-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_12654808-12936029

-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 snap_scaffold_6-snap.2674-T1
Valid prediction for snap_scaffold_6-snap.2700-T1
Valid prediction for Augustus_model.g10507.t1
Valid prediction for snap_scaffold_6-snap.2661-T1
Valid prediction for snap_scaffold_6-snap.2702-T1
Valid prediction for snap_scaffold_6-snap.2671-T1
Valid prediction for Augustus_model.g10523.t1
Valid prediction for Augustus_model.g10522.t1
Couldn't classify 228637, 228873
Couldn't classify 229091, 229219
Sorry, prediction pasa_asmbl_47982.p1 fails validation.
(GTG)	 AG	228637-228873	GT	AGG
(ACA)	 AG	229091-229219	GT	AGG
-recovered pasa_asmbl_47982.p1, internal, 228637, 228873
-recovered pasa_asmbl_47982.p1, internal, 229091, 229219
Valid prediction for Augustus_model.g10494.t1
Valid prediction for snap_scaffold_6-snap.2696-T1
Valid prediction for Augustus_model.g10519.t1
Valid prediction for snap_scaffold_6-snap.2688-T1
Valid prediction for GlimmerHMM_glimmerT_15694-T1
Valid prediction for GlimmerHMM_glimmerT_15671-T1
Valid prediction for pasa_asmbl_47453.p1
Valid prediction for GlimmerHMM_glimmerT_15699-T1
Valid prediction for Augustus_model.g10525.t1
Valid prediction for snap_scaffold_6-snap.2701-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g10526.t1
Valid prediction for Augustus_model.g10510.t1
Valid prediction for Augustus_model.g10503.t1
Couldn't classify 130244, 130597
Sorry, prediction pasa_asmbl_49346.p2 fails validation.
(GCG)	 AG	130244-130597	TG	AGT
Valid prediction for snap_scaffold_6-snap.2685-T1
Valid prediction for GlimmerHMM_glimmerT_15682-T1
Valid prediction for Augustus_model.g10515.t1
Valid prediction for snap_scaffold_6-snap.2690-T1
Valid prediction for GlimmerHMM_glimmerT_15685-T1
Valid prediction for snap_scaffold_6-snap.2653-T1
Valid prediction for GlimmerHMM_glimmerT_15695-T1
Valid prediction for snap_scaffold_6-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_15688-T1
Valid prediction for CodingQuarry_transcript_55269-T1
Valid prediction for GlimmerHMM_glimmerT_15697-T1
Valid prediction for snap_scaffold_6-snap.2689-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2695-T1
Valid prediction for snap_scaffold_6-snap.2694-T1
Valid prediction for GlimmerHMM_glimmerT_15676-T1
Couldn't classify 232671, 232874
Sorry, prediction pasa_asmbl_47440.p1 fails validation.
(GAG)	 AG	232671-232874	GT	AGG
(GAA)	 AG	232984-233223	GT	AGG
(TCC)	 AG	233437-233658	GC	AGG
(CTT)	 AG	234011-234193	GT	GGG
(ATA)	 AG	236800-237696	AG	AAA
-recovered pasa_asmbl_47440.p1, terminal, 236800, 237696
-recovered pasa_asmbl_47440.p1, internal, 232671, 232874
-recovered pasa_asmbl_47440.p1, internal, 232984, 233223
-recovered pasa_asmbl_47440.p1, internal, 233437, 233658
-recovered pasa_asmbl_47440.p1, internal, 234011, 234193
Valid prediction for snap_scaffold_6-snap.2659-T1
Valid prediction for CodingQuarry_transcript_55268-T1
Valid prediction for Augustus_model.g10527.t1
Valid prediction for GlimmerHMM_glimmerT_15690-T1
Valid prediction for snap_scaffold_6-snap.2697-T1
Valid prediction for CodingQuarry_transcript_55270-T1
Valid prediction for snap_scaffold_6-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_15683-T1
Valid prediction for GlimmerHMM_glimmerT_15693-T1
Valid prediction for snap_scaffold_6-snap.2692-T1
Valid prediction for Augustus_model.g10501.t1
Valid prediction for snap_scaffold_6-snap.2670-T1
Valid prediction for HiQ_model.g10518.t1
Valid prediction for GlimmerHMM_glimmerT_15684-T1
Valid prediction for snap_scaffold_6-snap.2668-T1
Couldn't classify 210834, 210971
Sorry, prediction pasa_asmbl_47435.p1 fails validation.
(GCC)	 AG	210834-210971	GT	TTG
(GCT)	 AG	211227-211298	GT	AGG
(AAA)	 AG	211738-211839	GT	GGG
(CTG)	 AG	212675-212720	GT	AGG
(TTC)	 AG	212856-212952	GT	AGG
(GGA)	 AG	213454-213567	GT	TGG
(GAT)	 AG	213928-214019	GT	GGG
(CTG)	 AG	214497-214594	GA	GAG
-recovered pasa_asmbl_47435.p1, terminal, 214497, 214594
-recovered pasa_asmbl_47435.p1, internal, 210834, 210971
-recovered pasa_asmbl_47435.p1, internal, 211227, 211298
-recovered pasa_asmbl_47435.p1, internal, 211738, 211839
-recovered pasa_asmbl_47435.p1, internal, 212675, 212720
-recovered pasa_asmbl_47435.p1, internal, 212856, 212952
-recovered pasa_asmbl_47435.p1, internal, 213454, 213567
-recovered pasa_asmbl_47435.p1, internal, 213928, 214019
Couldn't classify 218428, 218508
Couldn't classify 219614, 219709
Sorry, prediction pasa_asmbl_47439.p1 fails validation.
(TCA)	 GG	218428-218508	GT	ATG
(CAT)	 AG	218788-218955	GT	AGG
(GAG)	 AG	219123-219329	GT	CTG
(GGT)	 AG	219614-219709	GA	GAG
-recovered pasa_asmbl_47439.p1, internal, 218788, 218955
-recovered pasa_asmbl_47439.p1, internal, 219123, 219329
Valid prediction for Augustus_model.g10521.t1
Valid prediction for HiQ_model.g10524.t1
Valid prediction for GlimmerHMM_glimmerT_15698-T1
Valid prediction for snap_scaffold_6-snap.2669-T1
Valid prediction for HiQ_model.g10520.t1
Valid prediction for snap_scaffold_6-snap.2672-T1
Valid prediction for Augustus_model.g10505.t1
Valid prediction for snap_scaffold_6-snap.2675-T1
Valid prediction for Augustus_model.g10504.t1
Valid prediction for GlimmerHMM_glimmerT_15678-T1
Valid prediction for Augustus_model.g10493.t1
Valid prediction for snap_scaffold_6-snap.2658-T1
Valid prediction for snap_scaffold_6-snap.2699-T1
Valid prediction for snap_scaffold_6-snap.2691-T1
Valid prediction for Augustus_model.g10502.t1
Valid prediction for GlimmerHMM_glimmerT_15674-T1
Valid prediction for GlimmerHMM_glimmerT_15675-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.g10508.t1
Valid prediction for Augustus_model.g10509.t1
Valid prediction for Augustus_model.g10506.t1
Valid prediction for GlimmerHMM_glimmerT_15700-T1
Valid prediction for Augustus_model.g10495.t1
Valid prediction for Augustus_model.g10514.t1
Valid prediction for Augustus_model.g10513.t1
Valid prediction for GlimmerHMM_glimmerT_15672-T1
Valid prediction for Augustus_model.g10490.t1
Valid prediction for Augustus_model.g10516.t1
Valid prediction for snap_scaffold_6-snap.2655-T1
Valid prediction for GlimmerHMM_glimmerT_15689-T1
Valid prediction for snap_scaffold_6-snap.2654-T1
Valid prediction for GlimmerHMM_glimmerT_15670-T1
Valid prediction for pasa_asmbl_48848.p2
Valid prediction for Augustus_model.g10500.t1
Valid prediction for snap_scaffold_6-snap.2656-T1
Valid prediction for CodingQuarry_transcript_55267-T1
Valid prediction for GlimmerHMM_glimmerT_15687-T1
Valid prediction for GlimmerHMM_glimmerT_15681-T1
Valid prediction for Augustus_model.g10496.t1
Valid prediction for Augustus_model.g10511.t1
Valid prediction for GlimmerHMM_glimmerT_15679-T1
Valid prediction for snap_scaffold_6-snap.2660-T1
Valid prediction for snap_scaffold_6-snap.2687-T1
Valid prediction for snap_scaffold_6-snap.2683-T1
Valid prediction for snap_scaffold_6-snap.2664-T1
Valid prediction for Augustus_model.g10497.t1
Valid prediction for Augustus_model.g10498.t1
Valid prediction for Augustus_model.g10489.t1
Valid prediction for snap_scaffold_6-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_15677-T1
Valid prediction for snap_scaffold_6-snap.2652-T1
Valid prediction for GlimmerHMM_glimmerT_15701-T1
Valid prediction for snap_scaffold_6-snap.2686-T1
Valid prediction for snap_scaffold_6-snap.2684-T1
Valid prediction for Augustus_model.g10512.t1
Valid prediction for snap_scaffold_6-snap.2657-T1
Couldn't classify 95507, 95608
Sorry, prediction pasa_asmbl_48853.p1 fails validation.
(ATG)	 GA	92996-94729	GT	AAG
(TCC)	 AG	95507-95608	GT	AGG
-recovered pasa_asmbl_48853.p1, initial, 92996, 94729
-recovered pasa_asmbl_48853.p1, internal, 95507, 95608
Valid prediction for snap_scaffold_6-snap.2678-T1
Valid prediction for snap_scaffold_6-snap.2662-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2682-T1
Valid prediction for Augustus_model.g10488.t1
Valid prediction for Augustus_model.g10528.t1
Valid prediction for Augustus_model.g10491.t1
Valid prediction for GlimmerHMM_glimmerT_15680-T1
Valid prediction for snap_scaffold_6-snap.2673-T1
Valid prediction for snap_scaffold_6-snap.2681-T1
Valid prediction for Augustus_model.g10517.t1
Valid prediction for Augustus_model.g10492.t1
Valid prediction for snap_scaffold_6-snap.2676-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15696-T1
Couldn't classify 1261, 1569
Sorry, prediction pasa_asmbl_47455.p1 fails validation.
(CCC)	 GC	1261-1569	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_15673-T1
Valid prediction for GlimmerHMM_glimmerT_15686-T1
Valid prediction for snap_scaffold_6-snap.2665-T1
Valid prediction for GlimmerHMM_glimmerT_15691-T1
Valid prediction for snap_scaffold_6-snap.2677-T1
Valid prediction for Augustus_model.g10499.t1
Valid prediction for snap_scaffold_6-snap.2666-T1
Couldn't classify 101199, 101293
Couldn't classify 103269, 103495
Sorry, prediction pasa_asmbl_49396.p1 fails validation.
(CAG)	 CT	101199-101293	GT	AGG
(TGA)	 AG	101500-101576	GT	AGG
(TGT)	 AG	101738-101884	GT	AGG
(GTT)	 AG	103269-103495	GG	AAG
-recovered pasa_asmbl_49396.p1, internal, 101500, 101576
-recovered pasa_asmbl_49396.p1, internal, 101738, 101884
Valid prediction for Augustus_model.g10487.t1
Valid prediction for snap_scaffold_6-snap.2663-T1
Valid prediction for snap_scaffold_6-snap.2667-T1
Valid prediction for snap_scaffold_6-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_15692-T1

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

-building trellis in range 1 - 281222
-exon list size: 343


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
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    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 45 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 44 predictions persist after filtering for low support