-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_160560-363472

-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_10-snap.59-T1
Valid prediction for Augustus_model.g15934.t1
Valid prediction for GlimmerHMM_glimmerT_23932-T1
Valid prediction for GlimmerHMM_glimmerT_23928-T1
Valid prediction for snap_scaffold_10-snap.56-T1
Valid prediction for snap_scaffold_10-snap.76-T1
Couldn't classify 19729, 20736
Sorry, prediction pasa_asmbl_2847.p1 fails validation.
(GTT)	 GA	19729-20736	CT	TAC
Valid prediction for GlimmerHMM_glimmerT_23941-T1
Valid prediction for Augustus_model.g15928.t1
Valid prediction for GlimmerHMM_glimmerT_23913-T1
Couldn't classify 42590, 42991
Sorry, prediction pasa_asmbl_3920.p1 fails validation.
(ATG)	 TC	42590-42991	TC	ACT
Valid prediction for GlimmerHMM_glimmerT_23942-T1
Valid prediction for GlimmerHMM_glimmerT_23940-T1
Valid prediction for Augustus_model.g15943.t1
Valid prediction for snap_scaffold_10-snap.63-T1
Valid prediction for snap_scaffold_10-snap.68-T1
Valid prediction for GlimmerHMM_glimmerT_23917-T1
Valid prediction for snap_scaffold_10-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_23909-T1
Valid prediction for Augustus_model.g15938.t1
Valid prediction for GlimmerHMM_glimmerT_23919-T1
Couldn't classify 3231, 3452
Sorry, prediction pasa_asmbl_2843.p1 fails validation.
(GAG)	 AG	3231-3452	GT	CGG
(GAC)	 AG	5627-5718	GT	CGG
(GGA)	 AG	5843-5965	GT	AGG
(TAA)	 AG	6493-6673	GA	GAG
-recovered pasa_asmbl_2843.p1, terminal, 6493, 6673
-recovered pasa_asmbl_2843.p1, internal, 3231, 3452
-recovered pasa_asmbl_2843.p1, internal, 5627, 5718
-recovered pasa_asmbl_2843.p1, internal, 5843, 5965
Valid prediction for snap_scaffold_10-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_23939-T1
Valid prediction for Augustus_model.g15922.t1
Valid prediction for Augustus_model.g15931.t1
Valid prediction for GlimmerHMM_glimmerT_23921-T1
Valid prediction for Augustus_model.g15947.t1
Valid prediction for HiQ_model.g15916.t1
Valid prediction for GlimmerHMM_glimmerT_23923-T1
Valid prediction for GlimmerHMM_glimmerT_23924-T1
Valid prediction for Augustus_model.g15932.t1
Valid prediction for snap_scaffold_10-snap.40-T1
Valid prediction for snap_scaffold_10-snap.53-T1
Valid prediction for Augustus_model.g15919.t1
Valid prediction for snap_scaffold_10-snap.75-T1
Valid prediction for Augustus_model.g15923.t1
Valid prediction for snap_scaffold_10-snap.55-T1
Valid prediction for snap_scaffold_10-snap.70-T1
Valid prediction for Augustus_model.g15925.t1
Valid prediction for snap_scaffold_10-snap.60-T1
Valid prediction for snap_scaffold_10-snap.52-T1
Valid prediction for snap_scaffold_10-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_23937-T1
Valid prediction for Augustus_model.g15930.t1
Valid prediction for Augustus_model.g15948.t1
Valid prediction for snap_scaffold_10-snap.47-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: -)Couldn't classify 49114, 49365
Sorry, prediction pasa_asmbl_3928.p1 fails validation.
(ATG)	 GC	48812-48928	GT	AAG
(GCT)	 AG	49114-49365	AT	CCA
-recovered pasa_asmbl_3928.p1, initial, 48812, 48928
Couldn't classify 25440, 25536
Couldn't classify 31902, 32015
Sorry, prediction pasa_asmbl_3932.p1 fails validation.
(CAG)	 TT	25440-25536	GT	GGG
(GAG)	 AG	25674-25780	GC	AGG
(CAT)	 AG	25989-26047	GT	AAG
(TAA)	 AG	26146-26287	GT	AGG
(TTC)	 AG	26390-26479	GT	AGG
(CTG)	 AG	28547-28654	GT	AGG
(GTG)	 AG	28762-28849	GT	ATG
(CGG)	 AG	29174-29310	GT	AAG
(CTA)	 AG	29711-29929	GT	TGG
(ACT)	 AG	31902-32015	GT	AGG
-recovered pasa_asmbl_3932.p1, internal, 25674, 25780
-recovered pasa_asmbl_3932.p1, internal, 25989, 26047
-recovered pasa_asmbl_3932.p1, internal, 26146, 26287
-recovered pasa_asmbl_3932.p1, internal, 26390, 26479
-recovered pasa_asmbl_3932.p1, internal, 28547, 28654
-recovered pasa_asmbl_3932.p1, internal, 28762, 28849
-recovered pasa_asmbl_3932.p1, internal, 29174, 29310
-recovered pasa_asmbl_3932.p1, internal, 29711, 29929
-recovered pasa_asmbl_3932.p1, internal, 31902, 32015
Valid prediction for snap_scaffold_10-snap.61-T1
Valid prediction for Augustus_model.g15937.t1
Valid prediction for GlimmerHMM_glimmerT_23934-T1
Valid prediction for GlimmerHMM_glimmerT_23935-T1
Valid prediction for GlimmerHMM_glimmerT_23929-T1
Couldn't classify 178114, 178827
Sorry, prediction pasa_asmbl_3874.p1 fails validation.
(CAT)	 TA	178114-178827	NN	GGN
Couldn't classify 158130, 158253
Sorry, prediction pasa_asmbl_3925.p1 fails validation.
(ATG)	 AA	152996-153055	GT	AGG
(GTT)	 AG	153692-153830	GT	CCG
(CTG)	 AG	153972-154090	GT	AGG
(GCA)	 AG	154258-154332	GT	AGG
(GCG)	 AG	154673-154780	GT	AGG
(GTA)	 AG	155046-155124	GT	AGG
(AGA)	 AG	155211-155322	GT	AAG
(TCC)	 AG	155483-155572	GT	AAG
(TTC)	 AG	155661-155833	GT	AGG
(GTG)	 AG	155926-156038	GT	AGG
(TTT)	 AG	156123-156330	GT	TGG
(GGA)	 AG	156464-156553	GT	AGG
(GCG)	 AG	157380-157560	GT	GGG
(GTA)	 AG	157706-157805	GT	ACG
(ACC)	 AG	157903-158054	GT	ATG
(TTC)	 AG	158130-158253	AG	ACA
-recovered pasa_asmbl_3925.p1, initial, 152996, 153055
add_exon() Sorry, pasa_asmbl_3925.p1 155661-155833-terminal-2 is invalid.
-recovered pasa_asmbl_3925.p1, terminal, 155661, 155833
-recovered pasa_asmbl_3925.p1, internal, 153692, 153830
-recovered pasa_asmbl_3925.p1, internal, 153972, 154090
-recovered pasa_asmbl_3925.p1, internal, 154258, 154332
-recovered pasa_asmbl_3925.p1, internal, 154673, 154780
-recovered pasa_asmbl_3925.p1, internal, 155046, 155124
-recovered pasa_asmbl_3925.p1, internal, 155211, 155322
-recovered pasa_asmbl_3925.p1, internal, 155483, 155572
-recovered pasa_asmbl_3925.p1, internal, 155661, 155833
-recovered pasa_asmbl_3925.p1, internal, 155926, 156038
-recovered pasa_asmbl_3925.p1, internal, 156123, 156330
-recovered pasa_asmbl_3925.p1, internal, 156464, 156553
-recovered pasa_asmbl_3925.p1, internal, 157380, 157560
-recovered pasa_asmbl_3925.p1, internal, 157706, 157805
-recovered pasa_asmbl_3925.p1, internal, 157903, 158054
Valid prediction for GlimmerHMM_glimmerT_23920-T1
Valid prediction for snap_scaffold_10-snap.44-T1
Valid prediction for snap_scaffold_10-snap.58-T1
Couldn't classify 18893, 19066
Sorry, prediction pasa_asmbl_3938.p1 fails validation.
(AGT)	 AG	18893-19066	GT	TGG
(ACT)	 AG	20030-20068	GT	AGG
(GAA)	 AG	21293-21457	TG	AGT
-recovered pasa_asmbl_3938.p1, terminal, 21293, 21457
-recovered pasa_asmbl_3938.p1, internal, 18893, 19066
-recovered pasa_asmbl_3938.p1, internal, 20030, 20068
Valid prediction for Augustus_model.g15927.t1
Valid prediction for CodingQuarry_transcript_5243-T1
Couldn't classify 52417, 52719
Sorry, prediction pasa_asmbl_3927.p1 fails validation.
(GGA)	 CT	52417-52719	GT	AAG
Valid prediction for snap_scaffold_10-snap.73-T1
Valid prediction for snap_scaffold_10-snap.57-T1
Valid prediction for Augustus_model.g15944.t1
Valid prediction for Augustus_model.g15918.t1
Couldn't classify 35277, 35498
Couldn't classify 37424, 37642
Sorry, prediction pasa_asmbl_3930.p1 fails validation.
(GAC)	 TT	35277-35498	GT	TGG
(GAA)	 AG	36595-36691	GT	AGG
(GAG)	 AG	36855-36946	GT	TGG
(GTG)	 AG	37424-37642	TA	GGT
-recovered pasa_asmbl_3930.p1, internal, 36595, 36691
-recovered pasa_asmbl_3930.p1, internal, 36855, 36946
Valid prediction for snap_scaffold_10-snap.77-T1
Valid prediction for Augustus_model.g15920.t1
Valid prediction for Augustus_model.g15936.t1
Valid prediction for snap_scaffold_10-snap.67-T1
Valid prediction for Augustus_model.g15929.t1
Valid prediction for GlimmerHMM_glimmerT_23914-T1
Valid prediction for snap_scaffold_10-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_23936-T1
Valid prediction for HiQ_model.g15945.t1
Valid prediction for snap_scaffold_10-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_23910-T1
Valid prediction for Augustus_model.g15926.t1
Valid prediction for CodingQuarry_transcript_5245-T1
Valid prediction for GlimmerHMM_glimmerT_23930-T1
Valid prediction for GlimmerHMM_glimmerT_23926-T1
Valid prediction for GlimmerHMM_glimmerT_23925-T1
Couldn't classify 158130, 158253
Sorry, prediction pasa_asmbl_3924.p1 fails validation.
(ATG)	 AA	154745-154780	GT	AGG
(GTA)	 AG	155046-155124	GT	AGG
(AGA)	 AG	155211-155322	GT	AAG
(TCC)	 AG	155483-155572	GT	AAG
(TTC)	 AG	155661-155833	GT	AGG
(GTG)	 AG	155926-156038	GT	AGG
(TTT)	 AG	156123-156330	GT	TGG
(GGA)	 AG	156464-156553	GT	AGG
(GCG)	 AG	157380-157560	GT	GGG
(GTA)	 AG	157706-157805	GT	ACG
(ACC)	 AG	157903-158054	GT	ATG
(TTC)	 AG	158130-158253	AG	ACA
-recovered pasa_asmbl_3924.p1, initial, 154745, 154780
add_exon() Sorry, pasa_asmbl_3924.p1 155661-155833-terminal-2 is invalid.
-recovered pasa_asmbl_3924.p1, terminal, 155661, 155833
-recovered pasa_asmbl_3924.p1, internal, 155046, 155124
-recovered pasa_asmbl_3924.p1, internal, 155211, 155322
-recovered pasa_asmbl_3924.p1, internal, 155483, 155572
-recovered pasa_asmbl_3924.p1, internal, 155661, 155833
-recovered pasa_asmbl_3924.p1, internal, 155926, 156038
-recovered pasa_asmbl_3924.p1, internal, 156123, 156330
-recovered pasa_asmbl_3924.p1, internal, 156464, 156553
-recovered pasa_asmbl_3924.p1, internal, 157380, 157560
-recovered pasa_asmbl_3924.p1, internal, 157706, 157805
-recovered pasa_asmbl_3924.p1, internal, 157903, 158054
Valid prediction for snap_scaffold_10-snap.49-T1
Valid prediction for Augustus_model.g15935.t1
Valid prediction for GlimmerHMM_glimmerT_23943-T1
Valid prediction for snap_scaffold_10-snap.54-T1
Valid prediction for Augustus_model.g15933.t1
Couldn't classify 171373, 171615
Sorry, prediction pasa_asmbl_3916.p1 fails validation.
(AGA)	 CT	171373-171615	GT	AGG
(TAC)	 AG	171701-171824	GT	CGG
(ACG)	 AG	172077-172142	GT	AGG
(AAA)	 AG	172241-172338	GT	AGG
(ACT)	 AG	172449-172553	GT	TGG
(CCT)	 AG	172764-172892	GT	AGG
(GAT)	 AG	172979-173101	AA	GAA
-recovered pasa_asmbl_3916.p1, terminal, 172979, 173101
-recovered pasa_asmbl_3916.p1, internal, 171701, 171824
-recovered pasa_asmbl_3916.p1, internal, 172077, 172142
-recovered pasa_asmbl_3916.p1, internal, 172241, 172338
-recovered pasa_asmbl_3916.p1, internal, 172449, 172553
-recovered pasa_asmbl_3916.p1, internal, 172764, 172892
Valid prediction for snap_scaffold_10-snap.69-T1
Valid prediction for snap_scaffold_10-snap.42-T1
Valid prediction for Augustus_model.g15917.t1
Valid prediction for Augustus_model.g15939.t1
Valid prediction for Augustus_model.g15942.t1
Valid prediction for HiQ_model.g15924.t1
Valid prediction for GlimmerHMM_glimmerT_23922-T1
Valid prediction for GlimmerHMM_glimmerT_23931-T1
Valid prediction for snap_scaffold_10-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_23912-T1
Valid prediction for snap_scaffold_10-snap.72-T1
Valid prediction for Augustus_model.g15949.t1
Valid prediction for snap_scaffold_10-snap.51-T1
Valid prediction for snap_scaffold_10-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_23918-T1
Couldn't classify 56344, 56670
Sorry, prediction pasa_asmbl_2848.p1 fails validation.
(GTT)	 CT	56344-56670	TG	CGT
Valid prediction for Augustus_model.g15941.t1
Valid prediction for snap_scaffold_10-snap.65-T1
Valid prediction for CodingQuarry_transcript_5242-T1
Valid prediction for GlimmerHMM_glimmerT_23911-T1
Valid prediction for GlimmerHMM_glimmerT_23933-T1
Valid prediction for snap_scaffold_10-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_23916-T1
Valid prediction for snap_scaffold_10-snap.43-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23927-T1
Valid prediction for Augustus_model.g15940.t1
Valid prediction for Augustus_model.g15946.t1
Valid prediction for CodingQuarry_transcript_5246-T1
Valid prediction for snap_scaffold_10-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_23938-T1
Valid prediction for snap_scaffold_10-snap.50-T1
Valid prediction for GlimmerHMM_glimmerT_23915-T1
Valid prediction for HiQ_model.g15921.t1

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

-building trellis in range 1 - 202913
-exon list size: 322


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 42 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 192786 - 202913
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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