-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_322903-509081

-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 CodingQuarry_transcript_28425-T1
Valid prediction for snap_scaffold_2-snap.81-T1
Valid prediction for Augustus_model.g2078.t1
Valid prediction for snap_scaffold_2-snap.114-T1
Valid prediction for snap_scaffold_2-snap.116-T1
Valid prediction for HiQ_model.g2082.t1
Valid prediction for GlimmerHMM_glimmerT_3046-T1
Valid prediction for snap_scaffold_2-snap.92-T1
Valid prediction for GlimmerHMM_glimmerT_3062-T1
Valid prediction for snap_scaffold_2-snap.101-T1
Valid prediction for snap_scaffold_2-snap.113-T1
Valid prediction for snap_scaffold_2-snap.85-T1
Valid prediction for snap_scaffold_2-snap.88-T1
Valid prediction for snap_scaffold_2-snap.78-T1
Valid prediction for snap_scaffold_2-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_3045-T1
Valid prediction for GlimmerHMM_glimmerT_3049-T1
Valid prediction for GlimmerHMM_glimmerT_3056-T1
Valid prediction for snap_scaffold_2-snap.110-T1
Valid prediction for GlimmerHMM_glimmerT_3042-T1
Valid prediction for GlimmerHMM_glimmerT_3059-T1
Valid prediction for snap_scaffold_2-snap.93-T1
Valid prediction for snap_scaffold_2-snap.98-T1
Valid prediction for snap_scaffold_2-snap.104-T1
Valid prediction for snap_scaffold_2-snap.90-T1
Valid prediction for snap_scaffold_2-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_3055-T1
Valid prediction for Augustus_model.g2073.t1
Valid prediction for GlimmerHMM_glimmerT_3048-T1
Valid prediction for snap_scaffold_2-snap.111-T1
Valid prediction for snap_scaffold_2-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_3052-T1
Valid prediction for snap_scaffold_2-snap.89-T1
Valid prediction for GlimmerHMM_glimmerT_3057-T1
Valid prediction for snap_scaffold_2-snap.99-T1
Valid prediction for snap_scaffold_2-snap.76-T1
Valid prediction for snap_scaffold_2-snap.82-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_2-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_3061-T1
Valid prediction for GlimmerHMM_glimmerT_3043-T1
Valid prediction for snap_scaffold_2-snap.94-T1
Couldn't classify 14735, 14842
Couldn't classify 17233, 17348
Sorry, prediction pasa_asmbl_22808.p1 fails validation.
(CAG)	 CC	14735-14842	GT	AGG
(GTA)	 AG	15942-16094	GT	AGG
(TCG)	 AG	16948-17014	GT	TGG
(AAA)	 AG	17233-17348	GG	ACG
-recovered pasa_asmbl_22808.p1, internal, 15942, 16094
-recovered pasa_asmbl_22808.p1, internal, 16948, 17014
Valid prediction for CodingQuarry_transcript_28422-T1
Valid prediction for snap_scaffold_2-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_3058-T1
Valid prediction for GlimmerHMM_glimmerT_3047-T1
Valid prediction for snap_scaffold_2-snap.108-T1
Valid prediction for Augustus_model.g2074.t1
Valid prediction for snap_scaffold_2-snap.86-T1
Valid prediction for Augustus_model.g2075.t1
Valid prediction for snap_scaffold_2-snap.112-T1
Valid prediction for snap_scaffold_2-snap.103-T1
Couldn't classify 18968, 19240
Sorry, prediction pasa_asmbl_22802.p1 fails validation.
(CAG)	 GA	18968-19240	GT	AGG
(GAT)	 AG	19645-19845	GT	GGG
(GAC)	 AG	20203-20310	GT	ATG
(CGG)	 AG	21557-21728	GT	CGG
(GCC)	 AG	22917-23131	GT	AGG
(TTA)	 AG	23431-24175	GT	TGG
(CTT)	 AG	24431-24576	GT	AGG
(GAG)	 AG	24695-24899	GT	AGG
(CAG)	 AG	25208-25345	GT	CAG
(TGG)	 AG	25566-25699	GT	TGG
(GTG)	 AG	25948-26055	GT	CTG
(CAG)	 AG	27137-27320	GT	GGG
(CAG)	 AG	27916-27992	GT	AGG
(GAC)	 AG	28330-28485	GT	AGG
(GGC)	 AG	28752-28903	GT	AAG
(AAT)	 AG	29140-29320	AT	GAA
-recovered pasa_asmbl_22802.p1, terminal, 29140, 29320
-recovered pasa_asmbl_22802.p1, internal, 19645, 19845
-recovered pasa_asmbl_22802.p1, internal, 20203, 20310
-recovered pasa_asmbl_22802.p1, internal, 21557, 21728
-recovered pasa_asmbl_22802.p1, internal, 22917, 23131
-recovered pasa_asmbl_22802.p1, internal, 23431, 24175
-recovered pasa_asmbl_22802.p1, internal, 24431, 24576
-recovered pasa_asmbl_22802.p1, internal, 24695, 24899
-recovered pasa_asmbl_22802.p1, internal, 25208, 25345
-recovered pasa_asmbl_22802.p1, internal, 25566, 25699
-recovered pasa_asmbl_22802.p1, internal, 25948, 26055
-recovered pasa_asmbl_22802.p1, internal, 27137, 27320
-recovered pasa_asmbl_22802.p1, internal, 27916, 27992
-recovered pasa_asmbl_22802.p1, internal, 28330, 28485
-recovered pasa_asmbl_22802.p1, internal, 28752, 28903
Valid prediction for snap_scaffold_2-snap.117-T1
Valid prediction for snap_scaffold_2-snap.95-T1
Valid prediction for snap_scaffold_2-snap.100-T1
Valid prediction for snap_scaffold_2-snap.106-T1
Valid prediction for Augustus_model.g2081.t1
Valid prediction for Augustus_model.g2072.t1
Valid prediction for GlimmerHMM_glimmerT_3054-T1
Valid prediction for Augustus_model.g2079.t1
Valid prediction for Augustus_model.g2077.t1
Valid prediction for snap_scaffold_2-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_3050-T1
Valid prediction for snap_scaffold_2-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_3040-T1
Valid prediction for Augustus_model.g2080.t1
Valid prediction for GlimmerHMM_glimmerT_3051-T1
Valid prediction for pasa_asmbl_22805.p1
Valid prediction for snap_scaffold_2-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_3053-T1
Valid prediction for GlimmerHMM_glimmerT_3039-T1
Valid prediction for snap_scaffold_2-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_3044-T1
Valid prediction for snap_scaffold_2-snap.115-T1
Valid prediction for CodingQuarry_transcript_28424-T1
Valid prediction for snap_scaffold_2-snap.96-T1
Couldn't classify 14285, 14372
Sorry, prediction pasa_asmbl_22810.p1 fails validation.
(ATG)	 GG	11027-11104	GT	TGG
(GGT)	 AG	12221-12292	GT	TGG
(GTG)	 AG	12508-12635	GT	AGG
(GGT)	 AG	12910-13085	GT	AAG
(CAG)	 AG	13344-13548	GT	AGG
(GAG)	 AG	13811-14014	GT	AGG
(GCT)	 AG	14285-14372	AT	AGA
-recovered pasa_asmbl_22810.p1, initial, 11027, 11104
-recovered pasa_asmbl_22810.p1, internal, 12221, 12292
-recovered pasa_asmbl_22810.p1, internal, 12508, 12635
-recovered pasa_asmbl_22810.p1, internal, 12910, 13085
-recovered pasa_asmbl_22810.p1, internal, 13344, 13548
-recovered pasa_asmbl_22810.p1, internal, 13811, 14014
Valid prediction for snap_scaffold_2-snap.91-T1
Valid prediction for Augustus_model.g2076.t1
Valid prediction for GlimmerHMM_glimmerT_3041-T1
Valid prediction for snap_scaffold_2-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_3060-T1
Valid prediction for snap_scaffold_2-snap.83-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12660, rend_intergenic: 4676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15831, rend_intergenic: 12772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33178, rend_intergenic: 28957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38413, rend_intergenic: 33652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48711, rend_intergenic: 44623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64638, rend_intergenic: 62013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71542, rend_intergenic: 68039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96758, rend_intergenic: 77690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102503, rend_intergenic: 97803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105423, rend_intergenic: 105012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112295, rend_intergenic: 105478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129527, rend_intergenic: 113300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137421, rend_intergenic: 131254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140740, rend_intergenic: 139267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145978, rend_intergenic: 145097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153656, rend_intergenic: 147713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163421, rend_intergenic: 159596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164639, rend_intergenic: 164402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174774, rend_intergenic: 164942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177005, rend_intergenic: 174843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184285, rend_intergenic: 182848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186179
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 12660, rend_intergenic: 4676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15831, rend_intergenic: 12772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33178, rend_intergenic: 28957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38413, rend_intergenic: 33652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48711, rend_intergenic: 44623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64638, rend_intergenic: 62013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71542, rend_intergenic: 68039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96758, rend_intergenic: 77690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102503, rend_intergenic: 97803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105423, rend_intergenic: 105012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112295, rend_intergenic: 105478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129527, rend_intergenic: 113300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137421, rend_intergenic: 131254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140740, rend_intergenic: 139267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145978, rend_intergenic: 145097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153656, rend_intergenic: 147713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163421, rend_intergenic: 159596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164639, rend_intergenic: 164402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174774, rend_intergenic: 164942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177005, rend_intergenic: 174843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184285, rend_intergenic: 182848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support