-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_634601-910619

-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_50377-T1
Valid prediction for Augustus_model.g33637.t1
Valid prediction for GlimmerHMM_glimmerT_50379-T1
Valid prediction for Augustus_model.g33634.t1
Valid prediction for snap_scaffold_23-snap.94-T1
Valid prediction for snap_scaffold_23-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_50392-T1
Valid prediction for snap_scaffold_23-snap.95-T1
Valid prediction for snap_scaffold_23-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_50399-T1
Valid prediction for GlimmerHMM_glimmerT_50381-T1
Valid prediction for snap_scaffold_23-snap.108-T1
Valid prediction for snap_scaffold_23-snap.98-T1
Valid prediction for Augustus_model.g33644.t1
Valid prediction for GlimmerHMM_glimmerT_50387-T1
Valid prediction for GlimmerHMM_glimmerT_50382-T1
Valid prediction for snap_scaffold_23-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_50391-T1
Valid prediction for GlimmerHMM_glimmerT_50398-T1
Valid prediction for snap_scaffold_23-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_50397-T1
Valid prediction for Augustus_model.g33622.t1
Valid prediction for Augustus_model.g33639.t1
Valid prediction for snap_scaffold_23-snap.105-T1
Valid prediction for snap_scaffold_23-snap.91-T1
Valid prediction for snap_scaffold_23-snap.89-T1
Valid prediction for Augustus_model.g33633.t1
Valid prediction for Augustus_model.g33643.t1
Valid prediction for snap_scaffold_23-snap.88-T1
Valid prediction for Augustus_model.g33619.t1
Valid prediction for snap_scaffold_23-snap.112-T1
Valid prediction for snap_scaffold_23-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_50405-T1
Valid prediction for snap_scaffold_23-snap.109-T1
Valid prediction for snap_scaffold_23-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_50394-T1
Valid prediction for Augustus_model.g33618.t1
Valid prediction for Augustus_model.g33620.t1
Valid prediction for snap_scaffold_23-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_50376-T1
Valid prediction for GlimmerHMM_glimmerT_50384-T1
Valid prediction for GlimmerHMM_glimmerT_50395-T1
Valid prediction for Augustus_model.g33625.t1
Valid prediction for GlimmerHMM_glimmerT_50402-T1
Valid prediction for snap_scaffold_23-snap.111-T1
Valid prediction for Augustus_model.g33627.t1
Valid prediction for Augustus_model.g33623.t1
Valid prediction for Augustus_model.g33641.t1
Valid prediction for Augustus_model.g33636.t1
Valid prediction for snap_scaffold_23-snap.90-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 CodingQuarry_transcript_35543-T1
Valid prediction for snap_scaffold_23-snap.99-T1
Valid prediction for GlimmerHMM_glimmerT_50383-T1
Valid prediction for snap_scaffold_23-snap.117-T1
Couldn't classify 149613, 149778
Couldn't classify 152669, 152817
Sorry, prediction pasa_asmbl_30603.p1 fails validation.
(GTA)	 AG	149613-149778	GT	GGG
(GAA)	 AG	151260-151434	GT	CGG
(TTA)	 AG	151666-151771	GT	GTG
(TCC)	 AG	152047-152245	GT	AGG
(ACA)	 AG	152669-152817	GT	AGG
-recovered pasa_asmbl_30603.p1, internal, 149613, 149778
-recovered pasa_asmbl_30603.p1, internal, 151260, 151434
-recovered pasa_asmbl_30603.p1, internal, 151666, 151771
-recovered pasa_asmbl_30603.p1, internal, 152047, 152245
-recovered pasa_asmbl_30603.p1, internal, 152669, 152817
Valid prediction for snap_scaffold_23-snap.107-T1
Couldn't classify 159520, 159750
Sorry, prediction pasa_asmbl_30602.p1 fails validation.
(ATC)	 AG	159520-159750	GT	AGG
(AAA)	 AG	159915-159981	GT	AAG
(GAC)	 AG	162513-162620	GT	TGG
(GAT)	 AG	162733-162780	GT	AGG
(GAT)	 AG	164271-164392	GG	GAG
-recovered pasa_asmbl_30602.p1, terminal, 164271, 164392
-recovered pasa_asmbl_30602.p1, internal, 159520, 159750
-recovered pasa_asmbl_30602.p1, internal, 159915, 159981
-recovered pasa_asmbl_30602.p1, internal, 162513, 162620
-recovered pasa_asmbl_30602.p1, internal, 162733, 162780
Valid prediction for HiQ_model.g33626.t1
Valid prediction for snap_scaffold_23-snap.110-T1
Valid prediction for snap_scaffold_23-snap.115-T1
Valid prediction for snap_scaffold_23-snap.116-T1
Couldn't classify 86123, 86291
Couldn't classify 88059, 88259
Sorry, prediction pasa_asmbl_30614.p1 fails validation.
(AAG)	 AG	86123-86291	GT	AGG
(ATT)	 AG	86530-86735	GT	AGG
(ATC)	 AG	88059-88259	CC	TGC
add_exon() Sorry, pasa_asmbl_30614.p1 86123-86291-terminal-3 is invalid.
-recovered pasa_asmbl_30614.p1, terminal, 86123, 86291
-recovered pasa_asmbl_30614.p1, internal, 86123, 86291
-recovered pasa_asmbl_30614.p1, internal, 86530, 86735
Valid prediction for GlimmerHMM_glimmerT_50404-T1
Valid prediction for GlimmerHMM_glimmerT_50401-T1
Valid prediction for snap_scaffold_23-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_50378-T1
Valid prediction for Augustus_model.g33631.t1
Valid prediction for snap_scaffold_23-snap.102-T1
Valid prediction for snap_scaffold_23-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_50389-T1
Valid prediction for snap_scaffold_23-snap.96-T1
Valid prediction for GlimmerHMM_glimmerT_50400-T1
Valid prediction for HiQ_model.g33630.t1
Valid prediction for Augustus_model.g33629.t1
Valid prediction for Augustus_model.g33621.t1
Valid prediction for Augustus_model.g33638.t1
Couldn't classify 109306, 109623
Sorry, prediction pasa_asmbl_30609.p5 fails validation.
(ATG)	 AG	109306-109623	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_50393-T1
Valid prediction for Augustus_model.g33635.t1
Valid prediction for snap_scaffold_23-snap.92-T1
Valid prediction for Augustus_model.g33645.t1
Valid prediction for Augustus_model.g33624.t1
Valid prediction for Augustus_model.g33632.t1
Valid prediction for snap_scaffold_23-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_50403-T1
Valid prediction for GlimmerHMM_glimmerT_50396-T1
Valid prediction for Augustus_model.g33640.t1
Valid prediction for Augustus_model.g33642.t1
Valid prediction for GlimmerHMM_glimmerT_50390-T1
Valid prediction for snap_scaffold_23-snap.113-T1
Couldn't classify 70248, 70403
Couldn't classify 71775, 71888
Sorry, prediction pasa_asmbl_31210.p1 fails validation.
(AAG)	 TG	70248-70403	GT	AGG
(CGT)	 AG	70602-70717	GT	AGG
(AAA)	 AG	70920-71075	GT	AGG
(AGT)	 AG	71220-71328	GT	AGG
(ATT)	 AG	71775-71888	GG	AAG
-recovered pasa_asmbl_31210.p1, internal, 70602, 70717
-recovered pasa_asmbl_31210.p1, internal, 70920, 71075
-recovered pasa_asmbl_31210.p1, internal, 71220, 71328
Valid prediction for GlimmerHMM_glimmerT_50388-T1
Valid prediction for snap_scaffold_23-snap.106-T1
Valid prediction for Augustus_model.g33628.t1
Valid prediction for snap_scaffold_23-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_50380-T1
Valid prediction for GlimmerHMM_glimmerT_50386-T1
Valid prediction for GlimmerHMM_glimmerT_50385-T1
Valid prediction for snap_scaffold_23-snap.120-T1
Valid prediction for Augustus_model.g33646.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 166245, rend_intergenic: 165381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 276019
-exon list size: 270


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
2.9    
3.3    
3.7    
4.0    
4.4    
4.8    
5.1    
5.5    
5.9    
6.2    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.6    
9.9    
10.3    
10.7    
11.0    
11.4    
11.8    
12.1    
12.5    
12.9    
13.2    
13.6    
14.0    
14.3    
14.7    
15.1    
15.4    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
21.0    
21.3    
21.7    
22.1    
22.4    
22.8    
23.2    
23.5    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.5    
26.8    
27.2    
27.6    
27.9    
28.3    
28.7    
29.0    
29.4    
29.8    
30.1    
30.5    
30.9    
31.2    
31.6    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
34.9    
35.3    
35.7    
36.0    
36.4    
36.8    
37.1    
37.5    
37.9    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.4    
43.8    
44.1    
44.5    
44.9    
45.2    
45.6    
46.0    
46.3    
46.7    
47.1    
47.4    
47.8    
48.2    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.8    
52.2    
52.6    
52.9    
53.3    
53.7    
54.0    
54.4    
54.8    
55.1    
55.5    
55.9    
56.2    
56.6    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.1    
62.5    
62.9    
63.2    
63.6    
64.0    
64.3    
64.7    
65.1    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.4    
68.8    
69.1    
69.5    
69.9    
70.2    
70.6    
71.0    
71.3    
71.7    
72.1    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.5    
76.8    
77.2    
77.6    
77.9    
78.3    
78.7    
79.0    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.6    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.1    
87.5    
87.9    
88.2    
88.6    
89.0    
89.3    
89.7    
90.1    
90.4    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.8    
94.1    
94.5    
94.9    
95.2    
95.6    
96.0    
96.3    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 166245, rend_intergenic: 165381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 252838 - 276019
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 252838 - 268000
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 257966 - 268000
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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