-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_1774329-1955789

-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.g17600.t1
Valid prediction for GlimmerHMM_glimmerT_26594-T1
Valid prediction for snap_scaffold_11-snap.450-T1
Valid prediction for snap_scaffold_11-snap.462-T1
Valid prediction for Augustus_model.g17611.t1
Valid prediction for snap_scaffold_11-snap.481-T1
Valid prediction for snap_scaffold_11-snap.451-T1
Valid prediction for snap_scaffold_11-snap.449-T1
Valid prediction for Augustus_model.g17595.t1
Valid prediction for snap_scaffold_11-snap.467-T1
Valid prediction for GlimmerHMM_glimmerT_26568-T1
Valid prediction for GlimmerHMM_glimmerT_26586-T1
Valid prediction for GlimmerHMM_glimmerT_26584-T1
Valid prediction for Augustus_model.g17597.t1
Couldn't classify 104277, 104600
Sorry, prediction pasa_asmbl_5343.p1 fails validation.
(ATG)	 AT	104277-104600	AT	TGA
Valid prediction for GlimmerHMM_glimmerT_26600-T1
Valid prediction for GlimmerHMM_glimmerT_26588-T1
Valid prediction for snap_scaffold_11-snap.468-T1
Valid prediction for snap_scaffold_11-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_26592-T1
Valid prediction for Augustus_model.g17605.t1
Valid prediction for GlimmerHMM_glimmerT_26571-T1
Valid prediction for GlimmerHMM_glimmerT_26589-T1
Valid prediction for snap_scaffold_11-snap.484-T1
Valid prediction for Augustus_model.g17601.t1
Valid prediction for snap_scaffold_11-snap.443-T1
Valid prediction for GlimmerHMM_glimmerT_26576-T1
Valid prediction for GlimmerHMM_glimmerT_26577-T1
Valid prediction for snap_scaffold_11-snap.477-T1
Valid prediction for GlimmerHMM_glimmerT_26585-T1
Couldn't classify 17404, 17514
Couldn't classify 18604, 18624
Sorry, prediction pasa_asmbl_5342.p1 fails validation.
(AAG)	 TC	17404-17514	GT	AGG
(GAT)	 AG	17752-17955	GT	AGG
(AAC)	 AG	18048-18173	GT	ATG
(GCG)	 AG	18604-18624	CT	AGC
-recovered pasa_asmbl_5342.p1, internal, 17752, 17955
-recovered pasa_asmbl_5342.p1, internal, 18048, 18173
Valid prediction for GlimmerHMM_glimmerT_26578-T1
Valid prediction for GlimmerHMM_glimmerT_26593-T1
Valid prediction for Augustus_model.g17606.t1
Valid prediction for snap_scaffold_11-snap.460-T1
Valid prediction for pasa_asmbl_5344.p1
Valid prediction for GlimmerHMM_glimmerT_26580-T1
Valid prediction for snap_scaffold_11-snap.471-T1
Valid prediction for snap_scaffold_11-snap.453-T1
Valid prediction for snap_scaffold_11-snap.445-T1
Valid prediction for snap_scaffold_11-snap.485-T1
Valid prediction for Augustus_model.g17604.t1
Valid prediction for snap_scaffold_11-snap.486-T1
Valid prediction for snap_scaffold_11-snap.459-T1
Valid prediction for snap_scaffold_11-snap.480-T1
Valid prediction for snap_scaffold_11-snap.476-T1
Valid prediction for Augustus_model.g17603.t1
Valid prediction for CodingQuarry_transcript_7981-T1
Valid prediction for GlimmerHMM_glimmerT_26591-T1
Valid prediction for snap_scaffold_11-snap.446-T1
Valid prediction for snap_scaffold_11-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_26596-T1
Valid prediction for GlimmerHMM_glimmerT_26569-T1
Valid prediction for snap_scaffold_11-snap.463-T1
Valid prediction for Augustus_model.g17608.t1
Valid prediction for snap_scaffold_11-snap.441-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_11-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_26583-T1
Valid prediction for GlimmerHMM_glimmerT_26599-T1
Valid prediction for GlimmerHMM_glimmerT_26572-T1
Couldn't classify 130660, 130813
Couldn't classify 132829, 132865
Sorry, prediction pasa_asmbl_6450.p1 fails validation.
(GGG)	 CA	130660-130813	GT	AGG
(GGT)	 AG	130918-130997	GT	AGG
(GAC)	 AG	132497-132555	GT	GAG
(TTT)	 AG	132829-132865	CA	GCC
-recovered pasa_asmbl_6450.p1, internal, 130918, 130997
-recovered pasa_asmbl_6450.p1, internal, 132497, 132555
Valid prediction for snap_scaffold_11-snap.483-T1
Valid prediction for snap_scaffold_11-snap.461-T1
Valid prediction for snap_scaffold_11-snap.458-T1
Valid prediction for snap_scaffold_11-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_26587-T1
Valid prediction for snap_scaffold_11-snap.448-T1
Valid prediction for Augustus_model.g17610.t1
Valid prediction for snap_scaffold_11-snap.479-T1
Valid prediction for snap_scaffold_11-snap.470-T1
Valid prediction for Augustus_model.g17594.t1
Valid prediction for Augustus_model.g17609.t1
Valid prediction for snap_scaffold_11-snap.440-T1
Valid prediction for snap_scaffold_11-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_26579-T1
Valid prediction for snap_scaffold_11-snap.475-T1
Valid prediction for snap_scaffold_11-snap.444-T1
Valid prediction for Augustus_model.g17598.t1
Valid prediction for GlimmerHMM_glimmerT_26570-T1
Valid prediction for snap_scaffold_11-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_26582-T1
Valid prediction for snap_scaffold_11-snap.466-T1
Valid prediction for snap_scaffold_11-snap.464-T1
Valid prediction for GlimmerHMM_glimmerT_26590-T1
Couldn't classify 33398, 33509
Couldn't classify 33778, 33965
Sorry, prediction pasa_asmbl_6458.p1 fails validation.
(CGG)	 TA	33398-33509	GT	AGG
(TGG)	 AG	33778-33965	GT	ATG
-recovered pasa_asmbl_6458.p1, internal, 33778, 33965
Valid prediction for snap_scaffold_11-snap.487-T1
Valid prediction for snap_scaffold_11-snap.452-T1
Valid prediction for Augustus_model.g17596.t1
Valid prediction for snap_scaffold_11-snap.472-T1
Valid prediction for snap_scaffold_11-snap.457-T1
Valid prediction for snap_scaffold_11-snap.436-T1
Valid prediction for snap_scaffold_11-snap.439-T1
Valid prediction for GlimmerHMM_glimmerT_26597-T1
Valid prediction for GlimmerHMM_glimmerT_26598-T1
Valid prediction for GlimmerHMM_glimmerT_26581-T1
Valid prediction for snap_scaffold_11-snap.478-T1
Valid prediction for snap_scaffold_11-snap.447-T1
Couldn't classify 124285, 124608
Sorry, prediction pasa_asmbl_6452.p1 fails validation.
(GCC)	 CA	124285-124608	TC	GCT
Valid prediction for snap_scaffold_11-snap.456-T1
Couldn't classify 132497, 132498
Sorry, prediction CodingQuarry_transcript_7979-T1 fails validation.
(ATG)	 GC	130720-130813	GT	AGG
(GGT)	 AG	130918-131007	GT	ATG
(GAC)	 AG	132497-132498	CA	GAC
-recovered CodingQuarry_transcript_7979-T1, initial, 130720, 130813
-recovered CodingQuarry_transcript_7979-T1, internal, 130918, 131007
Valid prediction for GlimmerHMM_glimmerT_26573-T1
Valid prediction for Augustus_model.g17607.t1
Valid prediction for snap_scaffold_11-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_26574-T1
Valid prediction for snap_scaffold_11-snap.469-T1
Valid prediction for Augustus_model.g17602.t1
Valid prediction for Augustus_model.g17599.t1
Valid prediction for GlimmerHMM_glimmerT_26575-T1
Valid prediction for GlimmerHMM_glimmerT_26595-T1
Valid prediction for snap_scaffold_11-snap.442-T1
Valid prediction for snap_scaffold_11-snap.465-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8507, rend_intergenic: 7340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20324, rend_intergenic: 17797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27387, rend_intergenic: 21494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29452, rend_intergenic: 27520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39939, rend_intergenic: 39026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45744, rend_intergenic: 40519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70036, rend_intergenic: 64568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73186, rend_intergenic: 70980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85408, rend_intergenic: 80984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90564, rend_intergenic: 89280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96364, rend_intergenic: 92672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113291, rend_intergenic: 111897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116758, rend_intergenic: 113546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129778, rend_intergenic: 118557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135806, rend_intergenic: 130100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139412, rend_intergenic: 136310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147033, rend_intergenic: 141959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172554, rend_intergenic: 155561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181461
-exon list size: 432


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8507, rend_intergenic: 7340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20324, rend_intergenic: 17797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27387, rend_intergenic: 21494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29452, rend_intergenic: 27520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39939, rend_intergenic: 39026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45744, rend_intergenic: 40519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70036, rend_intergenic: 64568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73186, rend_intergenic: 70980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85408, rend_intergenic: 80984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90564, rend_intergenic: 89280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96364, rend_intergenic: 92672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113291, rend_intergenic: 111897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116758, rend_intergenic: 113546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129778, rend_intergenic: 118557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135806, rend_intergenic: 130100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139412, rend_intergenic: 136310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147033, rend_intergenic: 141959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172554, rend_intergenic: 155561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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