-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_885250-1111454

-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_6-snap.247-T1
Valid prediction for snap_scaffold_6-snap.232-T1
Valid prediction for snap_scaffold_6-snap.246-T1
Valid prediction for snap_scaffold_6-snap.237-T1
Valid prediction for snap_scaffold_6-snap.209-T1
Valid prediction for snap_scaffold_6-snap.241-T1
Valid prediction for snap_scaffold_6-snap.215-T1
Valid prediction for snap_scaffold_6-snap.224-T1
Valid prediction for snap_scaffold_6-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_13994-T1
Valid prediction for snap_scaffold_6-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_13979-T1
Valid prediction for snap_scaffold_6-snap.222-T1
Valid prediction for Augustus_model.g9299.t1
Valid prediction for GlimmerHMM_glimmerT_13991-T1
Valid prediction for snap_scaffold_6-snap.236-T1
Valid prediction for snap_scaffold_6-snap.212-T1
Valid prediction for snap_scaffold_6-snap.228-T1
Valid prediction for snap_scaffold_6-snap.227-T1
Valid prediction for snap_scaffold_6-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_14000-T1
Valid prediction for GlimmerHMM_glimmerT_13992-T1
Valid prediction for snap_scaffold_6-snap.245-T1
Valid prediction for GlimmerHMM_glimmerT_13985-T1
Valid prediction for GlimmerHMM_glimmerT_14002-T1
Couldn't classify 196694, 196843
Sorry, prediction pasa_asmbl_46685.p1 fails validation.
(GGT)	 AC	196694-196843	GT	AGG
(GCT)	 AG	197957-198032	GT	AGG
(TGC)	 AG	198478-198625	GT	AAG
(GCT)	 AG	199352-199477	GT	TGG
(CAA)	 AG	200487-200584	GT	AGG
(GTG)	 AG	201510-201679	GT	TGG
(GAG)	 AG	202237-202451	GT	AGG
(TTT)	 AG	202731-202842	GT	AGG
(TCT)	 AG	203602-203717	GT	AGG
(TAC)	 AG	204142-204241	GT	AGG
(GAG)	 AG	204461-204665	GT	AGG
(ACG)	 AG	204974-205146	GT	AGG
(GCA)	 AG	205412-205564	GT	AGG
(GCC)	 AG	205896-206104	GT	TGG
(GTA)	 AG	206548-206665	GT	TGG
(GTG)	 AG	207076-207204	GT	AGG
(GCT)	 AG	207400-207474	GT	AGG
(GTG)	 AG	208013-208175	GT	AGG
(CCG)	 AG	208520-208605	CC	AGC
-recovered pasa_asmbl_46685.p1, terminal, 200487, 200584
-recovered pasa_asmbl_46685.p1, terminal, 208520, 208605
-recovered pasa_asmbl_46685.p1, internal, 197957, 198032
-recovered pasa_asmbl_46685.p1, internal, 198478, 198625
-recovered pasa_asmbl_46685.p1, internal, 199352, 199477
-recovered pasa_asmbl_46685.p1, internal, 200487, 200584
-recovered pasa_asmbl_46685.p1, internal, 201510, 201679
-recovered pasa_asmbl_46685.p1, internal, 202237, 202451
-recovered pasa_asmbl_46685.p1, internal, 202731, 202842
-recovered pasa_asmbl_46685.p1, internal, 203602, 203717
-recovered pasa_asmbl_46685.p1, internal, 204142, 204241
-recovered pasa_asmbl_46685.p1, internal, 204461, 204665
-recovered pasa_asmbl_46685.p1, internal, 204974, 205146
-recovered pasa_asmbl_46685.p1, internal, 205412, 205564
-recovered pasa_asmbl_46685.p1, internal, 205896, 206104
-recovered pasa_asmbl_46685.p1, internal, 206548, 206665
-recovered pasa_asmbl_46685.p1, internal, 207076, 207204
-recovered pasa_asmbl_46685.p1, internal, 207400, 207474
-recovered pasa_asmbl_46685.p1, internal, 208013, 208175
Valid prediction for GlimmerHMM_glimmerT_13977-T1
Valid prediction for snap_scaffold_6-snap.226-T1
Valid prediction for snap_scaffold_6-snap.239-T1
Valid prediction for snap_scaffold_6-snap.234-T1
Valid prediction for Augustus_model.g9297.t1
Couldn't classify 220916, 221647
Sorry, prediction pasa_asmbl_46687.p1 fails validation.
(ACA)	 CC	220916-221647	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_13998-T1
Valid prediction for GlimmerHMM_glimmerT_13983-T1
Valid prediction for GlimmerHMM_glimmerT_13986-T1
Valid prediction for GlimmerHMM_glimmerT_13995-T1
Valid prediction for GlimmerHMM_glimmerT_13988-T1
Valid prediction for snap_scaffold_6-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_13984-T1
Valid prediction for GlimmerHMM_glimmerT_14001-T1
Valid prediction for snap_scaffold_6-snap.214-T1
Valid prediction for HiQ_model.g9298.t1
Valid prediction for snap_scaffold_6-snap.243-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_6-snap.223-T1
Valid prediction for Augustus_model.g9294.t1
Valid prediction for snap_scaffold_6-snap.251-T1
Valid prediction for Augustus_model.g9293.t1
Valid prediction for GlimmerHMM_glimmerT_13980-T1
Valid prediction for snap_scaffold_6-snap.235-T1
Valid prediction for snap_scaffold_6-snap.231-T1
Valid prediction for snap_scaffold_6-snap.217-T1
Valid prediction for snap_scaffold_6-snap.219-T1
Valid prediction for snap_scaffold_6-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_13973-T1
Valid prediction for GlimmerHMM_glimmerT_13972-T1
Valid prediction for Augustus_model.g9295.t1
Valid prediction for GlimmerHMM_glimmerT_13978-T1
Valid prediction for GlimmerHMM_glimmerT_13996-T1
Valid prediction for snap_scaffold_6-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_13987-T1
Valid prediction for GlimmerHMM_glimmerT_13982-T1
Couldn't classify 179482, 179518
Sorry, prediction pasa_asmbl_48091.p1 fails validation.
(GAA)	 TC	179482-179518	GT	AGG
(TTG)	 AG	179935-180135	GT	TGG
(TGC)	 AG	180619-180792	GT	AGG
(TCA)	 AG	181090-181278	GT	TTG
(TTG)	 AG	181394-181508	GT	CCG
(GGA)	 AG	182699-182825	GT	AGG
(AAT)	 AG	182978-182986	AA	AAA
-recovered pasa_asmbl_48091.p1, terminal, 182978, 182986
-recovered pasa_asmbl_48091.p1, internal, 179935, 180135
-recovered pasa_asmbl_48091.p1, internal, 180619, 180792
-recovered pasa_asmbl_48091.p1, internal, 181090, 181278
-recovered pasa_asmbl_48091.p1, internal, 181394, 181508
-recovered pasa_asmbl_48091.p1, internal, 182699, 182825
Valid prediction for GlimmerHMM_glimmerT_13993-T1
Valid prediction for GlimmerHMM_glimmerT_13975-T1
Valid prediction for snap_scaffold_6-snap.233-T1
Valid prediction for snap_scaffold_6-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_13997-T1
Valid prediction for snap_scaffold_6-snap.240-T1
Valid prediction for Augustus_model.g9296.t1
Valid prediction for snap_scaffold_6-snap.221-T1
Valid prediction for GlimmerHMM_glimmerT_13989-T1
Valid prediction for GlimmerHMM_glimmerT_13999-T1
Valid prediction for GlimmerHMM_glimmerT_13974-T1
Valid prediction for snap_scaffold_6-snap.211-T1
Valid prediction for snap_scaffold_6-snap.225-T1
Valid prediction for snap_scaffold_6-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_13976-T1
Valid prediction for snap_scaffold_6-snap.242-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13981-T1
Valid prediction for snap_scaffold_6-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_13990-T1
Valid prediction for snap_scaffold_6-snap.210-T1
Valid prediction for snap_scaffold_6-snap.249-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5874, rend_intergenic: 2106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24603, rend_intergenic: 5998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36069, rend_intergenic: 24951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37132, rend_intergenic: 36378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52264, rend_intergenic: 37228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67795, rend_intergenic: 64854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74370, rend_intergenic: 71548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76030, rend_intergenic: 75009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95349, rend_intergenic: 79174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101340, rend_intergenic: 95677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103501, rend_intergenic: 101483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107279, rend_intergenic: 103674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108149, rend_intergenic: 107722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133369, rend_intergenic: 108192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134496, rend_intergenic: 133484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137295, rend_intergenic: 134514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146930, rend_intergenic: 143154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149385, rend_intergenic: 147100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152065, rend_intergenic: 149427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154293, rend_intergenic: 152195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163212, rend_intergenic: 154623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177148, rend_intergenic: 163380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193127, rend_intergenic: 178520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210091, rend_intergenic: 197989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226205
-exon list size: 379


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
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9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 5874, rend_intergenic: 2106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24603, rend_intergenic: 5998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36069, rend_intergenic: 24951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37132, rend_intergenic: 36378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52264, rend_intergenic: 37228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67795, rend_intergenic: 64854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74370, rend_intergenic: 71548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76030, rend_intergenic: 75009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95349, rend_intergenic: 79174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101340, rend_intergenic: 95677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103501, rend_intergenic: 101483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107279, rend_intergenic: 103674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108149, rend_intergenic: 107722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133369, rend_intergenic: 108192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134496, rend_intergenic: 133484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137295, rend_intergenic: 134514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146930, rend_intergenic: 143154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149385, rend_intergenic: 147100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152065, rend_intergenic: 149427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154293, rend_intergenic: 152195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163212, rend_intergenic: 154623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177148, rend_intergenic: 163380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193127, rend_intergenic: 178520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210091, rend_intergenic: 197989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support