-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_16247505-16520113

-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_11-snap.3356-T1
Valid prediction for snap_scaffold_11-snap.3348-T1
Valid prediction for snap_scaffold_11-snap.3344-T1
Valid prediction for Augustus_model.g18868.t1
Valid prediction for GlimmerHMM_glimmerT_28496-T1
Valid prediction for snap_scaffold_11-snap.3342-T1
Valid prediction for snap_scaffold_11-snap.3340-T1
Valid prediction for Augustus_model.g18874.t1
Valid prediction for snap_scaffold_11-snap.3334-T1
Valid prediction for GlimmerHMM_glimmerT_28484-T1
Valid prediction for GlimmerHMM_glimmerT_28482-T1
Valid prediction for pasa_asmbl_6154.p1
Valid prediction for pasa_asmbl_6152.p1
Couldn't classify 255292, 255696
Sorry, prediction pasa_asmbl_6153.p1 fails validation.
(TCA)	 CA	255292-255696	AT	CTA
Valid prediction for GlimmerHMM_glimmerT_28489-T1
Valid prediction for snap_scaffold_11-snap.3324-T1
Valid prediction for snap_scaffold_11-snap.3341-T1
Valid prediction for Augustus_model.g18871.t1
Valid prediction for GlimmerHMM_glimmerT_28502-T1
Valid prediction for GlimmerHMM_glimmerT_28500-T1
Valid prediction for snap_scaffold_11-snap.3357-T1
Valid prediction for Augustus_model.g18862.t1
Valid prediction for GlimmerHMM_glimmerT_28487-T1
Couldn't classify 174104, 174261
Sorry, prediction pasa_asmbl_6348.p1 fails validation.
(ATG)	 CC	173518-173686	GT	AGG
(GTA)	 AG	174104-174261	CC	GGC
-recovered pasa_asmbl_6348.p1, initial, 173518, 173686
Valid prediction for snap_scaffold_11-snap.3350-T1
Valid prediction for GlimmerHMM_glimmerT_28494-T1
Valid prediction for GlimmerHMM_glimmerT_28493-T1
Valid prediction for snap_scaffold_11-snap.3330-T1
Valid prediction for snap_scaffold_11-snap.3360-T1
Valid prediction for CodingQuarry_transcript_8334-T1
Valid prediction for snap_scaffold_11-snap.3339-T1
Valid prediction for snap_scaffold_11-snap.3322-T1
Valid prediction for snap_scaffold_11-snap.3358-T1
Couldn't classify 262647, 262790
Couldn't classify 263445, 263541
Sorry, prediction pasa_asmbl_6255.p1 fails validation.
(AGG)	 CC	262647-262790	GT	AGG
(AAT)	 AG	263005-263121	GT	AGG
(GCT)	 AG	263266-263345	GT	CAG
(CGC)	 AG	263445-263541	GG	GGG
-recovered pasa_asmbl_6255.p1, internal, 263005, 263121
-recovered pasa_asmbl_6255.p1, internal, 263266, 263345
Couldn't classify 261057, 261104
Couldn't classify 261820, 261922
Sorry, prediction pasa_asmbl_6155.p1 fails validation.
(GAG)	 AG	261057-261104	GT	AGG
(GAG)	 AG	261231-261347	GT	AGG
(ATA)	 AG	261478-261557	GT	GGG
(GAT)	 AG	261820-261922	GA	AGG
-recovered pasa_asmbl_6155.p1, internal, 261057, 261104
-recovered pasa_asmbl_6155.p1, internal, 261231, 261347
-recovered pasa_asmbl_6155.p1, internal, 261478, 261557
Valid prediction for snap_scaffold_11-snap.3343-T1
Valid prediction for snap_scaffold_11-snap.3320-T1
Valid prediction for GlimmerHMM_glimmerT_28486-T1
Valid prediction for snap_scaffold_11-snap.3359-T1
Valid prediction for snap_scaffold_11-snap.3332-T1
Valid prediction for GlimmerHMM_glimmerT_28498-T1
Valid prediction for snap_scaffold_11-snap.3325-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28495-T1
Valid prediction for snap_scaffold_11-snap.3338-T1
Valid prediction for snap_scaffold_11-snap.3355-T1
Valid prediction for Augustus_model.g18867.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 HiQ_model.g18875.t1
Valid prediction for GlimmerHMM_glimmerT_28501-T1
Valid prediction for snap_scaffold_11-snap.3337-T1
Valid prediction for snap_scaffold_11-snap.3353-T1
Valid prediction for Augustus_model.g18866.t1
Valid prediction for Augustus_model.g18870.t1
Valid prediction for snap_scaffold_11-snap.3326-T1
Valid prediction for GlimmerHMM_glimmerT_28499-T1
Valid prediction for snap_scaffold_11-snap.3336-T1
Valid prediction for GlimmerHMM_glimmerT_28490-T1
Valid prediction for GlimmerHMM_glimmerT_28483-T1
Valid prediction for Augustus_model.g18876.t1
Valid prediction for snap_scaffold_11-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_28492-T1
Valid prediction for CodingQuarry_transcript_8340-T1
Valid prediction for pasa_asmbl_7294.p1
Valid prediction for snap_scaffold_11-snap.3335-T1
Valid prediction for pasa_asmbl_7222.p2
Valid prediction for snap_scaffold_11-snap.3319-T1
Valid prediction for HiQ_model.g18873.t1
Valid prediction for snap_scaffold_11-snap.3321-T1
Valid prediction for CodingQuarry_transcript_8338-T1
Valid prediction for CodingQuarry_transcript_8337-T1
Valid prediction for CodingQuarry_transcript_8335-T1
Valid prediction for HiQ_model.g18872.t1
Valid prediction for snap_scaffold_11-snap.3346-T1
Valid prediction for pasa_asmbl_7221.p1
Valid prediction for GlimmerHMM_glimmerT_28504-T1
Valid prediction for GlimmerHMM_glimmerT_28497-T1
Valid prediction for Augustus_model.g18864.t1
Valid prediction for snap_scaffold_11-snap.3327-T1
Valid prediction for snap_scaffold_11-snap.3354-T1
Valid prediction for GlimmerHMM_glimmerT_28503-T1
Valid prediction for snap_scaffold_11-snap.3361-T1
Valid prediction for snap_scaffold_11-snap.3323-T1
Valid prediction for snap_scaffold_11-snap.3351-T1
Valid prediction for snap_scaffold_11-snap.3349-T1
Valid prediction for Augustus_model.g18863.t1
Valid prediction for snap_scaffold_11-snap.3328-T1
Valid prediction for Augustus_model.g18869.t1
Valid prediction for GlimmerHMM_glimmerT_28485-T1
Valid prediction for GlimmerHMM_glimmerT_28491-T1
Valid prediction for GlimmerHMM_glimmerT_28488-T1
Valid prediction for snap_scaffold_11-snap.3317-T1
Valid prediction for snap_scaffold_11-snap.3345-T1
Valid prediction for CodingQuarry_transcript_8336-T1
Valid prediction for Augustus_model.g18865.t1
Valid prediction for snap_scaffold_11-snap.3352-T1
Valid prediction for snap_scaffold_11-snap.3318-T1
Valid prediction for pasa_asmbl_7224.p1
Valid prediction for snap_scaffold_11-snap.3331-T1
Valid prediction for snap_scaffold_11-snap.3347-T1
Valid prediction for snap_scaffold_11-snap.3329-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28856, rend_intergenic: 26685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272609
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 28856, rend_intergenic: 26685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16535
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 2 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 - 12392
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 - 10203
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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