-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_8700326-8884202

-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 Augustus_model.g32259.t1
Valid prediction for snap_scaffold_21-snap.1861-T1
Valid prediction for GlimmerHMM_glimmerT_48270-T1
Valid prediction for Augustus_model.g32258.t1
Valid prediction for snap_scaffold_21-snap.1865-T1
Valid prediction for snap_scaffold_21-snap.1896-T1
Valid prediction for snap_scaffold_21-snap.1869-T1
Valid prediction for snap_scaffold_21-snap.1884-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1877-T1
Valid prediction for snap_scaffold_21-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_48280-T1
Valid prediction for GlimmerHMM_glimmerT_48278-T1
Valid prediction for snap_scaffold_21-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_48286-T1
Valid prediction for snap_scaffold_21-snap.1849-T1
Valid prediction for snap_scaffold_21-snap.1898-T1
Valid prediction for GlimmerHMM_glimmerT_48273-T1
Valid prediction for snap_scaffold_21-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_48261-T1
Valid prediction for GlimmerHMM_glimmerT_48277-T1
Valid prediction for snap_scaffold_21-snap.1872-T1
Valid prediction for Augustus_model.g32243.t1
Valid prediction for GlimmerHMM_glimmerT_48289-T1
Valid prediction for Augustus_model.g32255.t1
Valid prediction for snap_scaffold_21-snap.1854-T1
Valid prediction for snap_scaffold_21-snap.1860-T1
Valid prediction for Augustus_model.g32252.t1
Valid prediction for snap_scaffold_21-snap.1880-T1
Valid prediction for CodingQuarry_transcript_32682-T1
Valid prediction for Augustus_model.g32251.t1
Valid prediction for GlimmerHMM_glimmerT_48281-T1
Valid prediction for Augustus_model.g32248.t1
Valid prediction for snap_scaffold_21-snap.1852-T1
Valid prediction for snap_scaffold_21-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_48272-T1
Valid prediction for GlimmerHMM_glimmerT_48266-T1
Valid prediction for snap_scaffold_21-snap.1866-T1
Valid prediction for snap_scaffold_21-snap.1858-T1
Valid prediction for snap_scaffold_21-snap.1874-T1
Valid prediction for Augustus_model.g32250.t1
Valid prediction for snap_scaffold_21-snap.1851-T1
Valid prediction for snap_scaffold_21-snap.1891-T1
Valid prediction for snap_scaffold_21-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_48285-T1
Valid prediction for GlimmerHMM_glimmerT_48288-T1
Valid prediction for snap_scaffold_21-snap.1897-T1
Valid prediction for snap_scaffold_21-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_48264-T1
Valid prediction for GlimmerHMM_glimmerT_48262-T1
Valid prediction for snap_scaffold_21-snap.1881-T1
Valid prediction for Augustus_model.g32257.t1
Valid prediction for GlimmerHMM_glimmerT_48276-T1
Valid prediction for GlimmerHMM_glimmerT_48271-T1
Valid prediction for snap_scaffold_21-snap.1868-T1
Valid prediction for snap_scaffold_21-snap.1873-T1
Valid prediction for snap_scaffold_21-snap.1902-T1
Valid prediction for Augustus_model.g32249.t1
Valid prediction for snap_scaffold_21-snap.1889-T1
Valid prediction for GlimmerHMM_glimmerT_48283-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_21-snap.1886-T1
Valid prediction for pasa_asmbl_27943.p1
Valid prediction for snap_scaffold_21-snap.1856-T1
Valid prediction for snap_scaffold_21-snap.1857-T1
Valid prediction for HiQ_model.g32256.t1
Valid prediction for GlimmerHMM_glimmerT_48287-T1
Valid prediction for GlimmerHMM_glimmerT_48265-T1
Valid prediction for GlimmerHMM_glimmerT_48275-T1
Valid prediction for snap_scaffold_21-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_48291-T1
Valid prediction for snap_scaffold_21-snap.1892-T1
Valid prediction for snap_scaffold_21-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_48267-T1
Valid prediction for snap_scaffold_21-snap.1853-T1
Valid prediction for snap_scaffold_21-snap.1878-T1
Valid prediction for snap_scaffold_21-snap.1895-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1859-T1
Valid prediction for snap_scaffold_21-snap.1871-T1
Valid prediction for snap_scaffold_21-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_48282-T1
Valid prediction for CodingQuarry_transcript_32683-T1
Valid prediction for snap_scaffold_21-snap.1887-T1
Valid prediction for snap_scaffold_21-snap.1885-T1
Couldn't classify 40570, 40637
Sorry, prediction pasa_asmbl_27942.p1 fails validation.
(GAG)	 CT	40570-40637	GT	AGG
(ATT)	 AG	40973-41346	GT	AGG
(TGG)	 AG	41692-41777	CC	GAC
-recovered pasa_asmbl_27942.p1, terminal, 41692, 41777
-recovered pasa_asmbl_27942.p1, internal, 40973, 41346
Valid prediction for snap_scaffold_21-snap.1870-T1
Valid prediction for Augustus_model.g32253.t1
Valid prediction for snap_scaffold_21-snap.1875-T1
Valid prediction for Augustus_model.g32244.t1
Valid prediction for Augustus_model.g32254.t1
Valid prediction for snap_scaffold_21-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_48279-T1
Valid prediction for GlimmerHMM_glimmerT_48284-T1
Valid prediction for HiQ_model.g32260.t1
Valid prediction for snap_scaffold_21-snap.1848-T1
Valid prediction for snap_scaffold_21-snap.1867-T1
Valid prediction for CodingQuarry_transcript_32681-T1
Valid prediction for Augustus_model.g32261.t1
Valid prediction for GlimmerHMM_glimmerT_48290-T1
Valid prediction for snap_scaffold_21-snap.1879-T1
Valid prediction for Augustus_model.g32247.t1
Valid prediction for snap_scaffold_21-snap.1899-T1
Valid prediction for snap_scaffold_21-snap.1850-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g32245.t1
Valid prediction for Augustus_model.g32246.t1
Valid prediction for GlimmerHMM_glimmerT_48268-T1
Valid prediction for GlimmerHMM_glimmerT_48269-T1
Valid prediction for GlimmerHMM_glimmerT_48274-T1
Valid prediction for GlimmerHMM_glimmerT_48263-T1
Valid prediction for snap_scaffold_21-snap.1876-T1
Valid prediction for snap_scaffold_21-snap.1864-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5723, rend_intergenic: 3237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16349, rend_intergenic: 9642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17355, rend_intergenic: 16424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25454, rend_intergenic: 17692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28161, rend_intergenic: 25615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36614, rend_intergenic: 31859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37140, rend_intergenic: 36642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38478, rend_intergenic: 37194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42806, rend_intergenic: 40185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48835, rend_intergenic: 43515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50932, rend_intergenic: 49712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63084, rend_intergenic: 57802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71770, rend_intergenic: 63642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75349, rend_intergenic: 72124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82120, rend_intergenic: 78570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89970, rend_intergenic: 83682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92444, rend_intergenic: 91077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114683, rend_intergenic: 97093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115226, rend_intergenic: 114740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120020, rend_intergenic: 115532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134577, rend_intergenic: 127009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149734, rend_intergenic: 148112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151619, rend_intergenic: 150253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156439, rend_intergenic: 152353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161478, rend_intergenic: 156894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183877
-exon list size: 370


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 5723, rend_intergenic: 3237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16349, rend_intergenic: 9642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17355, rend_intergenic: 16424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25454, rend_intergenic: 17692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28161, rend_intergenic: 25615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36614, rend_intergenic: 31859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37140, rend_intergenic: 36642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38478, rend_intergenic: 37194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42806, rend_intergenic: 40185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48835, rend_intergenic: 43515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50932, rend_intergenic: 49712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63084, rend_intergenic: 57802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71770, rend_intergenic: 63642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75349, rend_intergenic: 72124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82120, rend_intergenic: 78570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89970, rend_intergenic: 83682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92444, rend_intergenic: 91077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114683, rend_intergenic: 97093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115226, rend_intergenic: 114740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120020, rend_intergenic: 115532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134577, rend_intergenic: 127009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149734, rend_intergenic: 148112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151619, rend_intergenic: 150253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156439, rend_intergenic: 152353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161478, rend_intergenic: 156894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support