-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_4796126-4994367

-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_25-snap.1004-T1
Valid prediction for GlimmerHMM_glimmerT_54090-T1
Valid prediction for snap_scaffold_25-snap.1026-T1
Valid prediction for GlimmerHMM_glimmerT_54077-T1
Valid prediction for CodingQuarry_transcript_38720-T1
Valid prediction for snap_scaffold_25-snap.1009-T1
Valid prediction for Augustus_model.g35892.t1
Valid prediction for GlimmerHMM_glimmerT_54074-T1
Valid prediction for GlimmerHMM_glimmerT_54086-T1
Valid prediction for snap_scaffold_25-snap.1033-T1
Valid prediction for snap_scaffold_25-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_54068-T1
Valid prediction for GlimmerHMM_glimmerT_54066-T1
Valid prediction for CodingQuarry_transcript_38719-T1
Valid prediction for snap_scaffold_25-snap.1015-T1
Valid prediction for snap_scaffold_25-snap.995-T1
Valid prediction for Augustus_model.g35888.t1
Valid prediction for Augustus_model.g35901.t1
Valid prediction for GlimmerHMM_glimmerT_54091-T1
Valid prediction for snap_scaffold_25-snap.1038-T1
Valid prediction for pasa_asmbl_33531.p1
Valid prediction for GlimmerHMM_glimmerT_54070-T1
Valid prediction for GlimmerHMM_glimmerT_54083-T1
Valid prediction for snap_scaffold_25-snap.1014-T1
Valid prediction for snap_scaffold_25-snap.1017-T1
Valid prediction for pasa_asmbl_33535.p1
Valid prediction for snap_scaffold_25-snap.1021-T1
Valid prediction for GlimmerHMM_glimmerT_54088-T1
Valid prediction for Augustus_model.g35898.t1
Valid prediction for snap_scaffold_25-snap.996-T1
Valid prediction for snap_scaffold_25-snap.1037-T1
Valid prediction for snap_scaffold_25-snap.993-T1
Valid prediction for HiQ_model.g35887.t1
Valid prediction for snap_scaffold_25-snap.1008-T1
Valid prediction for snap_scaffold_25-snap.1005-T1
Valid prediction for snap_scaffold_25-snap.1013-T1
Valid prediction for CodingQuarry_transcript_38714-T1
Valid prediction for snap_scaffold_25-snap.1007-T1
Valid prediction for snap_scaffold_25-snap.998-T1
Valid prediction for Augustus_model.g35895.t1
Valid prediction for snap_scaffold_25-snap.1011-T1
Valid prediction for snap_scaffold_25-snap.1036-T1
Valid prediction for Augustus_model.g35889.t1
Valid prediction for snap_scaffold_25-snap.1027-T1
Valid prediction for GlimmerHMM_glimmerT_54082-T1
Valid prediction for snap_scaffold_25-snap.992-T1
Valid prediction for CodingQuarry_transcript_38713-T1
Valid prediction for GlimmerHMM_glimmerT_54069-T1
Valid prediction for HiQ_model.g35885.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 Augustus_model.g35905.t1
Valid prediction for snap_scaffold_25-snap.991-T1
Valid prediction for pasa_asmbl_34229.p1
Valid prediction for GlimmerHMM_glimmerT_54075-T1
Valid prediction for Augustus_model.g35899.t1
Valid prediction for Augustus_model.g35904.t1
Valid prediction for snap_scaffold_25-snap.1019-T1
Valid prediction for snap_scaffold_25-snap.1034-T1
Valid prediction for snap_scaffold_25-snap.1039-T1
Valid prediction for snap_scaffold_25-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_54079-T1
Valid prediction for GlimmerHMM_glimmerT_54081-T1
Valid prediction for Augustus_model.g35902.t1
Valid prediction for GlimmerHMM_glimmerT_54072-T1
Valid prediction for snap_scaffold_25-snap.1025-T1
Valid prediction for snap_scaffold_25-snap.1030-T1
Valid prediction for snap_scaffold_25-snap.1001-T1
Valid prediction for Augustus_model.g35906.t1
Valid prediction for GlimmerHMM_glimmerT_54073-T1
Valid prediction for HiQ_model.g35886.t1
Valid prediction for snap_scaffold_25-snap.1012-T1
Valid prediction for snap_scaffold_25-snap.997-T1
Valid prediction for GlimmerHMM_glimmerT_54084-T1
Valid prediction for snap_scaffold_25-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_54092-T1
Valid prediction for GlimmerHMM_glimmerT_54085-T1
Valid prediction for Augustus_model.g35896.t1
Valid prediction for snap_scaffold_25-snap.1035-T1
Valid prediction for snap_scaffold_25-snap.1000-T1
Valid prediction for snap_scaffold_25-snap.1003-T1
Valid prediction for snap_scaffold_25-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_54076-T1
Valid prediction for GlimmerHMM_glimmerT_54094-T1
Valid prediction for snap_scaffold_25-snap.1032-T1
Valid prediction for snap_scaffold_25-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_54078-T1
Valid prediction for Augustus_model.g35893.t1
Valid prediction for GlimmerHMM_glimmerT_54071-T1
Valid prediction for CodingQuarry_transcript_38717-T1
Valid prediction for snap_scaffold_25-snap.1031-T1
Valid prediction for snap_scaffold_25-snap.1002-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_54089-T1
Valid prediction for Augustus_model.g35890.t1
Valid prediction for Augustus_model.g35900.t1
Valid prediction for HiQ_model.g35891.t1
Valid prediction for Augustus_model.g35884.t1
Valid prediction for Augustus_model.g35903.t1
Valid prediction for snap_scaffold_25-snap.994-T1
Valid prediction for Augustus_model.g35897.t1
Valid prediction for GlimmerHMM_glimmerT_54093-T1
Valid prediction for snap_scaffold_25-snap.1022-T1
Valid prediction for Augustus_model.g35894.t1
Valid prediction for snap_scaffold_25-snap.1010-T1
Couldn't classify 176697, 177247
Sorry, prediction pasa_asmbl_34226.p1 fails validation.
(TAC)	 AG	176697-177247	GT	AGG
(ATT)	 AG	177593-177712	GT	AAG
(GTT)	 AG	178105-178261	GT	AGG
(GCC)	 AG	178630-178735	GT	GGG
(ATA)	 AG	178890-179087	GT	AGG
(GGC)	 AG	179539-179731	GT	CGG
(GTT)	 AG	179872-179959	GT	AGG
(GTC)	 AG	180116-180262	GT	AGG
(GGT)	 AG	180709-180870	GC	AGG
-recovered pasa_asmbl_34226.p1, terminal, 180709, 180870
-recovered pasa_asmbl_34226.p1, internal, 176697, 177247
-recovered pasa_asmbl_34226.p1, internal, 177593, 177712
-recovered pasa_asmbl_34226.p1, internal, 178105, 178261
-recovered pasa_asmbl_34226.p1, internal, 178630, 178735
-recovered pasa_asmbl_34226.p1, internal, 178890, 179087
-recovered pasa_asmbl_34226.p1, internal, 179539, 179731
-recovered pasa_asmbl_34226.p1, internal, 179872, 179959
-recovered pasa_asmbl_34226.p1, internal, 180116, 180262
-recovered pasa_asmbl_34226.p1, internal, 180709, 180870
Valid prediction for GlimmerHMM_glimmerT_54087-T1
Valid prediction for snap_scaffold_25-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_54067-T1
Valid prediction for GlimmerHMM_glimmerT_54080-T1
Valid prediction for CodingQuarry_transcript_38716-T1
Valid prediction for snap_scaffold_25-snap.1020-T1
Valid prediction for snap_scaffold_25-snap.999-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20492, rend_intergenic: 16813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32088, rend_intergenic: 28328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51440, rend_intergenic: 33800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70063, rend_intergenic: 57343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72947, rend_intergenic: 70292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85028, rend_intergenic: 82867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87192, rend_intergenic: 85852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88989, rend_intergenic: 87445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104772, rend_intergenic: 95089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105285, rend_intergenic: 104806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124579, rend_intergenic: 105879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128946, rend_intergenic: 128096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131657, rend_intergenic: 129060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134887, rend_intergenic: 133414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149593, rend_intergenic: 139851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162184, rend_intergenic: 153631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184335, rend_intergenic: 181096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193409, rend_intergenic: 184488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194837, rend_intergenic: 193824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198242
-exon list size: 515


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 20492, rend_intergenic: 16813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32088, rend_intergenic: 28328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51440, rend_intergenic: 33800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70063, rend_intergenic: 57343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72947, rend_intergenic: 70292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85028, rend_intergenic: 82867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87192, rend_intergenic: 85852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88989, rend_intergenic: 87445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104772, rend_intergenic: 95089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105285, rend_intergenic: 104806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124579, rend_intergenic: 105879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128946, rend_intergenic: 128096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131657, rend_intergenic: 129060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134887, rend_intergenic: 133414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149593, rend_intergenic: 139851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162184, rend_intergenic: 153631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184335, rend_intergenic: 181096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193409, rend_intergenic: 184488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194837, rend_intergenic: 193824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support