-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_9826029-9982980

-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.g4657.t1
Valid prediction for GlimmerHMM_glimmerT_7142-T1
Valid prediction for snap_scaffold_3-snap.1943-T1
Valid prediction for snap_scaffold_3-snap.1948-T1
Valid prediction for snap_scaffold_3-snap.1953-T1
Valid prediction for snap_scaffold_3-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_7121-T1
Valid prediction for Augustus_model.g4644.t1
Valid prediction for snap_scaffold_3-snap.1966-T1
Valid prediction for Augustus_model.g4653.t1
Valid prediction for snap_scaffold_3-snap.1964-T1
Valid prediction for GlimmerHMM_glimmerT_7120-T1
Valid prediction for GlimmerHMM_glimmerT_7129-T1
Valid prediction for GlimmerHMM_glimmerT_7132-T1
Valid prediction for snap_scaffold_3-snap.1942-T1
Valid prediction for Augustus_model.g4641.t1
Valid prediction for GlimmerHMM_glimmerT_7143-T1
Valid prediction for GlimmerHMM_glimmerT_7137-T1
Valid prediction for snap_scaffold_3-snap.1944-T1
Valid prediction for pasa_asmbl_40240.p1
Valid prediction for GlimmerHMM_glimmerT_7134-T1
Valid prediction for snap_scaffold_3-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_7117-T1
Valid prediction for GlimmerHMM_glimmerT_7125-T1
Valid prediction for snap_scaffold_3-snap.1951-T1
Valid prediction for snap_scaffold_3-snap.1958-T1
Valid prediction for Augustus_model.g4649.t1
Valid prediction for Augustus_model.g4656.t1
Valid prediction for GlimmerHMM_glimmerT_7122-T1
Valid prediction for snap_scaffold_3-snap.1949-T1
Couldn't classify 151516, 151600
Couldn't classify 153281, 153333
Sorry, prediction pasa_asmbl_40241.p1 fails validation.
(TCC)	 CC	151516-151600	GT	CTG
(CAT)	 AG	151723-151825	GT	AGG
(GTT)	 AG	152502-152566	GT	CCG
(TCC)	 AG	153281-153333	AG	CCA
-recovered pasa_asmbl_40241.p1, internal, 151723, 151825
-recovered pasa_asmbl_40241.p1, internal, 152502, 152566
Valid prediction for snap_scaffold_3-snap.1957-T1
Valid prediction for HiQ_model.g4643.t1
Valid prediction for Augustus_model.g4640.t1
Valid prediction for Augustus_model.g4645.t1
Valid prediction for snap_scaffold_3-snap.1939-T1
Valid prediction for GlimmerHMM_glimmerT_7127-T1
Valid prediction for snap_scaffold_3-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_7119-T1
Valid prediction for CodingQuarry_transcript_46242-T1
Couldn't classify 13049, 13345
Sorry, prediction pasa_asmbl_40237.p2 fails validation.
(CGA)	 CC	13049-13345	CC	GCC
Valid prediction for Augustus_model.g4658.t1
Valid prediction for Augustus_model.g4648.t1
Valid prediction for snap_scaffold_3-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_7133-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_3-snap.1960-T1
Valid prediction for snap_scaffold_3-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_7138-T1
Valid prediction for HiQ_model.g4642.t1
Valid prediction for CodingQuarry_transcript_46241-T1
Valid prediction for snap_scaffold_3-snap.1954-T1
Valid prediction for snap_scaffold_3-snap.1956-T1
Valid prediction for snap_scaffold_3-snap.1940-T1
Valid prediction for GlimmerHMM_glimmerT_7131-T1
Valid prediction for Augustus_model.g4646.t1
Valid prediction for GlimmerHMM_glimmerT_7141-T1
Valid prediction for snap_scaffold_3-snap.1963-T1
Valid prediction for GlimmerHMM_glimmerT_7126-T1
Valid prediction for GlimmerHMM_glimmerT_7136-T1
Valid prediction for Augustus_model.g4652.t1
Valid prediction for snap_scaffold_3-snap.1946-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g4650.t1
Valid prediction for Augustus_model.g4651.t1
Valid prediction for Augustus_model.g4654.t1
Valid prediction for snap_scaffold_3-snap.1945-T1
Valid prediction for snap_scaffold_3-snap.1961-T1
Valid prediction for Augustus_model.g4647.t1
Valid prediction for GlimmerHMM_glimmerT_7140-T1
Valid prediction for Augustus_model.g4655.t1
Valid prediction for snap_scaffold_3-snap.1965-T1
Valid prediction for GlimmerHMM_glimmerT_7135-T1
Valid prediction for CodingQuarry_transcript_46240-T1
Valid prediction for GlimmerHMM_glimmerT_7139-T1
Valid prediction for snap_scaffold_3-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_7128-T1
Valid prediction for snap_scaffold_3-snap.1947-T1
Valid prediction for pasa_asmbl_39071.p1
Valid prediction for GlimmerHMM_glimmerT_7118-T1
Valid prediction for GlimmerHMM_glimmerT_7124-T1
Valid prediction for snap_scaffold_3-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_7123-T1
Valid prediction for GlimmerHMM_glimmerT_7130-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65296, rend_intergenic: 57722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72811, rend_intergenic: 68840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79190, rend_intergenic: 74037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86741, rend_intergenic: 83419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90405, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96106, rend_intergenic: 91266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137300, rend_intergenic: 106950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139005, rend_intergenic: 138151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145366, rend_intergenic: 139584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154408, rend_intergenic: 146016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156952
-exon list size: 294


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.0    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.7    
6.1    
6.4    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.9    
16.2    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.0    
27.4    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.8    
84.1    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.6    
93.9    
94.3    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
97.0    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 65296, rend_intergenic: 57722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72811, rend_intergenic: 68840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79190, rend_intergenic: 74037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86741, rend_intergenic: 83419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90405, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96106, rend_intergenic: 91266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137300, rend_intergenic: 106950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139005, rend_intergenic: 138151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145366, rend_intergenic: 139584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154408, rend_intergenic: 146016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support