-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_331341-530920

-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: +)Couldn't classify 86686, 86805
Couldn't classify 87406, 87828
Sorry, prediction pasa_asmbl_54700.p1 fails validation.
(GGG)	 CA	86686-86805	GT	AGG
(GTG)	 AG	87406-87828	GT	TGG
-recovered pasa_asmbl_54700.p1, internal, 87406, 87828
Valid prediction for GlimmerHMM_glimmerT_21493-T1
Valid prediction for snap_scaffold_9-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_21470-T1
Valid prediction for Augustus_model.g14295.t1
Valid prediction for snap_scaffold_9-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_21478-T1
Valid prediction for GlimmerHMM_glimmerT_21481-T1
Valid prediction for Augustus_model.g14293.t1
Couldn't classify 27407, 27595
Sorry, prediction pasa_asmbl_53756.p1 fails validation.
(GAT)	 TG	27407-27595	GT	AGG
(CTA)	 AG	28089-28226	GT	TGG
(GTG)	 AG	28576-28719	GT	AGG
(GAG)	 AG	29023-29220	GT	AGG
(GTG)	 AG	29303-30107	GT	AGG
(ACT)	 AG	30289-30420	GT	AGG
(GCC)	 AG	30798-30952	GT	AGG
(CTG)	 AG	31350-31595	GT	AGG
(GTT)	 AG	32014-32325	TT	AGT
-recovered pasa_asmbl_53756.p1, terminal, 32014, 32325
-recovered pasa_asmbl_53756.p1, internal, 28089, 28226
-recovered pasa_asmbl_53756.p1, internal, 28576, 28719
-recovered pasa_asmbl_53756.p1, internal, 29023, 29220
-recovered pasa_asmbl_53756.p1, internal, 29303, 30107
-recovered pasa_asmbl_53756.p1, internal, 30289, 30420
-recovered pasa_asmbl_53756.p1, internal, 30798, 30952
-recovered pasa_asmbl_53756.p1, internal, 31350, 31595
Valid prediction for snap_scaffold_9-snap.88-T1
Valid prediction for snap_scaffold_9-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_21471-T1
Valid prediction for Augustus_model.g14290.t1
Valid prediction for snap_scaffold_9-snap.103-T1
Valid prediction for snap_scaffold_9-snap.78-T1
Valid prediction for snap_scaffold_9-snap.111-T1
Valid prediction for snap_scaffold_9-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_21485-T1
Valid prediction for snap_scaffold_9-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_21490-T1
Valid prediction for snap_scaffold_9-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_21475-T1
Valid prediction for Augustus_model.g14291.t1
Valid prediction for snap_scaffold_9-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_21486-T1
Valid prediction for GlimmerHMM_glimmerT_21477-T1
Valid prediction for snap_scaffold_9-snap.108-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21467-T1
Valid prediction for snap_scaffold_9-snap.96-T1
Valid prediction for snap_scaffold_9-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_21473-T1
Couldn't classify 37074, 37176
Couldn't classify 43243, 43346
Sorry, prediction pasa_asmbl_53757.p1 fails validation.
(CGC)	 GA	37074-37176	GT	GGG
(GTA)	 AG	38232-38345	GT	CGG
(CCT)	 AG	39690-39749	GT	AGG
(TGT)	 AG	42272-42307	GT	AGG
(CGT)	 AG	43243-43346	GG	GGG
-recovered pasa_asmbl_53757.p1, internal, 38232, 38345
-recovered pasa_asmbl_53757.p1, internal, 39690, 39749
-recovered pasa_asmbl_53757.p1, internal, 42272, 42307
Valid prediction for snap_scaffold_9-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_21483-T1
Couldn't classify 24499, 24549
Couldn't classify 26097, 26458
Sorry, prediction pasa_asmbl_53754.p1 fails validation.
(GTG)	 CG	24499-24549	GT	AGG
(GCA)	 AG	24734-24887	GT	TGG
(GTG)	 AG	25390-25623	GT	GGG
(GCT)	 AG	26097-26458	AA	GGA
-recovered pasa_asmbl_53754.p1, internal, 24734, 24887
-recovered pasa_asmbl_53754.p1, internal, 25390, 25623
Valid prediction for snap_scaffold_9-snap.106-T1
Valid prediction for GlimmerHMM_glimmerT_21479-T1
Valid prediction for GlimmerHMM_glimmerT_21491-T1
Valid prediction for Augustus_model.g14292.t1
Couldn't classify 19719, 19958
Couldn't classify 20287, 20355
Sorry, prediction pasa_asmbl_54759.p2 fails validation.
(GAG)	 AC	19719-19958	GT	AGG
(GTG)	 AG	20287-20355	AA	GTA
Valid prediction for GlimmerHMM_glimmerT_21480-T1
Valid prediction for snap_scaffold_9-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_21469-T1
Couldn't classify 88253, 88648
Sorry, prediction pasa_asmbl_54719.p1 fails validation.
(CTC)	 AC	88253-88648	GT	GAG
Valid prediction for snap_scaffold_9-snap.94-T1
Valid prediction for GlimmerHMM_glimmerT_21468-T1
Valid prediction for snap_scaffold_9-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_21488-T1
Valid prediction for snap_scaffold_9-snap.98-T1
Valid prediction for snap_scaffold_9-snap.91-T1
Valid prediction for snap_scaffold_9-snap.104-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 GlimmerHMM_glimmerT_21476-T1
Valid prediction for GlimmerHMM_glimmerT_21492-T1
Valid prediction for snap_scaffold_9-snap.107-T1
Valid prediction for snap_scaffold_9-snap.113-T1
Valid prediction for snap_scaffold_9-snap.110-T1
Valid prediction for snap_scaffold_9-snap.86-T1
Valid prediction for Augustus_model.g14294.t1
Valid prediction for snap_scaffold_9-snap.85-T1
Valid prediction for snap_scaffold_9-snap.122-T1
Valid prediction for Augustus_model.g14296.t1
Valid prediction for GlimmerHMM_glimmerT_21482-T1
Valid prediction for snap_scaffold_9-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_21487-T1
Valid prediction for snap_scaffold_9-snap.77-T1
Valid prediction for snap_scaffold_9-snap.79-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.89-T1
Valid prediction for snap_scaffold_9-snap.81-T1
Valid prediction for snap_scaffold_9-snap.92-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21496-T1
Valid prediction for GlimmerHMM_glimmerT_21472-T1
Valid prediction for GlimmerHMM_glimmerT_21489-T1
Valid prediction for snap_scaffold_9-snap.99-T1
Valid prediction for snap_scaffold_9-snap.101-T1
Valid prediction for snap_scaffold_9-snap.95-T1
Valid prediction for Augustus_model.g14297.t1
Valid prediction for GlimmerHMM_glimmerT_21474-T1
Valid prediction for GlimmerHMM_glimmerT_21484-T1
Valid prediction for snap_scaffold_9-snap.120-T1
Valid prediction for snap_scaffold_9-snap.115-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_21466-T1
Valid prediction for GlimmerHMM_glimmerT_21494-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21495-T1
Valid prediction for snap_scaffold_9-snap.109-T1
Valid prediction for Augustus_model.g14298.t1
Valid prediction for snap_scaffold_9-snap.97-T1
Valid prediction for snap_scaffold_9-snap.83-T1
Valid prediction for snap_scaffold_9-snap.82-T1
Valid prediction for snap_scaffold_9-snap.105-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3578, rend_intergenic: 2242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22063, rend_intergenic: 5384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29361, rend_intergenic: 22536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38494, rend_intergenic: 29372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44643, rend_intergenic: 39674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57140, rend_intergenic: 46544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80469, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88648, rend_intergenic: 83890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97029, rend_intergenic: 91655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105601, rend_intergenic: 103197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117735, rend_intergenic: 112223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133948, rend_intergenic: 130926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146308, rend_intergenic: 140414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155853, rend_intergenic: 147679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161505, rend_intergenic: 158144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177614, rend_intergenic: 163763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186031, rend_intergenic: 183739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199580
-exon list size: 354


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.4    
74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 3578, rend_intergenic: 2242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22063, rend_intergenic: 5384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29361, rend_intergenic: 22536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38494, rend_intergenic: 29372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44643, rend_intergenic: 39674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57140, rend_intergenic: 46544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80469, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88648, rend_intergenic: 83890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97029, rend_intergenic: 91655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105601, rend_intergenic: 103197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117735, rend_intergenic: 112223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133948, rend_intergenic: 130926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146308, rend_intergenic: 140414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155853, rend_intergenic: 147679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161505, rend_intergenic: 158144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177614, rend_intergenic: 163763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186031, rend_intergenic: 183739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support