-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_2351292-2565441

-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_19-snap.539-T1
Valid prediction for snap_scaffold_19-snap.511-T1
Valid prediction for Augustus_model.g29032.t1
Valid prediction for snap_scaffold_19-snap.525-T1
Valid prediction for GlimmerHMM_glimmerT_43738-T1
Valid prediction for GlimmerHMM_glimmerT_43739-T1
Valid prediction for Augustus_model.g29036.t1
Valid prediction for Augustus_model.g29027.t1
Valid prediction for snap_scaffold_19-snap.543-T1
Valid prediction for Augustus_model.g29033.t1
Valid prediction for snap_scaffold_19-snap.506-T1
Valid prediction for snap_scaffold_19-snap.547-T1
Valid prediction for Augustus_model.g29037.t1
Valid prediction for snap_scaffold_19-snap.537-T1
Valid prediction for snap_scaffold_19-snap.538-T1
Valid prediction for snap_scaffold_19-snap.520-T1
Valid prediction for snap_scaffold_19-snap.527-T1
Valid prediction for snap_scaffold_19-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_43744-T1
Valid prediction for snap_scaffold_19-snap.533-T1
Valid prediction for snap_scaffold_19-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_43731-T1
Valid prediction for Augustus_model.g29031.t1
Valid prediction for snap_scaffold_19-snap.514-T1
Valid prediction for snap_scaffold_19-snap.522-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.521-T1
Valid prediction for snap_scaffold_19-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_43747-T1
Valid prediction for Augustus_model.g29029.t1
Valid prediction for snap_scaffold_19-snap.536-T1
Valid prediction for GlimmerHMM_glimmerT_43735-T1
Valid prediction for GlimmerHMM_glimmerT_43737-T1
Valid prediction for snap_scaffold_19-snap.513-T1
Valid prediction for Augustus_model.g29030.t1
Valid prediction for GlimmerHMM_glimmerT_43748-T1
Valid prediction for GlimmerHMM_glimmerT_43730-T1
Valid prediction for Augustus_model.g29034.t1
Valid prediction for GlimmerHMM_glimmerT_43728-T1
Valid prediction for GlimmerHMM_glimmerT_43734-T1
Valid prediction for snap_scaffold_19-snap.517-T1
Valid prediction for GlimmerHMM_glimmerT_43727-T1
Couldn't classify 20788, 20839
Sorry, prediction pasa_asmbl_21264.p1 fails validation.
(CAG)	 GA	20788-20839	GT	AGG
(CCT)	 AG	21621-21806	GT	TGG
(GCT)	 AG	24305-24459	GC	GAG
-recovered pasa_asmbl_21264.p1, terminal, 24305, 24459
-recovered pasa_asmbl_21264.p1, internal, 21621, 21806
-recovered pasa_asmbl_21264.p1, internal, 24305, 24459

-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_19-snap.510-T1
Valid prediction for snap_scaffold_19-snap.516-T1
Valid prediction for snap_scaffold_19-snap.528-T1
Valid prediction for snap_scaffold_19-snap.524-T1
Valid prediction for snap_scaffold_19-snap.512-T1
Valid prediction for snap_scaffold_19-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_43742-T1
Valid prediction for snap_scaffold_19-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_43740-T1
Valid prediction for snap_scaffold_19-snap.515-T1
Valid prediction for snap_scaffold_19-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_43736-T1
Valid prediction for snap_scaffold_19-snap.505-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43743-T1
Valid prediction for snap_scaffold_19-snap.542-T1
Valid prediction for snap_scaffold_19-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_43749-T1
Valid prediction for Augustus_model.g29035.t1
Valid prediction for snap_scaffold_19-snap.534-T1
Valid prediction for snap_scaffold_19-snap.507-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_43745-T1
Valid prediction for snap_scaffold_19-snap.535-T1
Valid prediction for snap_scaffold_19-snap.518-T1
Valid prediction for Augustus_model.g29028.t1
Valid prediction for snap_scaffold_19-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_43733-T1
Valid prediction for snap_scaffold_19-snap.529-T1
Valid prediction for snap_scaffold_19-snap.526-T1
Valid prediction for GlimmerHMM_glimmerT_43732-T1
Valid prediction for GlimmerHMM_glimmerT_43741-T1
Valid prediction for snap_scaffold_19-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_43729-T1
Valid prediction for GlimmerHMM_glimmerT_43746-T1
Valid prediction for snap_scaffold_19-snap.531-T1
Valid prediction for snap_scaffold_19-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_43726-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22881, rend_intergenic: 15467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29510, rend_intergenic: 23144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42667, rend_intergenic: 38316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55238, rend_intergenic: 51047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62736, rend_intergenic: 55750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68757, rend_intergenic: 66049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75191, rend_intergenic: 71117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81207, rend_intergenic: 75679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102855, rend_intergenic: 90500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105930, rend_intergenic: 104033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107883, rend_intergenic: 107531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139216, rend_intergenic: 108122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142093, rend_intergenic: 139760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146154, rend_intergenic: 142114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184859, rend_intergenic: 183155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190383, rend_intergenic: 185201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194229, rend_intergenic: 190606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197992, rend_intergenic: 194556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 179985, rend_intergenic: 179982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214150
-exon list size: 311


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.7    
8.0    
8.3    
8.6    
8.9    
9.3    
9.6    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.3    
15.7    
16.0    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.4    
20.8    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.3    
23.6    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.2    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.4    
36.7    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.5    
41.9    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.1    
58.5    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.3    
63.6    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.8    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.4    
76.7    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.2    
79.6    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.0    
84.3    
84.7    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.4    
90.7    
91.1    
91.4    
91.7    
92.0    
92.3    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 22881, rend_intergenic: 15467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29510, rend_intergenic: 23144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42667, rend_intergenic: 38316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55238, rend_intergenic: 51047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62736, rend_intergenic: 55750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68757, rend_intergenic: 66049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75191, rend_intergenic: 71117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81207, rend_intergenic: 75679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102855, rend_intergenic: 90500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105930, rend_intergenic: 104033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107883, rend_intergenic: 107531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139216, rend_intergenic: 108122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142093, rend_intergenic: 139760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146154, rend_intergenic: 142114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184859, rend_intergenic: 183155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190383, rend_intergenic: 185201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194229, rend_intergenic: 190606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197992, rend_intergenic: 194556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 179985, rend_intergenic: 179982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16474
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15466
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14514
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14107
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 12482