-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_16811297-16970620

-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: +)Couldn't classify 129948, 130079
Sorry, prediction GeneMark_model.54366_t fails validation.
(GAT)	 AG	129948-130079	GT	ATG
(GTG)	 AG	130658-130761	GT	GAG
(ACT)	 AG	132504-132724	GT	AAG
(GCA)	 AG	132809-133008	GT	TTG
(CCG)	 AG	133114-133206	GT	CTG
(CGC)	 AG	133249-133384	GT	GGG
(GAG)	 AG	133430-133665	GT	CTG
(GAG)	 AG	133901-134149	GT	CCG
(GAT)	 AG	135265-135444	GT	AGG
(CCC)	 AG	135649-135784	GT	AGG
(ATT)	 AG	136511-137461	GT	AGG
(GTC)	 AG	137972-138328	GT	GGG
(GTT)	 AG	138830-140730	GT	AGG
(CCC)	 AG	140814-140819	AG	GAA
-recovered GeneMark_model.54366_t, terminal, 130658, 130761
-recovered GeneMark_model.54366_t, terminal, 140814, 140819
-recovered GeneMark_model.54366_t, internal, 129948, 130079
-recovered GeneMark_model.54366_t, internal, 130658, 130761
-recovered GeneMark_model.54366_t, internal, 132504, 132724
-recovered GeneMark_model.54366_t, internal, 132809, 133008
-recovered GeneMark_model.54366_t, internal, 133114, 133206
-recovered GeneMark_model.54366_t, internal, 133249, 133384
-recovered GeneMark_model.54366_t, internal, 133430, 133665
-recovered GeneMark_model.54366_t, internal, 133901, 134149
-recovered GeneMark_model.54366_t, internal, 135265, 135444
-recovered GeneMark_model.54366_t, internal, 135649, 135784
-recovered GeneMark_model.54366_t, internal, 136511, 137461
-recovered GeneMark_model.54366_t, internal, 137972, 138328
-recovered GeneMark_model.54366_t, internal, 138830, 140730
Valid prediction for Augustus_model.g21096.t1
Valid prediction for GlimmerHMM_glimmerT_31554-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31550-T1
Valid prediction for snap_scaffold_12-snap.3281-T1
Valid prediction for snap_scaffold_12-snap.3251-T1
Valid prediction for GeneMark_model.54359_t
Valid prediction for Augustus_model.g21083.t1
Valid prediction for snap_scaffold_12-snap.3255-T1
Valid prediction for GlimmerHMM_glimmerT_31561-T1
Valid prediction for GeneMark_model.54351_t
Valid prediction for snap_scaffold_12-snap.3277-T1
Valid prediction for GlimmerHMM_glimmerT_31573-T1
Valid prediction for snap_scaffold_12-snap.3278-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.54354_t
Valid prediction for snap_scaffold_12-snap.3265-T1
Valid prediction for Augustus_model.g21081.t1
Valid prediction for GlimmerHMM_glimmerT_31566-T1
Valid prediction for snap_scaffold_12-snap.3274-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.54360_t
Valid prediction for snap_scaffold_12-snap.3262-T1
Valid prediction for Augustus_model.g21076.t1
Valid prediction for Augustus_model.g21091.t1
Valid prediction for GeneMark_model.54346_t
Valid prediction for snap_scaffold_12-snap.3272-T1
Valid prediction for snap_scaffold_12-snap.3258-T1
Valid prediction for GlimmerHMM_glimmerT_31547-T1
Valid prediction for Augustus_model.g21077.t1
Valid prediction for snap_scaffold_12-snap.3264-T1
Valid prediction for Augustus_model.g21073.t1
Valid prediction for GlimmerHMM_glimmerT_31570-T1
Valid prediction for snap_scaffold_12-snap.3257-T1
Valid prediction for GlimmerHMM_glimmerT_31575-T1
Valid prediction for Augustus_model.g21089.t1
Valid prediction for GeneMark_model.54371_t
Valid prediction for GlimmerHMM_glimmerT_31551-T1
Valid prediction for snap_scaffold_12-snap.3280-T1
Valid prediction for snap_scaffold_12-snap.3259-T1
Valid prediction for GlimmerHMM_glimmerT_31568-T1
Valid prediction for snap_scaffold_12-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_31548-T1
Valid prediction for Augustus_model.g21082.t1
Valid prediction for GeneMark_model.54361_t
Valid prediction for GeneMark_model.54348_t
Valid prediction for GlimmerHMM_glimmerT_31556-T1
Valid prediction for Augustus_model.g21074.t1
Valid prediction for snap_scaffold_12-snap.3260-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.54355_t
Valid prediction for snap_scaffold_12-snap.3254-T1
Valid prediction for GeneMark_model.54370_t
Valid prediction for GeneMark_model.54357_t
Valid prediction for GlimmerHMM_glimmerT_31545-T1
Valid prediction for GlimmerHMM_glimmerT_31563-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 Augustus_model.g21090.t1
Valid prediction for GeneMark_model.54358_t
Valid prediction for Augustus_model.g21072.t1
Valid prediction for snap_scaffold_12-snap.3269-T1
Valid prediction for GeneMark_model.54353_t
Valid prediction for snap_scaffold_12-snap.3284-T1
Valid prediction for snap_scaffold_12-snap.3256-T1
Valid prediction for GlimmerHMM_glimmerT_31560-T1
Valid prediction for GlimmerHMM_glimmerT_31558-T1
Valid prediction for GlimmerHMM_glimmerT_31565-T1
Valid prediction for snap_scaffold_12-snap.3266-T1
Valid prediction for GlimmerHMM_glimmerT_31555-T1
Valid prediction for GlimmerHMM_glimmerT_31564-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.54347_t
Valid prediction for GeneMark_model.54363_t
Valid prediction for Augustus_model.g21094.t1
Valid prediction for snap_scaffold_12-snap.3261-T1
Valid prediction for snap_scaffold_12-snap.3275-T1
Valid prediction for snap_scaffold_12-snap.3268-T1
Valid prediction for GlimmerHMM_glimmerT_31571-T1
Valid prediction for snap_scaffold_12-snap.3270-T1
Valid prediction for Augustus_model.g21071.t1
Valid prediction for GeneMark_model.54356_t
Valid prediction for GlimmerHMM_glimmerT_31546-T1
Valid prediction for GeneMark_model.54350_t
Valid prediction for Augustus_model.g21087.t1
Valid prediction for Augustus_model.g21092.t1
Valid prediction for GlimmerHMM_glimmerT_31552-T1
Valid prediction for snap_scaffold_12-snap.3253-T1
Valid prediction for GlimmerHMM_glimmerT_31544-T1
Valid prediction for GlimmerHMM_glimmerT_31562-T1
Valid prediction for Augustus_model.g21084.t1
Valid prediction for snap_scaffold_12-snap.3250-T1
Valid prediction for snap_scaffold_12-snap.3267-T1
Valid prediction for GeneMark_model.54365_t
Valid prediction for snap_scaffold_12-snap.3282-T1
Valid prediction for GlimmerHMM_glimmerT_31553-T1
Valid prediction for snap_scaffold_12-snap.3271-T1
Valid prediction for GlimmerHMM_glimmerT_31574-T1
Valid prediction for Augustus_model.g21079.t1
Valid prediction for GeneMark_model.54367_t
Valid prediction for Augustus_model.g21093.t1
Valid prediction for GeneMark_model.54362_t
Valid prediction for snap_scaffold_12-snap.3279-T1
Valid prediction for GeneMark_model.54352_t
Valid prediction for GlimmerHMM_glimmerT_31549-T1
Valid prediction for GlimmerHMM_glimmerT_31569-T1
Valid prediction for snap_scaffold_12-snap.3252-T1
Valid prediction for Augustus_model.g21086.t1
Valid prediction for GlimmerHMM_glimmerT_31572-T1
Valid prediction for GeneMark_model.54349_t
Valid prediction for snap_scaffold_12-snap.3283-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.54364_t
Valid prediction for Augustus_model.g21078.t1
Valid prediction for Augustus_model.g21070.t1
Valid prediction for Augustus_model.g21095.t1
Valid prediction for snap_scaffold_12-snap.3263-T1
Valid prediction for GeneMark_model.54369_t
Valid prediction for Augustus_model.g21075.t1
Valid prediction for GlimmerHMM_glimmerT_31557-T1
Valid prediction for snap_scaffold_12-snap.3276-T1
Valid prediction for Augustus_model.g21088.t1
Valid prediction for Augustus_model.g21080.t1
Valid prediction for GlimmerHMM_glimmerT_31559-T1
Valid prediction for Augustus_model.g21085.t1
Valid prediction for GeneMark_model.54372_t
Valid prediction for snap_scaffold_12-snap.3273-T1
Valid prediction for GlimmerHMM_glimmerT_31567-T1
Valid prediction for GlimmerHMM_glimmerT_31543-T1

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

-building trellis in range 1 - 159324
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 39 predictions from path traversal

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