62645, 62810
-recovered pasa_asmbl_38294.p1, internal, 62993, 63233
-recovered pasa_asmbl_38294.p1, internal, 63811, 63926
-recovered pasa_asmbl_38294.p1, internal, 64347, 64483
-recovered pasa_asmbl_38294.p1, internal, 64660, 64771
Valid prediction for GlimmerHMM_glimmerT_58814-T1
Valid prediction for snap_scaffold_28-snap.1252-T1
Valid prediction for Augustus_model.g38990.t1
Valid prediction for Augustus_model.g38974.t1
Valid prediction for Augustus_model.g38991.t1
Valid prediction for snap_scaffold_28-snap.1279-T1
Valid prediction for CodingQuarry_transcript_43679-T1
Valid prediction for GlimmerHMM_glimmerT_58816-T1
Valid prediction for snap_scaffold_28-snap.1258-T1
Valid prediction for snap_scaffold_28-snap.1277-T1
Valid prediction for CodingQuarry_transcript_43680-T1
Valid prediction for GlimmerHMM_glimmerT_58817-T1
Valid prediction for Augustus_model.g38973.t1
Couldn't classify 86317, 87052
Sorry, prediction pasa_asmbl_38293.p1 fails validation.
(CTG)	 CT	86317-87052	GT	GGG
(ACT)	 AG	89788-89868	GT	TGG
(GCA)	 AG	90123-90145	AG	GAA
-recovered pasa_asmbl_38293.p1, terminal, 90123, 90145
-recovered pasa_asmbl_38293.p1, internal, 89788, 89868
Valid prediction for GlimmerHMM_glimmerT_58806-T1
Valid prediction for snap_scaffold_28-snap.1249-T1
Valid prediction for Augustus_model.g38988.t1
Valid prediction for snap_scaffold_28-snap.1247-T1
Valid prediction for Augustus_model.g38972.t1
Valid prediction for GlimmerHMM_glimmerT_58812-T1
Valid prediction for snap_scaffold_28-snap.1245-T1
Valid prediction for snap_scaffold_28-snap.1282-T1
Valid prediction for HiQ_model.g38989.t1

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

-building trellis in range 1 - 236035
-exon list size: 261


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.0    
3.4    
3.8    
4.2    
4.6    
4.9    
5.3    
5.7    
6.1    
6.5    
6.8    
7.2    
7.6    
8.0    
8.4    
8.7    
9.1    
9.5    
9.9    
10.3    
10.6    
11.0    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
16.0    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.6    
19.0    
19.4    
19.8    
20.2    
20.5    
20.9    
21.3    
21.7    
22.1    
22.4    
22.8    
23.2    
23.6    
24.0    
24.3    
24.7    
25.1    
25.5    
25.9    
26.2    
26.6    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.7    
30.0    
30.4    
30.8    
31.2    
31.6    
31.9    
32.3    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
35.0    
35.4    
35.7    
36.1    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.8    
39.2    
39.5    
39.9    
40.3    
40.7    
41.1    
41.4    
41.8    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.5    
44.9    
45.2    
45.6    
46.0    
46.4    
46.8    
47.1    
47.5    
47.9    
48.3    
48.7    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.3    
51.7    
52.1    
52.5    
52.9    
53.2    
53.6    
54.0    
54.4    
54.8    
55.1    
55.5    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.2    
58.6    
58.9    
59.3    
59.7    
60.1    
60.5    
60.8    
61.2    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.9    
64.3    
64.6    
65.0    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.7    
68.1    
68.4    
68.8    
69.2    
69.6    
70.0    
70.3    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.4    
73.8    
74.1    
74.5    
74.9    
75.3    
75.7    
76.0    
76.4    
76.8    
77.2    
77.6    
77.9    
78.3    
78.7    
79.1    
79.5    
79.8    
80.2    
80.6    
81.0    
81.4    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.0    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
89.0    
89.4    
89.7    
90.1    
90.5    
90.9    
91.3    
91.6    
92.0    
92.4    
92.8    
93.2    
93.5    
93.9    
94.3    
94.7    
95.1    
95.4    
95.8    
96.2    
96.6    
97.0    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 40 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support