-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_5649563-5782061

-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.6464_t
Valid prediction for snap_scaffold_2-snap.1277-T1
Valid prediction for GeneMark_model.6475_t
Valid prediction for snap_scaffold_2-snap.1279-T1
Valid prediction for snap_scaffold_2-snap.1292-T1
Valid prediction for HiQ_model.g2631.t1
Couldn't classify 78979, 79008
Sorry, prediction pasa_asmbl_24465.p1 fails validation.
(CAA)	 TG	78979-79008	GT	GGG
(GTC)	 AG	79538-79640	GT	GGG
(CCA)	 AG	79747-79887	GT	ACG
(TCA)	 AG	80410-80525	GT	AGG
(GTC)	 AG	80715-80770	GT	AGG
(TGA)	 AG	80861-80892	GT	CAG
(GAG)	 AG	80987-81048	GT	AGG
(GCC)	 AG	81328-81396	GT	AGG
(TTT)	 AG	81556-81657	GT	TGG
(CTT)	 AG	81878-81950	GT	AGG
(ACA)	 AG	83090-83163	GC	GAG
-recovered pasa_asmbl_24465.p1, terminal, 83090, 83163
-recovered pasa_asmbl_24465.p1, internal, 79538, 79640
-recovered pasa_asmbl_24465.p1, internal, 79747, 79887
-recovered pasa_asmbl_24465.p1, internal, 80410, 80525
-recovered pasa_asmbl_24465.p1, internal, 80715, 80770
-recovered pasa_asmbl_24465.p1, internal, 80861, 80892
-recovered pasa_asmbl_24465.p1, internal, 80987, 81048
-recovered pasa_asmbl_24465.p1, internal, 81328, 81396
-recovered pasa_asmbl_24465.p1, internal, 81556, 81657
-recovered pasa_asmbl_24465.p1, internal, 81878, 81950
-recovered pasa_asmbl_24465.p1, internal, 83090, 83163
Valid prediction for Augustus_model.g2626.t1
Couldn't classify 64574, 64602
Couldn't classify 65937, 65976
Sorry, prediction pasa_asmbl_24457.p1 fails validation.
(TAT)	 AC	64574-64602	GT	AGG
(GGT)	 AG	64831-64899	GT	AGG
(TGT)	 AG	65008-65134	GC	AGG
(GTT)	 AG	65215-65280	GT	AAG
(TTC)	 AG	65365-65424	GT	AGG
(GGA)	 AG	65517-65606	GT	AGG
(GGA)	 AG	65711-65817	GT	AGG
(TGC)	 AG	65937-65976	CC	AAC
-recovered pasa_asmbl_24457.p1, internal, 64831, 64899
-recovered pasa_asmbl_24457.p1, internal, 65008, 65134
-recovered pasa_asmbl_24457.p1, internal, 65215, 65280
-recovered pasa_asmbl_24457.p1, internal, 65365, 65424
-recovered pasa_asmbl_24457.p1, internal, 65517, 65606
-recovered pasa_asmbl_24457.p1, internal, 65711, 65817
Valid prediction for GeneMark_model.6471_t
Valid prediction for GeneMark_model.6472_t
Valid prediction for GeneMark_model.6479_t
Valid prediction for CodingQuarry_transcript_28506-T1
Valid prediction for snap_scaffold_2-snap.1285-T1
Valid prediction for GeneMark_model.6482_t
Valid prediction for snap_scaffold_2-snap.1278-T1
Valid prediction for HiQ_model.g2632.t1
Valid prediction for CodingQuarry_transcript_28507-T1
Valid prediction for GlimmerHMM_glimmerT_3936-T1
Valid prediction for GeneMark_model.6461_t
Valid prediction for GeneMark_model.6477_t
Valid prediction for snap_scaffold_2-snap.1286-T1
Valid prediction for GeneMark_model.6463_t
Valid prediction for GlimmerHMM_glimmerT_3942-T1
Valid prediction for GlimmerHMM_glimmerT_3937-T1
Valid prediction for Augustus_model.g2624.t1
Valid prediction for snap_scaffold_2-snap.1294-T1
Valid prediction for GeneMark_model.6459_t
Valid prediction for GeneMark_model.6468_t
Valid prediction for snap_scaffold_2-snap.1275-T1
Valid prediction for CodingQuarry_transcript_28505-T1
Valid prediction for GeneMark_model.6470_t
Valid prediction for GlimmerHMM_glimmerT_3946-T1
Valid prediction for snap_scaffold_2-snap.1284-T1
Valid prediction for GlimmerHMM_glimmerT_3941-T1
Valid prediction for Augustus_model.g2630.t1
Valid prediction for snap_scaffold_2-snap.1290-T1
Valid prediction for snap_scaffold_2-snap.1276-T1
Valid prediction for Augustus_model.g2625.t1
Valid prediction for pasa_asmbl_24458.p1
Valid prediction for snap_scaffold_2-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_3945-T1
Couldn't classify 71560, 71656
Sorry, prediction pasa_asmbl_24464.p1 fails validation.
(CAT)	 CA	71560-71656	GT	AGG
(TGA)	 AG	73371-73460	GT	AGG
(AAG)	 AG	74022-74092	GT	AGG
(GTA)	 AG	74212-74314	GT	TGG
(AGA)	 AG	74511-74651	GT	CTG
(CTA)	 AG	75010-75125	GT	AGG
(AAA)	 AG	75245-75303	GT	GAG
(GAT)	 AG	75405-75424	GT	TGG
(ACA)	 AG	75517-75578	GT	AGG
(TCG)	 AG	75655-75723	GT	AGG
(TTT)	 AG	75966-76067	GT	AGG
(GTC)	 AG	76163-76235	GT	AGG
(ACG)	 AG	76553-76629	GC	AAG
add_exon() Sorry, pasa_asmbl_24464.p1 73371-73460-terminal-1 is invalid.
-recovered pasa_asmbl_24464.p1, terminal, 73371, 73460
-recovered pasa_asmbl_24464.p1, terminal, 76553, 76629
-recovered pasa_asmbl_24464.p1, internal, 73371, 73460
-recovered pasa_asmbl_24464.p1, internal, 74022, 74092
-recovered pasa_asmbl_24464.p1, internal, 74212, 74314
-recovered pasa_asmbl_24464.p1, internal, 74511, 74651
-recovered pasa_asmbl_24464.p1, internal, 75010, 75125
-recovered pasa_asmbl_24464.p1, internal, 75245, 75303
-recovered pasa_asmbl_24464.p1, internal, 75405, 75424
-recovered pasa_asmbl_24464.p1, internal, 75517, 75578
-recovered pasa_asmbl_24464.p1, internal, 75655, 75723
-recovered pasa_asmbl_24464.p1, internal, 75966, 76067
-recovered pasa_asmbl_24464.p1, internal, 76163, 76235
-recovered pasa_asmbl_24464.p1, internal, 76553, 76629
Couldn't classify 63364, 63423
Couldn't classify 64243, 64308
Sorry, prediction pasa_asmbl_25371.p1 fails validation.
(CAT)	 AA	63364-63423	GT	CGG
(TGC)	 AG	63546-63631	GT	GAG
(CCC)	 AG	63748-63882	GT	AGG
(TGA)	 AG	63962-64058	GT	CAG
(AAC)	 AG	64243-64308	GG	CAG
add_exon() Sorry, pasa_asmbl_25371.p1 63546-63631-terminal-2 is invalid.
-recovered pasa_asmbl_25371.p1, terminal, 63546, 63631
-recovered pasa_asmbl_25371.p1, internal, 63546, 63631
-recovered pasa_asmbl_25371.p1, internal, 63748, 63882
-recovered pasa_asmbl_25371.p1, internal, 63962, 64058
Valid prediction for GeneMark_model.6480_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 CodingQuarry_transcript_28504-T1
Valid prediction for GeneMark_model.6465_t
Valid prediction for snap_scaffold_2-snap.1291-T1
Valid prediction for snap_scaffold_2-snap.1289-T1
Valid prediction for snap_scaffold_2-snap.1288-T1
Valid prediction for GeneMark_model.6466_t
Valid prediction for GlimmerHMM_glimmerT_3939-T1
Valid prediction for GlimmerHMM_glimmerT_3940-T1
Valid prediction for GeneMark_model.6469_t
Valid prediction for CodingQuarry_transcript_28503-T1
Valid prediction for HiQ_model.g2628.t1
Valid prediction for snap_scaffold_2-snap.1280-T1
Valid prediction for GeneMark_model.6476_t
Valid prediction for GeneMark_model.6474_t
Valid prediction for snap_scaffold_2-snap.1283-T1
Valid prediction for snap_scaffold_2-snap.1281-T1
Valid prediction for HiQ_model.g2629.t1
Valid prediction for GeneMark_model.6481_t
Valid prediction for GlimmerHMM_glimmerT_3943-T1
Valid prediction for snap_scaffold_2-snap.1274-T1
Valid prediction for snap_scaffold_2-snap.1295-T1
Valid prediction for GeneMark_model.6462_t
Valid prediction for snap_scaffold_2-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_3938-T1
Valid prediction for GeneMark_model.6467_t
Valid prediction for GlimmerHMM_glimmerT_3944-T1
Valid prediction for Augustus_model.g2627.t1
Valid prediction for Augustus_model.g2633.t1
Valid prediction for GeneMark_model.6460_t
Couldn't classify 69365, 69393
Couldn't classify 73345, 73482
Sorry, prediction pasa_asmbl_23186.p1 fails validation.
(GCA)	 CG	69365-69393	GT	AGG
(GTC)	 AG	70146-70193	GT	TGG
(TAG)	 AG	70615-70795	GT	AGG
(CAC)	 AG	70902-71044	GT	AGG
(AGA)	 AG	71288-71384	GT	AGG
(GTC)	 AG	71554-71635	GT	AGG
(ACG)	 AG	71885-71970	GT	AGG
(GTG)	 AG	72055-72203	GT	AAG
(ACT)	 AG	72364-72610	GT	AGG
(TCG)	 AG	72814-72939	GT	AGG
(GGT)	 AG	73030-73182	GT	AGG
(GTG)	 AG	73345-73482	TA	GAT
-recovered pasa_asmbl_23186.p1, internal, 70146, 70193
-recovered pasa_asmbl_23186.p1, internal, 70615, 70795
-recovered pasa_asmbl_23186.p1, internal, 70902, 71044
-recovered pasa_asmbl_23186.p1, internal, 71288, 71384
-recovered pasa_asmbl_23186.p1, internal, 71554, 71635
-recovered pasa_asmbl_23186.p1, internal, 71885, 71970
-recovered pasa_asmbl_23186.p1, internal, 72055, 72203
-recovered pasa_asmbl_23186.p1, internal, 72364, 72610
-recovered pasa_asmbl_23186.p1, internal, 72814, 72939
-recovered pasa_asmbl_23186.p1, internal, 73030, 73182
Couldn't classify 46318, 46755
Sorry, prediction pasa_asmbl_23188.p1 fails validation.
(TCT)	 GT	46318-46755	CC	AGC
Valid prediction for pasa_asmbl_23181.p1
Valid prediction for snap_scaffold_2-snap.1282-T1

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

-building trellis in range 1 - 132499
-exon list size: 304


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
2.9    
3.3    
3.6    
3.9    
4.2    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.2    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.4    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.5    
26.8    
27.1    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.9    
73.2    
73.5    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.6    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.8    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.8    
96.1    
96.4    
96.7    
97.1    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 12 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support