-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_486427-620896

-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_51893-T1
Valid prediction for Augustus_model.g34606.t1
Valid prediction for pasa_asmbl_32026.p1
Valid prediction for snap_scaffold_24-snap.141-T1
Valid prediction for Augustus_model.g34605.t1
Valid prediction for GlimmerHMM_glimmerT_51890-T1
Valid prediction for GlimmerHMM_glimmerT_51902-T1
Valid prediction for Augustus_model.g34601.t1
Valid prediction for GlimmerHMM_glimmerT_51897-T1
Valid prediction for Augustus_model.g34602.t1
Valid prediction for snap_scaffold_24-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_51888-T1
Valid prediction for GlimmerHMM_glimmerT_51896-T1
Valid prediction for snap_scaffold_24-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_51899-T1
Valid prediction for snap_scaffold_24-snap.129-T1
Valid prediction for snap_scaffold_24-snap.152-T1
Valid prediction for snap_scaffold_24-snap.147-T1
Valid prediction for Augustus_model.g34604.t1
Valid prediction for snap_scaffold_24-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_51884-T1
Valid prediction for snap_scaffold_24-snap.143-T1
Valid prediction for snap_scaffold_24-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_51886-T1
Valid prediction for GlimmerHMM_glimmerT_51894-T1
Valid prediction for Augustus_model.g34600.t1
Valid prediction for GlimmerHMM_glimmerT_51887-T1
Valid prediction for Augustus_model.g34607.t1
Valid prediction for GlimmerHMM_glimmerT_51904-T1
Valid prediction for GlimmerHMM_glimmerT_51885-T1
Valid prediction for snap_scaffold_24-snap.122-T1
Couldn't classify 54007, 54129
Couldn't classify 56861, 56960
Sorry, prediction pasa_asmbl_32024.p1 fails validation.
(GGT)	 CA	54007-54129	GT	AGG
(GTG)	 AG	54417-54516	GT	AGG
(TGT)	 AG	54698-54829	GT	GAG
(GGA)	 AG	55477-55539	GT	GAG
(TAG)	 AG	55626-55767	GT	AGG
(TGT)	 AG	56861-56960	AG	CAA
-recovered pasa_asmbl_32024.p1, internal, 54417, 54516
-recovered pasa_asmbl_32024.p1, internal, 54698, 54829
-recovered pasa_asmbl_32024.p1, internal, 55477, 55539
-recovered pasa_asmbl_32024.p1, internal, 55626, 55767
Valid prediction for Augustus_model.g34603.t1
Valid prediction for snap_scaffold_24-snap.138-T1
Sorry, intron length (4) is less than minimum required (10)

-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_24-snap.133-T1
Valid prediction for Augustus_model.g34608.t1
Valid prediction for snap_scaffold_24-snap.124-T1
Valid prediction for snap_scaffold_24-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_51898-T1
Valid prediction for snap_scaffold_24-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_51903-T1
Valid prediction for snap_scaffold_24-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_51901-T1
Valid prediction for GlimmerHMM_glimmerT_51900-T1
Valid prediction for snap_scaffold_24-snap.125-T1
Valid prediction for snap_scaffold_24-snap.127-T1
Valid prediction for snap_scaffold_24-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_51905-T1
Valid prediction for snap_scaffold_24-snap.126-T1
Valid prediction for GlimmerHMM_glimmerT_51895-T1
Valid prediction for snap_scaffold_24-snap.135-T1
Valid prediction for snap_scaffold_24-snap.139-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.131-T1
Valid prediction for snap_scaffold_24-snap.148-T1
Valid prediction for snap_scaffold_24-snap.130-T1
Valid prediction for snap_scaffold_24-snap.151-T1
Valid prediction for snap_scaffold_24-snap.145-T1
Valid prediction for snap_scaffold_24-snap.134-T1
Valid prediction for GlimmerHMM_glimmerT_51892-T1
Valid prediction for GlimmerHMM_glimmerT_51891-T1
Valid prediction for snap_scaffold_24-snap.149-T1
Valid prediction for snap_scaffold_24-snap.150-T1
Valid prediction for snap_scaffold_24-snap.128-T1
Valid prediction for snap_scaffold_24-snap.142-T1
Valid prediction for snap_scaffold_24-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_51889-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12909, rend_intergenic: 7985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35899, rend_intergenic: 12960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42626, rend_intergenic: 41637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51783, rend_intergenic: 47381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63729, rend_intergenic: 52273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70857, rend_intergenic: 65407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76266, rend_intergenic: 72116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84984, rend_intergenic: 84376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93994, rend_intergenic: 85191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104117, rend_intergenic: 98043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105946, rend_intergenic: 104398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113369, rend_intergenic: 106670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126728, rend_intergenic: 113454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134363, rend_intergenic: 132165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134470
-exon list size: 297


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.4    
5.7    
6.0    
6.4    
6.7    
7.0    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.7    
16.1    
16.4    
16.7    
17.1    
17.4    
17.7    
18.1    
18.4    
18.7    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.5    
41.8    
42.1    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.5    
44.8    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.2    
55.5    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.9    
58.2    
58.5    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.3    
81.6    
81.9    
82.3    
82.6    
82.9    
83.3    
83.6    
83.9    
84.3    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
93.0    
93.3    
93.6    
94.0    
94.3    
94.6    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 12909, rend_intergenic: 7985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35899, rend_intergenic: 12960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42626, rend_intergenic: 41637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51783, rend_intergenic: 47381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63729, rend_intergenic: 52273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70857, rend_intergenic: 65407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76266, rend_intergenic: 72116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84984, rend_intergenic: 84376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93994, rend_intergenic: 85191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104117, rend_intergenic: 98043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105946, rend_intergenic: 104398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113369, rend_intergenic: 106670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126728, rend_intergenic: 113454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134363, rend_intergenic: 132165  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