-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_1735115-1995625

-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.400-T1
Valid prediction for GlimmerHMM_glimmerT_43667-T1
Valid prediction for Augustus_model.g28997.t1
Valid prediction for snap_scaffold_19-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_43676-T1
Valid prediction for snap_scaffold_19-snap.408-T1
Valid prediction for snap_scaffold_19-snap.394-T1
Valid prediction for snap_scaffold_19-snap.396-T1
Valid prediction for Augustus_model.g28993.t1
Valid prediction for Augustus_model.g28998.t1
Valid prediction for GlimmerHMM_glimmerT_43654-T1
Valid prediction for snap_scaffold_19-snap.390-T1
Valid prediction for snap_scaffold_19-snap.415-T1
Valid prediction for snap_scaffold_19-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_43656-T1
Valid prediction for GlimmerHMM_glimmerT_43660-T1
Valid prediction for Augustus_model.g28992.t1
Valid prediction for GlimmerHMM_glimmerT_43680-T1
Valid prediction for snap_scaffold_19-snap.401-T1
Valid prediction for snap_scaffold_19-snap.421-T1
Valid prediction for snap_scaffold_19-snap.404-T1
Valid prediction for snap_scaffold_19-snap.423-T1
Valid prediction for snap_scaffold_19-snap.416-T1
Valid prediction for snap_scaffold_19-snap.412-T1
Valid prediction for snap_scaffold_19-snap.383-T1
Valid prediction for snap_scaffold_19-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_43658-T1
Valid prediction for snap_scaffold_19-snap.391-T1
Valid prediction for snap_scaffold_19-snap.407-T1
Valid prediction for snap_scaffold_19-snap.420-T1
Valid prediction for snap_scaffold_19-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_43670-T1
Valid prediction for GlimmerHMM_glimmerT_43674-T1
Valid prediction for GlimmerHMM_glimmerT_43662-T1
Valid prediction for snap_scaffold_19-snap.386-T1
Valid prediction for snap_scaffold_19-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_43665-T1
Valid prediction for GlimmerHMM_glimmerT_43679-T1
Valid prediction for snap_scaffold_19-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_43664-T1
Valid prediction for Augustus_model.g28995.t1
Valid prediction for snap_scaffold_19-snap.389-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 GlimmerHMM_glimmerT_43668-T1
Valid prediction for GlimmerHMM_glimmerT_43671-T1
Valid prediction for GlimmerHMM_glimmerT_43678-T1
Valid prediction for Augustus_model.g28996.t1
Valid prediction for GlimmerHMM_glimmerT_43661-T1
Valid prediction for snap_scaffold_19-snap.403-T1
Valid prediction for snap_scaffold_19-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_43672-T1
Valid prediction for snap_scaffold_19-snap.422-T1
Valid prediction for snap_scaffold_19-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_43666-T1
Valid prediction for snap_scaffold_19-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_43673-T1
Valid prediction for snap_scaffold_19-snap.418-T1
Valid prediction for snap_scaffold_19-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_43681-T1
Valid prediction for GlimmerHMM_glimmerT_43663-T1
Valid prediction for snap_scaffold_19-snap.409-T1
Valid prediction for snap_scaffold_19-snap.424-T1
Valid prediction for snap_scaffold_19-snap.406-T1
Valid prediction for snap_scaffold_19-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_43655-T1
Valid prediction for snap_scaffold_19-snap.399-T1
Valid prediction for CodingQuarry_transcript_25600-T1
Valid prediction for Augustus_model.g28999.t1
Valid prediction for GlimmerHMM_glimmerT_43659-T1
Valid prediction for GlimmerHMM_glimmerT_43669-T1
Couldn't classify 254674, 254692
Couldn't classify 259738, 260174
Sorry, prediction pasa_asmbl_22047.p1 fails validation.
(CAG)	 TG	254674-254692	GT	AGG
(TTG)	 AG	257094-257287	GT	AGG
(AGC)	 AG	258517-258642	GT	TAG
(ACG)	 AG	258760-258937	GT	AGG
(ATT)	 AG	259396-259581	GT	GTG
(ATC)	 AG	259738-260174	CC	TCC
-recovered pasa_asmbl_22047.p1, internal, 257094, 257287
-recovered pasa_asmbl_22047.p1, internal, 258517, 258642
-recovered pasa_asmbl_22047.p1, internal, 258760, 258937
-recovered pasa_asmbl_22047.p1, internal, 259396, 259581
Valid prediction for Augustus_model.g28994.t1
Valid prediction for GlimmerHMM_glimmerT_43677-T1
Valid prediction for snap_scaffold_19-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_43675-T1
Valid prediction for snap_scaffold_19-snap.393-T1
Valid prediction for snap_scaffold_19-snap.397-T1
Valid prediction for Augustus_model.g28991.t1
Valid prediction for snap_scaffold_19-snap.419-T1
Valid prediction for snap_scaffold_19-snap.410-T1
Valid prediction for snap_scaffold_19-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_43657-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30420, rend_intergenic: 15330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42553, rend_intergenic: 30595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46264, rend_intergenic: 43717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59977, rend_intergenic: 46321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87435, rend_intergenic: 68819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97091, rend_intergenic: 92996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117903, rend_intergenic: 100842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122274, rend_intergenic: 118402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127619, rend_intergenic: 122407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135773, rend_intergenic: 132410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141024, rend_intergenic: 137870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153772, rend_intergenic: 148169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168520, rend_intergenic: 165262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241431, rend_intergenic: 236186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 93570, rend_intergenic: 93567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 260511
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 30420, rend_intergenic: 15330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42553, rend_intergenic: 30595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46264, rend_intergenic: 43717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59977, rend_intergenic: 46321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87435, rend_intergenic: 68819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97091, rend_intergenic: 92996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117903, rend_intergenic: 100842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122274, rend_intergenic: 118402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127619, rend_intergenic: 122407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135773, rend_intergenic: 132410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141024, rend_intergenic: 137870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153772, rend_intergenic: 148169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168520, rend_intergenic: 165262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241431, rend_intergenic: 236186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 93570, rend_intergenic: 93567  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