-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_123788-293799

-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.63-T1
Valid prediction for GlimmerHMM_glimmerT_43466-T1
Valid prediction for snap_scaffold_19-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_43460-T1
Valid prediction for GlimmerHMM_glimmerT_43463-T1
Valid prediction for Augustus_model.g28889.t1
Couldn't classify 165467, 165562
Sorry, prediction pasa_asmbl_21909.p1 fails validation.
(TCG)	 CC	165467-165562	GT	CGG
(GAG)	 AG	166111-166216	GT	AGG
(AGC)	 AG	166309-166442	CA	GAC
-recovered pasa_asmbl_21909.p1, terminal, 166309, 166442
-recovered pasa_asmbl_21909.p1, internal, 166111, 166216
Valid prediction for snap_scaffold_19-snap.37-T1
Valid prediction for Augustus_model.g28893.t1
Valid prediction for Augustus_model.g28896.t1
Valid prediction for HiQ_model.g28890.t1
Valid prediction for GlimmerHMM_glimmerT_43465-T1
Valid prediction for Augustus_model.g28895.t1
Valid prediction for snap_scaffold_19-snap.56-T1
Valid prediction for snap_scaffold_19-snap.58-T1
Valid prediction for Augustus_model.g28894.t1
Valid prediction for snap_scaffold_19-snap.51-T1
Valid prediction for CodingQuarry_transcript_25568-T1
Valid prediction for GlimmerHMM_glimmerT_43464-T1
Valid prediction for snap_scaffold_19-snap.61-T1
Valid prediction for snap_scaffold_19-snap.64-T1
Valid prediction for snap_scaffold_19-snap.38-T1
Valid prediction for CodingQuarry_transcript_25567-T1
Valid prediction for snap_scaffold_19-snap.46-T1
Valid prediction for snap_scaffold_19-snap.66-T1
Valid prediction for snap_scaffold_19-snap.65-T1
Valid prediction for snap_scaffold_19-snap.45-T1
Valid prediction for snap_scaffold_19-snap.36-T1
Valid prediction for snap_scaffold_19-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_43448-T1
Valid prediction for pasa_asmbl_21179.p1
Valid prediction for snap_scaffold_19-snap.44-T1
Valid prediction for snap_scaffold_19-snap.40-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43456-T1
Valid prediction for GlimmerHMM_glimmerT_43451-T1
Valid prediction for GlimmerHMM_glimmerT_43458-T1
Valid prediction for GlimmerHMM_glimmerT_43461-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 Augustus_model.g28892.t1
Valid prediction for snap_scaffold_19-snap.49-T1
Valid prediction for snap_scaffold_19-snap.42-T1
Valid prediction for GlimmerHMM_glimmerT_43457-T1
Valid prediction for GlimmerHMM_glimmerT_43455-T1
Valid prediction for GlimmerHMM_glimmerT_43452-T1
Valid prediction for snap_scaffold_19-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_43449-T1
Valid prediction for snap_scaffold_19-snap.34-T1
Valid prediction for snap_scaffold_19-snap.67-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43447-T1
Valid prediction for snap_scaffold_19-snap.35-T1
Valid prediction for pasa_asmbl_21984.p1
Valid prediction for Augustus_model.g28888.t1
Valid prediction for snap_scaffold_19-snap.50-T1
Valid prediction for Augustus_model.g28891.t1
Valid prediction for snap_scaffold_19-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_43450-T1
Valid prediction for GlimmerHMM_glimmerT_43459-T1
Valid prediction for snap_scaffold_19-snap.62-T1
Valid prediction for Augustus_model.g28887.t1
Valid prediction for snap_scaffold_19-snap.48-T1
Valid prediction for snap_scaffold_19-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_43453-T1
Valid prediction for snap_scaffold_19-snap.32-T1
Valid prediction for snap_scaffold_19-snap.60-T1
Valid prediction for snap_scaffold_19-snap.55-T1
Valid prediction for snap_scaffold_19-snap.33-T1
Valid prediction for snap_scaffold_19-snap.31-T1
Valid prediction for snap_scaffold_19-snap.43-T1
Valid prediction for snap_scaffold_19-snap.54-T1
Valid prediction for snap_scaffold_19-snap.39-T1
Valid prediction for snap_scaffold_19-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_43454-T1
Valid prediction for snap_scaffold_19-snap.57-T1
Valid prediction for snap_scaffold_19-snap.69-T1
Valid prediction for GlimmerHMM_glimmerT_43462-T1
Couldn't classify 164739, 164804
Sorry, prediction pasa_asmbl_22707.p1 fails validation.
(TTT)	 AG	164739-164804	GT	TGG
(ACA)	 AG	164953-165045	GT	AGG
(GTG)	 AG	165212-165465	GT	AAG
(GAT)	 AG	166274-166436	GT	AGG
(ATC)	 AG	167579-167725	GT	AAG
(GCT)	 AG	167838-167962	GT	GGG
(GAG)	 AG	168102-168219	AT	AGA
-recovered pasa_asmbl_22707.p1, terminal, 168102, 168219
-recovered pasa_asmbl_22707.p1, internal, 164739, 164804
-recovered pasa_asmbl_22707.p1, internal, 164953, 165045
-recovered pasa_asmbl_22707.p1, internal, 165212, 165465
-recovered pasa_asmbl_22707.p1, internal, 166274, 166436
-recovered pasa_asmbl_22707.p1, internal, 167579, 167725
-recovered pasa_asmbl_22707.p1, internal, 167838, 167962

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 44125, rend_intergenic: 41390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44875, rend_intergenic: 44675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52167, rend_intergenic: 44982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70880, rend_intergenic: 56462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84440, rend_intergenic: 77905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88448, rend_intergenic: 86497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106170, rend_intergenic: 94485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112081, rend_intergenic: 108129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119755, rend_intergenic: 116052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135458, rend_intergenic: 122614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139979, rend_intergenic: 139472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147016, rend_intergenic: 141081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158944, rend_intergenic: 155645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170012
-exon list size: 369


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    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
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 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 44125, rend_intergenic: 41390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44875, rend_intergenic: 44675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52167, rend_intergenic: 44982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70880, rend_intergenic: 56462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84440, rend_intergenic: 77905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88448, rend_intergenic: 86497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106170, rend_intergenic: 94485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112081, rend_intergenic: 108129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119755, rend_intergenic: 116052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135458, rend_intergenic: 122614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139979, rend_intergenic: 139472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147016, rend_intergenic: 141081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158944, rend_intergenic: 155645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support