-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_5585314-5743937

-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 pasa_asmbl_30888.p1
Valid prediction for snap_scaffold_23-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_52271-T1
Valid prediction for GlimmerHMM_glimmerT_52272-T1
Valid prediction for GeneMark_model.90659_t
Valid prediction for snap_scaffold_23-snap.1027-T1
Valid prediction for GeneMark_model.90668_t
Valid prediction for GlimmerHMM_glimmerT_52283-T1
Valid prediction for snap_scaffold_23-snap.1007-T1
Valid prediction for snap_scaffold_23-snap.1026-T1
Valid prediction for GeneMark_model.90663_t
Valid prediction for snap_scaffold_23-snap.995-T1
Valid prediction for GeneMark_model.90642_t
Valid prediction for snap_scaffold_23-snap.1031-T1
Valid prediction for Augustus_model.g35170.t1
Valid prediction for GeneMark_model.90648_t
Valid prediction for snap_scaffold_23-snap.1010-T1
Valid prediction for GeneMark_model.90671_t
Valid prediction for GlimmerHMM_glimmerT_52277-T1
Valid prediction for snap_scaffold_23-snap.1030-T1
Valid prediction for Augustus_model.g35171.t1
Couldn't classify 136179, 136886
Sorry, prediction pasa_asmbl_30887.p1 fails validation.
(CAG)	 AG	136179-136886	GT	AGG
(GAG)	 AG	137737-137861	GT	AGG
(GAA)	 AG	138044-139442	CC	GAC
-recovered pasa_asmbl_30887.p1, terminal, 138044, 139442
-recovered pasa_asmbl_30887.p1, internal, 136179, 136886
-recovered pasa_asmbl_30887.p1, internal, 137737, 137861
Valid prediction for GlimmerHMM_glimmerT_52268-T1
Valid prediction for snap_scaffold_23-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_52278-T1
Valid prediction for snap_scaffold_23-snap.1005-T1
Valid prediction for GeneMark_model.90655_t
Valid prediction for snap_scaffold_23-snap.1008-T1
Valid prediction for GlimmerHMM_glimmerT_52290-T1
Valid prediction for GlimmerHMM_glimmerT_52293-T1
Valid prediction for snap_scaffold_23-snap.994-T1
Valid prediction for GeneMark_model.90650_t
Valid prediction for GlimmerHMM_glimmerT_52269-T1
Valid prediction for snap_scaffold_23-snap.1028-T1
Valid prediction for GeneMark_model.90666_t
Valid prediction for HiQ_model.g35178.t1
Valid prediction for GeneMark_model.90641_t
Valid prediction for Augustus_model.g35180.t1
Valid prediction for GeneMark_model.90652_t
Valid prediction for GeneMark_model.90670_t
Valid prediction for CodingQuarry_transcript_35599-T1
Valid prediction for snap_scaffold_23-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_52286-T1
Valid prediction for GeneMark_model.90647_t
Valid prediction for snap_scaffold_23-snap.1011-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_52280-T1
Valid prediction for Augustus_model.g35162.t1
Valid prediction for GlimmerHMM_glimmerT_52291-T1
Valid prediction for snap_scaffold_23-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_52267-T1
Valid prediction for snap_scaffold_23-snap.1017-T1
Valid prediction for Augustus_model.g35181.t1
Valid prediction for GeneMark_model.90657_t
Valid prediction for GlimmerHMM_glimmerT_52284-T1
Valid prediction for Augustus_model.g35182.t1
Valid prediction for Augustus_model.g35163.t1
Valid prediction for Augustus_model.g35175.t1
Valid prediction for GeneMark_model.90664_t
Valid prediction for snap_scaffold_23-snap.1004-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.90645_t
Valid prediction for snap_scaffold_23-snap.1014-T1
Valid prediction for GeneMark_model.90636_t
Valid prediction for GlimmerHMM_glimmerT_52294-T1
Valid prediction for GeneMark_model.90632_t
Valid prediction for GeneMark_model.90644_t
Valid prediction for snap_scaffold_23-snap.1019-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.g35179.t1
Valid prediction for snap_scaffold_23-snap.998-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1006-T1
Valid prediction for CodingQuarry_transcript_35597-T1
Valid prediction for snap_scaffold_23-snap.1003-T1
Valid prediction for snap_scaffold_23-snap.1029-T1
Valid prediction for GeneMark_model.90665_t
Valid prediction for snap_scaffold_23-snap.1021-T1
Valid prediction for GeneMark_model.90667_t
Valid prediction for snap_scaffold_23-snap.1016-T1
Valid prediction for GeneMark_model.90651_t
Valid prediction for snap_scaffold_23-snap.1020-T1
Valid prediction for snap_scaffold_23-snap.1009-T1
Couldn't classify 113142, 113483
Sorry, prediction pasa_asmbl_31654.p1 fails validation.
(ATG)	 GT	113142-113483	AC	CCA
Valid prediction for snap_scaffold_23-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_52282-T1
Valid prediction for GeneMark_model.90654_t
Valid prediction for Augustus_model.g35165.t1
Valid prediction for GeneMark_model.90634_t
Valid prediction for GlimmerHMM_glimmerT_52273-T1
Valid prediction for Augustus_model.g35173.t1
Valid prediction for snap_scaffold_23-snap.1024-T1
Valid prediction for CodingQuarry_transcript_35594-T1
Valid prediction for Augustus_model.g35164.t1
Valid prediction for snap_scaffold_23-snap.1023-T1
Valid prediction for Augustus_model.g35174.t1
Valid prediction for GlimmerHMM_glimmerT_52292-T1
Valid prediction for HiQ_model.g35172.t1
Valid prediction for snap_scaffold_23-snap.1000-T1
Valid prediction for CodingQuarry_transcript_35596-T1
Valid prediction for snap_scaffold_23-snap.1025-T1
Valid prediction for GeneMark_model.90656_t
Valid prediction for CodingQuarry_transcript_35598-T1
Valid prediction for GeneMark_model.90643_t
Valid prediction for Augustus_model.g35161.t1
Valid prediction for Augustus_model.g35168.t1
Valid prediction for Augustus_model.g35169.t1
Valid prediction for GlimmerHMM_glimmerT_52275-T1
Valid prediction for GeneMark_model.90640_t
Valid prediction for Augustus_model.g35176.t1
Valid prediction for CodingQuarry_transcript_35595-T1
Valid prediction for GlimmerHMM_glimmerT_52285-T1
Valid prediction for Augustus_model.g35166.t1
Valid prediction for GlimmerHMM_glimmerT_52279-T1
Valid prediction for GeneMark_model.90660_t
Valid prediction for GlimmerHMM_glimmerT_52274-T1
Valid prediction for snap_scaffold_23-snap.1018-T1
Valid prediction for GeneMark_model.90658_t
Valid prediction for GeneMark_model.90638_t
Valid prediction for pasa_asmbl_31655.p1
Valid prediction for GlimmerHMM_glimmerT_52289-T1
Valid prediction for GlimmerHMM_glimmerT_52281-T1
Valid prediction for GeneMark_model.90635_t
Valid prediction for GlimmerHMM_glimmerT_52266-T1
Valid prediction for HiQ_model.g35177.t1
Valid prediction for GeneMark_model.90631_t
Valid prediction for GeneMark_model.90653_t
Valid prediction for HiQ_model.g35167.t1
Valid prediction for GeneMark_model.90669_t
Valid prediction for GlimmerHMM_glimmerT_52276-T1
Valid prediction for GeneMark_model.90661_t
Valid prediction for GeneMark_model.90637_t
Valid prediction for GeneMark_model.90649_t
Valid prediction for pasa_asmbl_31658.p1
Valid prediction for snap_scaffold_23-snap.1001-T1
Valid prediction for GeneMark_model.90646_t
Valid prediction for snap_scaffold_23-snap.1012-T1
Valid prediction for GlimmerHMM_glimmerT_52270-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52287-T1
Valid prediction for snap_scaffold_23-snap.997-T1
Valid prediction for pasa_asmbl_31646.p1
Valid prediction for GlimmerHMM_glimmerT_52288-T1
Valid prediction for GeneMark_model.90662_t
Valid prediction for snap_scaffold_23-snap.1002-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48856, rend_intergenic: 46634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73975, rend_intergenic: 67056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91566, rend_intergenic: 75838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97027, rend_intergenic: 94796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100316, rend_intergenic: 99943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105971, rend_intergenic: 103892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107580, rend_intergenic: 106845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113898, rend_intergenic: 107600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133218, rend_intergenic: 129699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146071, rend_intergenic: 144470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158624
-exon list size: 557


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.3    
1.4    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.7    
2.9    
3.0    
3.2    
3.4    
3.6    
3.8    
3.9    
4.1    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.1    
6.3    
6.4    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.1    
8.2    
8.4    
8.6    
8.8    
8.9    
9.1    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.3    
11.4    
11.6    
11.8    
12.0    
12.2    
12.3    
12.5    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.8    
14.0    
14.1    
14.3    
14.5    
14.7    
14.8    
15.0    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.1    
18.2    
18.4    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
25.9    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.6    
37.7    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.6    
42.8    
42.9    
43.1    
43.3    
43.5    
43.6    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.3    
45.4    
45.6    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.5    
48.7    
48.8    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.2    
51.3    
51.5    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.3    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 48856, rend_intergenic: 46634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73975, rend_intergenic: 67056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91566, rend_intergenic: 75838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97027, rend_intergenic: 94796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100316, rend_intergenic: 99943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105971, rend_intergenic: 103892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107580, rend_intergenic: 106845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113898, rend_intergenic: 107600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133218, rend_intergenic: 129699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146071, rend_intergenic: 144470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support