-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_1-298179

-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_23-snap.6-T1
Valid prediction for snap_scaffold_23-snap.4-T1
Valid prediction for Augustus_model.g34560.t1
Valid prediction for GeneMark_model.89686_t
Valid prediction for GeneMark_model.89673_t
Valid prediction for GlimmerHMM_glimmerT_51523-T1
Valid prediction for snap_scaffold_23-snap.3-T1
Valid prediction for snap_scaffold_23-snap.17-T1
Valid prediction for GeneMark_model.89661_t
Valid prediction for snap_scaffold_23-snap.16-T1
Couldn't classify 191838, 193382
Sorry, prediction pasa_asmbl_30591.p1 fails validation.
(ATG)	 AG	191838-193382	GG	CAG
Valid prediction for GeneMark_model.89670_t
Valid prediction for snap_scaffold_23-snap.15-T1
Valid prediction for GeneMark_model.89677_t
Valid prediction for GlimmerHMM_glimmerT_51527-T1
Valid prediction for GlimmerHMM_glimmerT_51525-T1
Valid prediction for Augustus_model.g34568.t1
Valid prediction for GlimmerHMM_glimmerT_51519-T1
Valid prediction for GlimmerHMM_glimmerT_51534-T1
Valid prediction for snap_scaffold_23-snap.13-T1
Valid prediction for Augustus_model.g34557.t1
Valid prediction for Augustus_model.g34565.t1
Valid prediction for Augustus_model.g34569.t1
Valid prediction for Augustus_model.g34561.t1
Valid prediction for GlimmerHMM_glimmerT_51512-T1
Couldn't classify 132680, 133407
Sorry, prediction pasa_asmbl_30584.p1 fails validation.
(ATG)	 TC	131609-131720	GT	AGG
(GCC)	 AG	132680-133407	CG	GGC
-recovered pasa_asmbl_30584.p1, initial, 131609, 131720
Valid prediction for Augustus_model.g34583.t1
Valid prediction for GeneMark_model.89666_t
Valid prediction for snap_scaffold_23-snap.20-T1
Valid prediction for GeneMark_model.89668_t
Valid prediction for GeneMark_model.89660_t
Valid prediction for snap_scaffold_23-snap.30-T1
Valid prediction for HiQ_model.g34576.t1
Valid prediction for Augustus_model.g34564.t1
Valid prediction for snap_scaffold_23-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_51533-T1
Valid prediction for snap_scaffold_23-snap.28-T1
Valid prediction for Augustus_model.g34577.t1
Valid prediction for CodingQuarry_transcript_35465-T1
Valid prediction for snap_scaffold_23-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_51518-T1
Valid prediction for GeneMark_model.89671_t
Valid prediction for GeneMark_model.89656_t
Couldn't classify 179614, 179698
Couldn't classify 180487, 180509
Sorry, prediction pasa_asmbl_31216.p1 fails validation.
(GCC)	 TA	179614-179698	GT	GGG
(CCA)	 AG	179933-180241	GT	AGG
(TTG)	 AG	180487-180509	GT	TGG
-recovered pasa_asmbl_31216.p1, internal, 179933, 180241
-recovered pasa_asmbl_31216.p1, internal, 180487, 180509
Valid prediction for GeneMark_model.89655_t
Valid prediction for GlimmerHMM_glimmerT_51531-T1
Valid prediction for snap_scaffold_23-snap.5-T1
Valid prediction for snap_scaffold_23-snap.14-T1
Valid prediction for snap_scaffold_23-snap.1-T1
Valid prediction for Augustus_model.g34572.t1
Valid prediction for Augustus_model.g34558.t1
Valid prediction for snap_scaffold_23-snap.7-T1
Valid prediction for snap_scaffold_23-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_51513-T1
Couldn't classify 171011, 171460
Sorry, prediction pasa_asmbl_31232.p1 fails validation.
(AAA)	 CG	171011-171460	AA	CCA
Valid prediction for Augustus_model.g34554.t1
Valid prediction for GeneMark_model.89665_t
Valid prediction for snap_scaffold_23-snap.29-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_51530-T1
Valid prediction for GeneMark_model.89684_t
Valid prediction for snap_scaffold_23-snap.27-T1
Couldn't classify 163076, 163232
Couldn't classify 165882, 165967
Sorry, prediction pasa_asmbl_30590.p1 fails validation.
(GAT)	 CG	163076-163232	GT	AGG
(TTT)	 AG	163871-164345	GT	AGG
(GTT)	 AG	165455-165591	GT	AGG
(CCT)	 AG	165882-165967	CA	CCC
-recovered pasa_asmbl_30590.p1, internal, 163871, 164345
-recovered pasa_asmbl_30590.p1, internal, 165455, 165591
Valid prediction for GlimmerHMM_glimmerT_51520-T1
Valid prediction for pasa_asmbl_30599.p1
Valid prediction for GlimmerHMM_glimmerT_51521-T1
Valid prediction for GlimmerHMM_glimmerT_51515-T1
Valid prediction for snap_scaffold_23-snap.19-T1
Valid prediction for HiQ_model.g34573.t1
Valid prediction for Augustus_model.g34566.t1
Couldn't classify 140301, 140475
Sorry, prediction pasa_asmbl_30585.p1 fails validation.
(CAG)	 CT	140301-140475	GT	AGG
(GAA)	 AG	140637-140742	GT	AGG
(GAA)	 AG	141066-141163	GT	ACG
(TTT)	 AG	141475-142013	AT	GAA
-recovered pasa_asmbl_30585.p1, terminal, 141475, 142013
-recovered pasa_asmbl_30585.p1, internal, 140637, 140742
-recovered pasa_asmbl_30585.p1, internal, 141066, 141163
Valid prediction for GeneMark_model.89681_t
Valid prediction for GeneMark_model.89654_t
Couldn't classify 156833, 156958
Sorry, prediction pasa_asmbl_30589.p1 fails validation.
(ATG)	 AA	155355-155384	GT	CGG
(ACA)	 AG	155477-155540	GT	AGG
(TGC)	 AG	156082-156185	GT	CAG
(AAA)	 AG	156298-156404	GT	TGG
(GGG)	 AG	156571-156637	GT	AGG
(ACT)	 AG	156833-156958	AG	TCA
-recovered pasa_asmbl_30589.p1, initial, 155355, 155384
-recovered pasa_asmbl_30589.p1, internal, 155477, 155540
-recovered pasa_asmbl_30589.p1, internal, 156082, 156185
-recovered pasa_asmbl_30589.p1, internal, 156298, 156404
-recovered pasa_asmbl_30589.p1, internal, 156571, 156637
Valid prediction for Augustus_model.g34562.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 GeneMark_model.89674_t
Valid prediction for pasa_asmbl_31289.p1
Valid prediction for snap_scaffold_23-snap.21-T1
Valid prediction for Augustus_model.g34567.t1
Valid prediction for Augustus_model.g34582.t1
Valid prediction for snap_scaffold_23-snap.32-T1
Valid prediction for snap_scaffold_23-snap.8-T1
Valid prediction for GeneMark_model.89653_t
Valid prediction for Augustus_model.g34578.t1
Valid prediction for GeneMark_model.89679_t
Valid prediction for GeneMark_model.89667_t
Valid prediction for GeneMark_model.89657_t
Couldn't classify 6144, 6270
Couldn't classify 8254, 8454
Sorry, prediction pasa_asmbl_31951.p1 fails validation.
(TCT)	 TG	6144-6270	GT	TGG
(GAA)	 AG	6364-6443	GT	TGG
(GCC)	 AG	8254-8454	TA	GGT
-recovered pasa_asmbl_31951.p1, internal, 6364, 6443
Valid prediction for Augustus_model.g34580.t1
Valid prediction for GeneMark_model.89676_t
Valid prediction for CodingQuarry_transcript_35466-T1
Valid prediction for Augustus_model.g34571.t1
Valid prediction for snap_scaffold_23-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_51526-T1
Valid prediction for CodingQuarry_transcript_35464-T1
Valid prediction for Augustus_model.g34574.t1
Valid prediction for snap_scaffold_23-snap.37-T1
Valid prediction for GeneMark_model.89659_t
Valid prediction for Augustus_model.g34570.t1
Valid prediction for snap_scaffold_23-snap.18-T1
Valid prediction for snap_scaffold_23-snap.33-T1
Valid prediction for GeneMark_model.89678_t
Valid prediction for snap_scaffold_23-snap.22-T1
Valid prediction for snap_scaffold_23-snap.38-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51524-T1
Valid prediction for HiQ_model.g34575.t1
Valid prediction for snap_scaffold_23-snap.31-T1
Valid prediction for GeneMark_model.89683_t
Valid prediction for Augustus_model.g34559.t1
Valid prediction for snap_scaffold_23-snap.9-T1
Valid prediction for GeneMark_model.89672_t
Valid prediction for GlimmerHMM_glimmerT_51536-T1
Valid prediction for GlimmerHMM_glimmerT_51517-T1
Valid prediction for GlimmerHMM_glimmerT_51529-T1
Valid prediction for snap_scaffold_23-snap.2-T1
Valid prediction for Augustus_model.g34555.t1
Valid prediction for GlimmerHMM_glimmerT_51532-T1
Valid prediction for snap_scaffold_23-snap.36-T1
Valid prediction for Augustus_model.g34563.t1
Valid prediction for GlimmerHMM_glimmerT_51535-T1
Valid prediction for snap_scaffold_23-snap.12-T1
Valid prediction for snap_scaffold_23-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_51522-T1
Valid prediction for GeneMark_model.89669_t
Valid prediction for Augustus_model.g34581.t1
Valid prediction for HiQ_model.g34579.t1
Couldn't classify 20950, 21034
Couldn't classify 24721, 24886
Sorry, prediction pasa_asmbl_31297.p1 fails validation.
(CAG)	 CC	20950-21034	GT	CCG
(CTG)	 AG	23293-23422	GT	AAG
(GCC)	 AG	23519-23589	GT	AGG
(GAT)	 AG	23696-23768	GT	AGG
(TGC)	 AG	24721-24886	GA	GAG
-recovered pasa_asmbl_31297.p1, internal, 23293, 23422
-recovered pasa_asmbl_31297.p1, internal, 23519, 23589
-recovered pasa_asmbl_31297.p1, internal, 23696, 23768
Valid prediction for GeneMark_model.89663_t
Valid prediction for snap_scaffold_23-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_51516-T1
Valid prediction for Augustus_model.g34556.t1
Valid prediction for GlimmerHMM_glimmerT_51528-T1
Valid prediction for GeneMark_model.89685_t
Valid prediction for GlimmerHMM_glimmerT_51514-T1
Valid prediction for snap_scaffold_23-snap.23-T1
Valid prediction for GeneMark_model.89658_t
Couldn't classify 25094, 25141
Sorry, prediction pasa_asmbl_31293.p1 fails validation.
(TTG)	 GA	25094-25141	GT	GGG
(TGT)	 AG	25237-25362	GT	AGG
(GCT)	 AG	25495-25615	GT	AGG
(ACT)	 AG	25811-25970	GT	AGG
(GCC)	 AG	26102-26191	GT	AAG
(GCA)	 AG	26363-26446	GT	AGG
(AAG)	 AG	26660-26711	AA	GAA
-recovered pasa_asmbl_31293.p1, terminal, 25495, 25615
add_exon() Sorry, pasa_asmbl_31293.p1 25811-25970-terminal-3 is invalid.
-recovered pasa_asmbl_31293.p1, terminal, 25811, 25970
-recovered pasa_asmbl_31293.p1, terminal, 26660, 26711
-recovered pasa_asmbl_31293.p1, internal, 25237, 25362
-recovered pasa_asmbl_31293.p1, internal, 25495, 25615
-recovered pasa_asmbl_31293.p1, internal, 25811, 25970
-recovered pasa_asmbl_31293.p1, internal, 26102, 26191
-recovered pasa_asmbl_31293.p1, internal, 26363, 26446

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

-building trellis in range 1 - 298179
-exon list size: 350


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
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    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
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    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21690
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 20194
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10484
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 1 - 10332