-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_5156108-5343360

-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_53763-T1
Valid prediction for snap_scaffold_24-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_53770-T1
Valid prediction for GlimmerHMM_glimmerT_53772-T1
Valid prediction for snap_scaffold_24-snap.1027-T1
Valid prediction for snap_scaffold_24-snap.1043-T1
Valid prediction for GeneMark_model.93797_t
Valid prediction for GeneMark_model.93782_t
Valid prediction for GeneMark_model.93773_t
Valid prediction for Augustus_model.g35993.t1
Valid prediction for snap_scaffold_24-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_53781-T1
Valid prediction for GeneMark_model.93799_t
Valid prediction for Augustus_model.g35988.t1
Valid prediction for snap_scaffold_24-snap.1048-T1
Valid prediction for snap_scaffold_24-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_53768-T1
Valid prediction for Augustus_model.g35991.t1
Valid prediction for snap_scaffold_24-snap.1042-T1
Valid prediction for Augustus_model.g36001.t1
Valid prediction for snap_scaffold_24-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_53771-T1
Valid prediction for GlimmerHMM_glimmerT_53761-T1
Valid prediction for GlimmerHMM_glimmerT_53762-T1
Valid prediction for GeneMark_model.93778_t
Valid prediction for GlimmerHMM_glimmerT_53780-T1
Valid prediction for Augustus_model.g35995.t1
Valid prediction for GlimmerHMM_glimmerT_53776-T1
Valid prediction for Augustus_model.g35989.t1
Valid prediction for GeneMark_model.93790_t
Valid prediction for snap_scaffold_24-snap.1031-T1
Valid prediction for snap_scaffold_24-snap.1041-T1
Valid prediction for GeneMark_model.93784_t
Valid prediction for GlimmerHMM_glimmerT_53777-T1
Valid prediction for GeneMark_model.93787_t
Valid prediction for GeneMark_model.93776_t
Valid prediction for HiQ_model.g35999.t1
Valid prediction for Augustus_model.g36002.t1
Valid prediction for Augustus_model.g35994.t1
Valid prediction for GlimmerHMM_glimmerT_53773-T1
Valid prediction for GeneMark_model.93795_t
Valid prediction for GlimmerHMM_glimmerT_53765-T1
Valid prediction for snap_scaffold_24-snap.1033-T1
Valid prediction for GlimmerHMM_glimmerT_53766-T1
Valid prediction for GlimmerHMM_glimmerT_53758-T1
Valid prediction for GeneMark_model.93786_t
Valid prediction for pasa_asmbl_32220.p1
Valid prediction for snap_scaffold_24-snap.1038-T1
Valid prediction for GeneMark_model.93788_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 pasa_asmbl_32873.p1
Valid prediction for GeneMark_model.93779_t
Valid prediction for GlimmerHMM_glimmerT_53774-T1
Valid prediction for GeneMark_model.93783_t
Valid prediction for snap_scaffold_24-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_53778-T1
Valid prediction for CodingQuarry_transcript_37235-T1
Couldn't classify 30391, 30589
Sorry, prediction pasa_asmbl_32881.p1 fails validation.
(CGC)	 GC	30391-30589	GT	TGG
(AGT)	 AG	31552-31647	GT	CAG
(ATG)	 AG	31883-31998	GT	AGG
(GAG)	 AG	32220-32418	GT	CCG
(TGT)	 AG	32938-33042	GT	AGG
(ATT)	 AG	33686-33777	GG	AGG
-recovered pasa_asmbl_32881.p1, initial, 31883, 31998
-recovered pasa_asmbl_32881.p1, terminal, 33686, 33777
-recovered pasa_asmbl_32881.p1, internal, 31552, 31647
-recovered pasa_asmbl_32881.p1, internal, 31883, 31998
-recovered pasa_asmbl_32881.p1, internal, 32220, 32418
-recovered pasa_asmbl_32881.p1, internal, 32938, 33042
Valid prediction for GlimmerHMM_glimmerT_53769-T1
Valid prediction for GlimmerHMM_glimmerT_53779-T1
Valid prediction for HiQ_model.g35998.t1
Valid prediction for GeneMark_model.93781_t
Valid prediction for GeneMark_model.93777_t
Valid prediction for snap_scaffold_24-snap.1050-T1
Valid prediction for pasa_asmbl_32871.p1
Valid prediction for GeneMark_model.93798_t
Valid prediction for GeneMark_model.93792_t
Valid prediction for snap_scaffold_24-snap.1030-T1
Valid prediction for snap_scaffold_24-snap.1028-T1
Valid prediction for snap_scaffold_24-snap.1040-T1
Valid prediction for pasa_asmbl_32887.p1
Valid prediction for GlimmerHMM_glimmerT_53767-T1
Couldn't classify 23421, 23675
Sorry, prediction pasa_asmbl_32884.p1 fails validation.
(TCT)	 AC	23421-23675	GT	TGG
(GTG)	 AG	23924-24028	GT	TGG
(GCC)	 AG	24360-24452	GT	AGG
(GAA)	 AG	24581-24622	TT	GAT
-recovered pasa_asmbl_32884.p1, terminal, 24581, 24622
-recovered pasa_asmbl_32884.p1, internal, 23924, 24028
-recovered pasa_asmbl_32884.p1, internal, 24360, 24452
Valid prediction for Augustus_model.g35987.t1
Valid prediction for GlimmerHMM_glimmerT_53764-T1
Valid prediction for snap_scaffold_24-snap.1026-T1
Valid prediction for snap_scaffold_24-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_53775-T1
Valid prediction for snap_scaffold_24-snap.1032-T1
Valid prediction for Augustus_model.g35997.t1
Valid prediction for GlimmerHMM_glimmerT_53759-T1
Valid prediction for HiQ_model.g36000.t1
Valid prediction for snap_scaffold_24-snap.1045-T1
Valid prediction for GeneMark_model.93774_t
Valid prediction for GeneMark_model.93793_t
Valid prediction for CodingQuarry_transcript_37234-T1
Couldn't classify 28199, 28306
Sorry, prediction pasa_asmbl_32883.p1 fails validation.
(ATG)	 AC	25854-25891	GT	AGG
(GCG)	 AG	27590-27743	GT	AGG
(GTG)	 AG	28199-28306	GA	GGG
-recovered pasa_asmbl_32883.p1, initial, 25854, 25891
-recovered pasa_asmbl_32883.p1, internal, 27590, 27743
Valid prediction for snap_scaffold_24-snap.1034-T1
Valid prediction for GeneMark_model.93794_t
Valid prediction for snap_scaffold_24-snap.1036-T1
Valid prediction for HiQ_model.g35992.t1
Valid prediction for snap_scaffold_24-snap.1046-T1
Valid prediction for snap_scaffold_24-snap.1025-T1
Valid prediction for GeneMark_model.93796_t
Valid prediction for GlimmerHMM_glimmerT_53757-T1
Valid prediction for GeneMark_model.93801_t
Valid prediction for GeneMark_model.93780_t
Valid prediction for GeneMark_model.93791_t
Valid prediction for HiQ_model.g35996.t1
Valid prediction for GeneMark_model.93775_t
Valid prediction for GeneMark_model.93785_t
Valid prediction for GeneMark_model.93800_t
Valid prediction for snap_scaffold_24-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_53760-T1
Valid prediction for snap_scaffold_24-snap.1044-T1
Couldn't classify 23032, 23105
Sorry, prediction pasa_asmbl_32885.p1 fails validation.
(ATG)	 CC	21090-21161	GT	TTG
(AAA)	 AG	21268-21396	GT	ACG
(GAA)	 AG	21531-21594	GT	AGG
(CGG)	 AG	21792-21922	GT	CGG
(TAC)	 AG	22021-22103	GT	AGG
(TCA)	 AG	22261-22444	GT	AGG
(GTC)	 AG	22631-22696	GT	GCG
(GGT)	 AG	22840-22942	GT	CGG
(GCG)	 AG	23032-23105	AC	GTA
-recovered pasa_asmbl_32885.p1, initial, 21090, 21161
-recovered pasa_asmbl_32885.p1, internal, 21268, 21396
-recovered pasa_asmbl_32885.p1, internal, 21531, 21594
-recovered pasa_asmbl_32885.p1, internal, 21792, 21922
-recovered pasa_asmbl_32885.p1, internal, 22021, 22103
-recovered pasa_asmbl_32885.p1, internal, 22261, 22444
-recovered pasa_asmbl_32885.p1, internal, 22631, 22696
-recovered pasa_asmbl_32885.p1, internal, 22840, 22942
Couldn't classify 36966, 37024
Sorry, prediction pasa_asmbl_32875.p2 fails validation.
(GCA)	 AC	36966-37024	GT	ATG
(CTC)	 AG	37395-37527	GT	AGG
(CTG)	 AG	37669-37814	GT	AAG
(GAG)	 AG	38001-38065	GT	AGG
(ACT)	 AG	38198-38436	GT	GGG
(GTC)	 AG	38641-38702	GT	GAG
(TGT)	 AG	38861-39014	GT	TGG
(CTG)	 AG	39166-39259	GT	AGG
(AGT)	 AG	41766-41914	AG	GAA
-recovered pasa_asmbl_32875.p2, terminal, 41766, 41914
-recovered pasa_asmbl_32875.p2, internal, 37395, 37527
-recovered pasa_asmbl_32875.p2, internal, 37669, 37814
-recovered pasa_asmbl_32875.p2, internal, 38001, 38065
-recovered pasa_asmbl_32875.p2, internal, 38198, 38436
-recovered pasa_asmbl_32875.p2, internal, 38641, 38702
-recovered pasa_asmbl_32875.p2, internal, 38861, 39014
-recovered pasa_asmbl_32875.p2, internal, 39166, 39259
Valid prediction for Augustus_model.g35990.t1

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

-building trellis in range 1 - 187253
-exon list size: 365


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.5    
3.8    
4.1    
4.4    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
9.0    
9.3    
9.5    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20816
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19458
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13496
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10941
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support