-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_9118739-9307546

-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_15-snap.1902-T1
Valid prediction for Augustus_model.g24429.t1
Valid prediction for snap_scaffold_15-snap.1890-T1
Valid prediction for snap_scaffold_15-snap.1907-T1
Valid prediction for Augustus_model.g24421.t1
Valid prediction for GlimmerHMM_glimmerT_36670-T1
Valid prediction for GlimmerHMM_glimmerT_36679-T1
Valid prediction for snap_scaffold_15-snap.1900-T1
Valid prediction for snap_scaffold_15-snap.1915-T1
Valid prediction for Augustus_model.g24433.t1
Valid prediction for GlimmerHMM_glimmerT_36685-T1
Valid prediction for Augustus_model.g24434.t1
Valid prediction for Augustus_model.g24426.t1
Valid prediction for GlimmerHMM_glimmerT_36692-T1
Valid prediction for Augustus_model.g24423.t1
Valid prediction for GlimmerHMM_glimmerT_36684-T1
Valid prediction for snap_scaffold_15-snap.1884-T1
Valid prediction for snap_scaffold_15-snap.1901-T1
Valid prediction for GlimmerHMM_glimmerT_36680-T1
Valid prediction for Augustus_model.g24417.t1
Valid prediction for GlimmerHMM_glimmerT_36683-T1
Valid prediction for snap_scaffold_15-snap.1917-T1
Valid prediction for Augustus_model.g24416.t1
Valid prediction for GlimmerHMM_glimmerT_36693-T1
Valid prediction for GlimmerHMM_glimmerT_36677-T1
Valid prediction for snap_scaffold_15-snap.1913-T1
Valid prediction for Augustus_model.g24415.t1
Valid prediction for Augustus_model.g24422.t1
Valid prediction for GlimmerHMM_glimmerT_36678-T1
Valid prediction for Augustus_model.g24428.t1
Valid prediction for snap_scaffold_15-snap.1888-T1
Valid prediction for snap_scaffold_15-snap.1904-T1
Valid prediction for snap_scaffold_15-snap.1919-T1
Valid prediction for snap_scaffold_15-snap.1910-T1
Valid prediction for snap_scaffold_15-snap.1903-T1
Valid prediction for snap_scaffold_15-snap.1885-T1
Valid prediction for snap_scaffold_15-snap.1914-T1
Valid prediction for snap_scaffold_15-snap.1906-T1
Couldn't classify 93492, 93506
Sorry, prediction pasa_asmbl_15380.p1 fails validation.
(AAA)	 TC	93492-93506	GT	AGG
(ACT)	 AG	93828-94001	GT	ATG
(AGC)	 AG	95288-95419	GT	AGG
(GGC)	 AG	95545-95670	GT	GGG
(CCT)	 AG	95817-95980	GT	CTG
(GAA)	 AG	96128-96263	GT	CGG
(GAT)	 AG	97006-97059	CC	AAC
-recovered pasa_asmbl_15380.p1, terminal, 97006, 97059
-recovered pasa_asmbl_15380.p1, internal, 93828, 94001
-recovered pasa_asmbl_15380.p1, internal, 95288, 95419
-recovered pasa_asmbl_15380.p1, internal, 95545, 95670
-recovered pasa_asmbl_15380.p1, internal, 95817, 95980
-recovered pasa_asmbl_15380.p1, internal, 96128, 96263
Valid prediction for snap_scaffold_15-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_36686-T1
Valid prediction for snap_scaffold_15-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_36689-T1
Valid prediction for Augustus_model.g24419.t1
Couldn't classify 167946, 167984
Sorry, prediction pasa_asmbl_15382.p1 fails validation.
(GTA)	 AA	167946-167984	GT	AGG
(AGA)	 AG	168613-168742	GT	AAG
(CTG)	 AG	169227-169296	GT	CTG
(GCA)	 AG	169647-169737	GT	AGG
(CGC)	 AG	170520-170657	GT	CAG
(GCA)	 AG	170819-170859	GT	AGG
(CGA)	 AG	171077-171179	GT	AGG
(TCT)	 AG	171290-171362	GT	CGG
(ACA)	 AG	171530-171612	GT	AGG
(AGT)	 AG	171826-171921	AG	GAA
add_exon() Sorry, pasa_asmbl_15382.p1 168613-168742-terminal-3 is invalid.
-recovered pasa_asmbl_15382.p1, terminal, 168613, 168742
-recovered pasa_asmbl_15382.p1, terminal, 171826, 171921
-recovered pasa_asmbl_15382.p1, internal, 168613, 168742
-recovered pasa_asmbl_15382.p1, internal, 169227, 169296
-recovered pasa_asmbl_15382.p1, internal, 169647, 169737
-recovered pasa_asmbl_15382.p1, internal, 170520, 170657
-recovered pasa_asmbl_15382.p1, internal, 170819, 170859
-recovered pasa_asmbl_15382.p1, internal, 171077, 171179
-recovered pasa_asmbl_15382.p1, internal, 171290, 171362
-recovered pasa_asmbl_15382.p1, internal, 171530, 171612
Valid prediction for snap_scaffold_15-snap.1893-T1
Valid prediction for Augustus_model.g24414.t1
Valid prediction for Augustus_model.g24431.t1
Valid prediction for snap_scaffold_15-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_36687-T1
Valid prediction for snap_scaffold_15-snap.1905-T1
Valid prediction for Augustus_model.g24425.t1
Valid prediction for snap_scaffold_15-snap.1918-T1
Valid prediction for Augustus_model.g24418.t1
Valid prediction for CodingQuarry_transcript_18092-T1
Valid prediction for Augustus_model.g24412.t1
Valid prediction for GlimmerHMM_glimmerT_36682-T1
Valid prediction for Augustus_model.g24427.t1
Valid prediction for snap_scaffold_15-snap.1899-T1
Valid prediction for snap_scaffold_15-snap.1911-T1
Valid prediction for snap_scaffold_15-snap.1920-T1
Valid prediction for snap_scaffold_15-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_36694-T1
Couldn't classify 76527, 76764
Couldn't classify 77203, 77394
Sorry, prediction pasa_asmbl_15379.p1 fails validation.
(TGG)	 AC	76527-76764	GT	TGG
(TGC)	 AG	76935-77044	GT	AGG
(ATC)	 AG	77203-77394	AA	CCA
-recovered pasa_asmbl_15379.p1, internal, 76935, 77044
Valid prediction for GlimmerHMM_glimmerT_36691-T1
Valid prediction for GlimmerHMM_glimmerT_36672-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_15-snap.1897-T1
Valid prediction for GlimmerHMM_glimmerT_36671-T1
Valid prediction for GlimmerHMM_glimmerT_36675-T1
Valid prediction for GlimmerHMM_glimmerT_36690-T1
Valid prediction for snap_scaffold_15-snap.1898-T1
Valid prediction for GlimmerHMM_glimmerT_36676-T1
Valid prediction for HiQ_model.g24420.t1
Valid prediction for Augustus_model.g24432.t1
Valid prediction for Augustus_model.g24424.t1
Valid prediction for snap_scaffold_15-snap.1887-T1
Valid prediction for snap_scaffold_15-snap.1908-T1
Valid prediction for snap_scaffold_15-snap.1922-T1
Valid prediction for snap_scaffold_15-snap.1889-T1
Valid prediction for snap_scaffold_15-snap.1916-T1
Valid prediction for Augustus_model.g24413.t1
Valid prediction for GlimmerHMM_glimmerT_36673-T1
Valid prediction for pasa_asmbl_14377.p1
Valid prediction for snap_scaffold_15-snap.1886-T1
Valid prediction for snap_scaffold_15-snap.1891-T1
Valid prediction for snap_scaffold_15-snap.1892-T1
Valid prediction for GlimmerHMM_glimmerT_36674-T1
Valid prediction for snap_scaffold_15-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_36688-T1
Valid prediction for GlimmerHMM_glimmerT_36681-T1
Valid prediction for Augustus_model.g24430.t1
Valid prediction for CodingQuarry_transcript_18091-T1
Valid prediction for snap_scaffold_15-snap.1895-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26294, rend_intergenic: 23955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39452, rend_intergenic: 29442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52789, rend_intergenic: 39468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66015, rend_intergenic: 52807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82019, rend_intergenic: 68203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97059, rend_intergenic: 92697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185371, rend_intergenic: 173630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188808
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 26294, rend_intergenic: 23955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39452, rend_intergenic: 29442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52789, rend_intergenic: 39468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66015, rend_intergenic: 52807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82019, rend_intergenic: 68203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97059, rend_intergenic: 92697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185371, rend_intergenic: 173630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support