-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1-301619

-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 Augustus_model.g33564.t1
Valid prediction for snap_scaffold_23-snap.31-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50314-T1
Valid prediction for GlimmerHMM_glimmerT_50334-T1
Couldn't classify 179614, 179698
Couldn't classify 180487, 180509
Sorry, prediction pasa_asmbl_31972.p1 fails validation.
(GCC)	 TA	179614-179698	GT	GGG
(CCA)	 AG	179933-180241	GT	AGG
(TTG)	 AG	180487-180509	GT	TGG
-recovered pasa_asmbl_31972.p1, internal, 179933, 180241
-recovered pasa_asmbl_31972.p1, internal, 180487, 180509
Valid prediction for snap_scaffold_23-snap.6-T1
Valid prediction for snap_scaffold_23-snap.29-T1
Valid prediction for Augustus_model.g33573.t1
Valid prediction for Augustus_model.g33570.t1
Valid prediction for GlimmerHMM_glimmerT_50306-T1
Valid prediction for snap_scaffold_23-snap.13-T1
Valid prediction for Augustus_model.g33583.t1
Valid prediction for Augustus_model.g33560.t1
Valid prediction for GlimmerHMM_glimmerT_50316-T1
Valid prediction for GlimmerHMM_glimmerT_50319-T1
Valid prediction for snap_scaffold_23-snap.10-T1
Valid prediction for Augustus_model.g33569.t1
Valid prediction for snap_scaffold_23-snap.8-T1
Couldn't classify 191431, 191485
Couldn't classify 191788, 193382
Sorry, prediction pasa_asmbl_31283.p1 fails validation.
(TCT)	 GG	191431-191485	GT	AGG
(TGA)	 AG	191788-193382	GG	CAG
Valid prediction for snap_scaffold_23-snap.17-T1
Valid prediction for CodingQuarry_transcript_35533-T1
Valid prediction for GlimmerHMM_glimmerT_50329-T1
Valid prediction for snap_scaffold_23-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_50324-T1
Couldn't classify 140301, 140475
Sorry, prediction pasa_asmbl_31276.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_31276.p1, terminal, 141475, 142013
-recovered pasa_asmbl_31276.p1, internal, 140637, 140742
-recovered pasa_asmbl_31276.p1, internal, 141066, 141163
Valid prediction for snap_scaffold_23-snap.9-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_50320-T1
Valid prediction for Augustus_model.g33558.t1
Valid prediction for GlimmerHMM_glimmerT_50307-T1
Couldn't classify 171011, 171460
Sorry, prediction pasa_asmbl_31282.p1 fails validation.
(AAA)	 CG	171011-171460	AA	CCA
Valid prediction for snap_scaffold_23-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_50335-T1
Valid prediction for Augustus_model.g33555.t1
Valid prediction for snap_scaffold_23-snap.30-T1
Valid prediction for Augustus_model.g33565.t1
Couldn't classify 156833, 156958
Sorry, prediction pasa_asmbl_31280.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_31280.p1, initial, 155355, 155384
-recovered pasa_asmbl_31280.p1, internal, 155477, 155540
-recovered pasa_asmbl_31280.p1, internal, 156082, 156185
-recovered pasa_asmbl_31280.p1, internal, 156298, 156404
-recovered pasa_asmbl_31280.p1, internal, 156571, 156637
Valid prediction for GlimmerHMM_glimmerT_50310-T1
Valid prediction for Augustus_model.g33559.t1
Valid prediction for GlimmerHMM_glimmerT_50322-T1
Valid prediction for GlimmerHMM_glimmerT_50326-T1
Valid prediction for snap_scaffold_23-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_50308-T1
Valid prediction for Augustus_model.g33563.t1
Valid prediction for snap_scaffold_23-snap.2-T1
Valid prediction for snap_scaffold_23-snap.1-T1
Valid prediction for Augustus_model.g33567.t1
Couldn't classify 132680, 133407
Sorry, prediction pasa_asmbl_31275.p1 fails validation.
(ATG)	 TC	131609-131720	GT	AGG
(GCC)	 AG	132680-133407	CG	GGC
-recovered pasa_asmbl_31275.p1, initial, 131609, 131720
Valid prediction for Augustus_model.g33566.t1
Valid prediction for snap_scaffold_23-snap.20-T1
Valid prediction for snap_scaffold_23-snap.5-T1
Valid prediction for pasa_asmbl_31291.p1
Valid prediction for snap_scaffold_23-snap.32-T1
Couldn't classify 163076, 163232
Couldn't classify 165882, 165967
Sorry, prediction pasa_asmbl_31281.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_31281.p1, internal, 163871, 164345
-recovered pasa_asmbl_31281.p1, internal, 165455, 165591
Valid prediction for snap_scaffold_23-snap.4-T1
Valid prediction for HiQ_model.g33574.t1
Valid prediction for GlimmerHMM_glimmerT_50331-T1
Valid prediction for snap_scaffold_23-snap.11-T1
Valid prediction for Augustus_model.g33578.t1
Valid prediction for HiQ_model.g33577.t1
Valid prediction for GlimmerHMM_glimmerT_50317-T1
Valid prediction for Augustus_model.g33562.t1
Valid prediction for snap_scaffold_23-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_50311-T1
Valid prediction for snap_scaffold_23-snap.15-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 snap_scaffold_23-snap.21-T1
Valid prediction for Augustus_model.g33561.t1
Valid prediction for Augustus_model.g33572.t1
Valid prediction for snap_scaffold_23-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_50330-T1
Valid prediction for GlimmerHMM_glimmerT_50325-T1
Valid prediction for GlimmerHMM_glimmerT_50332-T1
Valid prediction for GlimmerHMM_glimmerT_50336-T1
Valid prediction for GlimmerHMM_glimmerT_50328-T1
Valid prediction for HiQ_model.g33580.t1
Valid prediction for snap_scaffold_23-snap.3-T1
Couldn't classify 9584, 9710
Couldn't classify 11694, 11894
Sorry, prediction pasa_asmbl_31214.p1 fails validation.
(TCT)	 TG	9584-9710	GT	TGG
(GAA)	 AG	9804-9883	GT	TGG
(GCC)	 AG	11694-11894	TA	GGT
-recovered pasa_asmbl_31214.p1, internal, 9804, 9883
Valid prediction for GlimmerHMM_glimmerT_50321-T1
Valid prediction for snap_scaffold_23-snap.12-T1
Valid prediction for snap_scaffold_23-snap.37-T1
Valid prediction for snap_scaffold_23-snap.27-T1
Valid prediction for snap_scaffold_23-snap.22-T1
Valid prediction for Augustus_model.g33579.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_50327-T1
Couldn't classify 28534, 28581
Sorry, prediction pasa_asmbl_30575.p1 fails validation.
(TTG)	 GA	28534-28581	GT	GGG
(TGT)	 AG	28677-28802	GT	AGG
(GCT)	 AG	28935-29055	GT	AGG
(ACT)	 AG	29251-29410	GT	AGG
(GCC)	 AG	29542-29631	GT	AAG
(GCA)	 AG	29803-29886	GT	AGG
(AAG)	 AG	30100-30151	AA	GAA
-recovered pasa_asmbl_30575.p1, terminal, 28935, 29055
add_exon() Sorry, pasa_asmbl_30575.p1 29251-29410-terminal-3 is invalid.
-recovered pasa_asmbl_30575.p1, terminal, 29251, 29410
-recovered pasa_asmbl_30575.p1, terminal, 30100, 30151
-recovered pasa_asmbl_30575.p1, internal, 28677, 28802
-recovered pasa_asmbl_30575.p1, internal, 28935, 29055
-recovered pasa_asmbl_30575.p1, internal, 29251, 29410
-recovered pasa_asmbl_30575.p1, internal, 29542, 29631
-recovered pasa_asmbl_30575.p1, internal, 29803, 29886
Valid prediction for snap_scaffold_23-snap.18-T1
Valid prediction for Augustus_model.g33556.t1
Valid prediction for GlimmerHMM_glimmerT_50318-T1
Valid prediction for snap_scaffold_23-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_50315-T1
Valid prediction for snap_scaffold_23-snap.34-T1
Valid prediction for Augustus_model.g33568.t1
Valid prediction for CodingQuarry_transcript_35532-T1
Valid prediction for snap_scaffold_23-snap.39-T1
Valid prediction for HiQ_model.g33576.t1
Valid prediction for snap_scaffold_23-snap.33-T1
Valid prediction for snap_scaffold_23-snap.26-T1
Valid prediction for Augustus_model.g33582.t1
Valid prediction for GlimmerHMM_glimmerT_50333-T1
Valid prediction for pasa_asmbl_30572.p1
Valid prediction for GlimmerHMM_glimmerT_50312-T1
Valid prediction for snap_scaffold_23-snap.28-T1
Valid prediction for snap_scaffold_23-snap.36-T1
Valid prediction for Augustus_model.g33571.t1
Valid prediction for GlimmerHMM_glimmerT_50309-T1
Valid prediction for Augustus_model.g33557.t1
Valid prediction for Augustus_model.g33581.t1
Couldn't classify 24390, 24474
Couldn't classify 28161, 28326
Sorry, prediction pasa_asmbl_30579.p1 fails validation.
(CAG)	 CC	24390-24474	GT	CCG
(CTG)	 AG	26733-26862	GT	AAG
(GCC)	 AG	26959-27029	GT	AGG
(GAT)	 AG	27136-27208	GT	AGG
(TGC)	 AG	28161-28326	GA	GAG
-recovered pasa_asmbl_30579.p1, internal, 26733, 26862
-recovered pasa_asmbl_30579.p1, internal, 26959, 27029
-recovered pasa_asmbl_30579.p1, internal, 27136, 27208
Valid prediction for Augustus_model.g33575.t1
Valid prediction for GlimmerHMM_glimmerT_50323-T1
Valid prediction for GlimmerHMM_glimmerT_50313-T1
Valid prediction for snap_scaffold_23-snap.24-T1
Valid prediction for Augustus_model.g33584.t1
Valid prediction for CodingQuarry_transcript_35534-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 136504, rend_intergenic: 136501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 301619
-exon list size: 279


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.6    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.8    
7.1    
7.5    
7.8    
8.2    
8.5    
8.9    
9.3    
9.6    
10.0    
10.3    
10.7    
11.0    
11.4    
11.7    
12.1    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.4    
21.7    
22.1    
22.4    
22.8    
23.1    
23.5    
23.8    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.7    
38.1    
38.4    
38.8    
39.1    
39.5    
39.9    
40.2    
40.6    
40.9    
41.3    
41.6    
42.0    
42.3    
42.7    
43.1    
43.4    
43.8    
44.1    
44.5    
44.8    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.0    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
52.0    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.2    
55.5    
55.9    
56.2    
56.6    
56.9    
57.3    
57.7    
58.0    
58.4    
58.7    
59.1    
59.4    
59.8    
60.1    
60.5    
60.9    
61.2    
61.6    
61.9    
62.3    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.2    
76.5    
76.9    
77.2    
77.6    
77.9    
78.3    
78.6    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.4    
90.7    
91.1    
91.5    
91.8    
92.2    
92.5    
92.9    
93.2    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.4    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 136504, rend_intergenic: 136501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21690
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 16356