-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_228450-362554

-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 GlimmerHMM_glimmerT_26332-T1
Valid prediction for Augustus_model.g17476.t1
Valid prediction for snap_scaffold_11-snap.48-T1
Valid prediction for snap_scaffold_11-snap.63-T1
Valid prediction for snap_scaffold_11-snap.51-T1
Valid prediction for GlimmerHMM_glimmerT_26329-T1
Valid prediction for snap_scaffold_11-snap.74-T1
Valid prediction for CodingQuarry_transcript_7946-T1
Valid prediction for snap_scaffold_11-snap.65-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.54-T1
Valid prediction for Augustus_model.g17469.t1
Valid prediction for snap_scaffold_11-snap.68-T1
Valid prediction for HiQ_model.g17475.t1
Valid prediction for pasa_asmbl_5285.p1
Valid prediction for snap_scaffold_11-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_26326-T1
Valid prediction for snap_scaffold_11-snap.71-T1
Valid prediction for CodingQuarry_transcript_7945-T1
Valid prediction for GlimmerHMM_glimmerT_26336-T1
Valid prediction for GlimmerHMM_glimmerT_26324-T1
Valid prediction for GlimmerHMM_glimmerT_26339-T1
Valid prediction for snap_scaffold_11-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_26337-T1
Valid prediction for Augustus_model.g17468.t1
Valid prediction for GlimmerHMM_glimmerT_26341-T1
Valid prediction for snap_scaffold_11-snap.69-T1
Valid prediction for GlimmerHMM_glimmerT_26322-T1
Valid prediction for GlimmerHMM_glimmerT_26325-T1
Valid prediction for snap_scaffold_11-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_26340-T1
Valid prediction for Augustus_model.g17471.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_26323-T1
Valid prediction for GlimmerHMM_glimmerT_26327-T1
Valid prediction for snap_scaffold_11-snap.56-T1
Valid prediction for pasa_asmbl_6389.p1
Valid prediction for snap_scaffold_11-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_26334-T1
Couldn't classify 31923, 32018
Sorry, prediction pasa_asmbl_7316.p1 fails validation.
(ATG)	 AG	29705-29810	GT	AGG
(GAG)	 AG	30513-30713	GT	CGG
(GGT)	 AG	30792-30974	GT	AGG
(GGG)	 AG	31097-31122	GT	AGG
(GAC)	 AG	31923-32018	TA	CAT
-recovered pasa_asmbl_7316.p1, initial, 29705, 29810
add_exon() Sorry, pasa_asmbl_7316.p1 30792-30974-terminal-1 is invalid.
-recovered pasa_asmbl_7316.p1, terminal, 30792, 30974
-recovered pasa_asmbl_7316.p1, internal, 29705, 29810
-recovered pasa_asmbl_7316.p1, internal, 30513, 30713
-recovered pasa_asmbl_7316.p1, internal, 30792, 30974
-recovered pasa_asmbl_7316.p1, internal, 31097, 31122
Valid prediction for snap_scaffold_11-snap.70-T1
Valid prediction for snap_scaffold_11-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_26328-T1
Valid prediction for GlimmerHMM_glimmerT_26331-T1
Valid prediction for snap_scaffold_11-snap.49-T1
Valid prediction for CodingQuarry_transcript_7943-T1
Valid prediction for GlimmerHMM_glimmerT_26333-T1
Valid prediction for Augustus_model.g17472.t1
Valid prediction for snap_scaffold_11-snap.50-T1
Valid prediction for snap_scaffold_11-snap.73-T1
Valid prediction for snap_scaffold_11-snap.72-T1
Valid prediction for CodingQuarry_transcript_7944-T1
Valid prediction for GlimmerHMM_glimmerT_26338-T1
Valid prediction for snap_scaffold_11-snap.57-T1
Valid prediction for GlimmerHMM_glimmerT_26335-T1
Valid prediction for snap_scaffold_11-snap.60-T1
Valid prediction for HiQ_model.g17470.t1
Valid prediction for snap_scaffold_11-snap.64-T1
Valid prediction for snap_scaffold_11-snap.67-T1
Valid prediction for snap_scaffold_11-snap.55-T1
Valid prediction for Augustus_model.g17474.t1
Valid prediction for Augustus_model.g17477.t1
Valid prediction for Augustus_model.g17473.t1
Valid prediction for GlimmerHMM_glimmerT_26330-T1
Valid prediction for snap_scaffold_11-snap.75-T1
Valid prediction for snap_scaffold_11-snap.53-T1
Valid prediction for snap_scaffold_11-snap.62-T1
Couldn't classify 37748, 37872
Couldn't classify 39041, 39184
Sorry, prediction pasa_asmbl_6394.p1 fails validation.
(GCT)	 CT	37748-37872	GT	AGG
(CTG)	 AG	38804-38918	GT	AGG
(GAA)	 AG	39041-39184	AC	CAA
-recovered pasa_asmbl_6394.p1, internal, 38804, 38918

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8059, rend_intergenic: 7050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12866, rend_intergenic: 9786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26885, rend_intergenic: 23370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81770, rend_intergenic: 78741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99521, rend_intergenic: 88146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103333, rend_intergenic: 100990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116514, rend_intergenic: 114241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120937, rend_intergenic: 117505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127893, rend_intergenic: 123941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130053, rend_intergenic: 127930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134105
-exon list size: 242


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.5    
2.9    
3.3    
3.7    
4.1    
4.5    
4.9    
5.3    
5.7    
6.1    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.7    
11.1    
11.5    
11.9    
12.3    
12.7    
13.1    
13.5    
13.9    
14.3    
14.8    
15.2    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
18.0    
18.4    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.1    
22.5    
23.0    
23.4    
23.8    
24.2    
24.6    
25.0    
25.4    
25.8    
26.2    
26.6    
27.0    
27.5    
27.9    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.7    
36.1    
36.5    
36.9    
37.3    
37.7    
38.1    
38.5    
38.9    
39.3    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.9    
44.3    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.7    
56.1    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.7    
61.1    
61.5    
61.9    
62.3    
62.7    
63.1    
63.5    
63.9    
64.3    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.1    
72.5    
73.0    
73.4    
73.8    
74.2    
74.6    
75.0    
75.4    
75.8    
76.2    
76.6    
77.0    
77.5    
77.9    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.6    
82.0    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.8    
85.2    
85.7    
86.1    
86.5    
86.9    
87.3    
87.7    
88.1    
88.5    
88.9    
89.3    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.9    
94.3    
94.7    
95.1    
95.5    
95.9    
96.3    
96.7    
97.1    
97.5    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 8059, rend_intergenic: 7050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12866, rend_intergenic: 9786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26885, rend_intergenic: 23370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81770, rend_intergenic: 78741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99521, rend_intergenic: 88146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103333, rend_intergenic: 100990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116514, rend_intergenic: 114241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120937, rend_intergenic: 117505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127893, rend_intergenic: 123941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130053, rend_intergenic: 127930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support