-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_3224462-3358607

-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_23-snap.642-T1
Valid prediction for snap_scaffold_23-snap.633-T1
Valid prediction for GlimmerHMM_glimmerT_51992-T1
Valid prediction for snap_scaffold_23-snap.653-T1
Valid prediction for GeneMark_model.90301_t
Valid prediction for GeneMark_model.90298_t
Valid prediction for GlimmerHMM_glimmerT_51998-T1
Valid prediction for GlimmerHMM_glimmerT_52012-T1
Valid prediction for GeneMark_model.90305_t
Valid prediction for snap_scaffold_23-snap.657-T1
Valid prediction for Augustus_model.g34957.t1
Valid prediction for GlimmerHMM_glimmerT_52009-T1
Valid prediction for CodingQuarry_transcript_35537-T1
Valid prediction for GeneMark_model.90302_t
Valid prediction for GeneMark_model.90315_t
Valid prediction for snap_scaffold_23-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_51993-T1
Valid prediction for GeneMark_model.90303_t
Valid prediction for GlimmerHMM_glimmerT_51991-T1
Valid prediction for GeneMark_model.90289_t
Valid prediction for GeneMark_model.90295_t
Valid prediction for Augustus_model.g34943.t1
Valid prediction for GlimmerHMM_glimmerT_51996-T1
Valid prediction for HiQ_model.g34940.t1
Valid prediction for snap_scaffold_23-snap.644-T1
Valid prediction for Augustus_model.g34941.t1
Valid prediction for GlimmerHMM_glimmerT_52010-T1
Valid prediction for GeneMark_model.90287_t
Valid prediction for GeneMark_model.90308_t
Valid prediction for GeneMark_model.90318_t
Valid prediction for GlimmerHMM_glimmerT_52001-T1
Valid prediction for GeneMark_model.90314_t
Valid prediction for pasa_asmbl_30733.p1
Valid prediction for GeneMark_model.90312_t
Valid prediction for GeneMark_model.90320_t
Valid prediction for GeneMark_model.90307_t
Valid prediction for snap_scaffold_23-snap.634-T1
Valid prediction for snap_scaffold_23-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_51989-T1
Valid prediction for GeneMark_model.90299_t
Valid prediction for snap_scaffold_23-snap.655-T1
Valid prediction for pasa_asmbl_30730.p1
Valid prediction for GeneMark_model.90286_t
Valid prediction for GeneMark_model.90310_t
Valid prediction for snap_scaffold_23-snap.649-T1
Valid prediction for Augustus_model.g34953.t1
Valid prediction for snap_scaffold_23-snap.635-T1
Valid prediction for GlimmerHMM_glimmerT_52005-T1
Couldn't classify 19900, 20047
Sorry, prediction pasa_asmbl_30732.p1 fails validation.
(ATG)	 CC	18684-18723	GT	ATG
(TTG)	 AG	19316-19439	GT	AGG
(AAA)	 AG	19682-19801	GT	AAG
(TAC)	 AG	19900-20047	GG	CAG
-recovered pasa_asmbl_30732.p1, initial, 18684, 18723
-recovered pasa_asmbl_30732.p1, internal, 19316, 19439
-recovered pasa_asmbl_30732.p1, internal, 19682, 19801
Valid prediction for Augustus_model.g34950.t1
Valid prediction for snap_scaffold_23-snap.638-T1
Valid prediction for snap_scaffold_23-snap.651-T1
Valid prediction for GlimmerHMM_glimmerT_51987-T1
Valid prediction for snap_scaffold_23-snap.647-T1
Valid prediction for GlimmerHMM_glimmerT_52000-T1
Valid prediction for snap_scaffold_23-snap.641-T1
Valid prediction for GeneMark_model.90306_t
Valid prediction for CodingQuarry_transcript_35538-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_52007-T1
Valid prediction for GeneMark_model.90300_t
Valid prediction for Augustus_model.g34944.t1
Valid prediction for GeneMark_model.90297_t
Valid prediction for GlimmerHMM_glimmerT_52006-T1
Valid prediction for snap_scaffold_23-snap.636-T1
Valid prediction for snap_scaffold_23-snap.640-T1
Valid prediction for Augustus_model.g34952.t1
Valid prediction for GeneMark_model.90304_t
Valid prediction for snap_scaffold_23-snap.654-T1
Valid prediction for Augustus_model.g34946.t1
Valid prediction for GlimmerHMM_glimmerT_51985-T1
Valid prediction for GeneMark_model.90294_t
Valid prediction for GlimmerHMM_glimmerT_52008-T1
Valid prediction for GlimmerHMM_glimmerT_51990-T1
Valid prediction for GlimmerHMM_glimmerT_51986-T1
Valid prediction for GeneMark_model.90313_t
Valid prediction for Augustus_model.g34938.t1
Valid prediction for GeneMark_model.90285_t
Valid prediction for Augustus_model.g34949.t1
Valid prediction for CodingQuarry_transcript_35536-T1
Valid prediction for snap_scaffold_23-snap.650-T1
Valid prediction for Augustus_model.g34954.t1
Valid prediction for GlimmerHMM_glimmerT_51997-T1
Valid prediction for GeneMark_model.90288_t
Valid prediction for GeneMark_model.90309_t
Valid prediction for Augustus_model.g34951.t1
Valid prediction for snap_scaffold_23-snap.645-T1
Valid prediction for GeneMark_model.90311_t
Valid prediction for Augustus_model.g34942.t1
Valid prediction for snap_scaffold_23-snap.656-T1
Valid prediction for pasa_asmbl_31508.p1
Valid prediction for snap_scaffold_23-snap.639-T1
Valid prediction for snap_scaffold_23-snap.631-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52011-T1
Valid prediction for GeneMark_model.90292_t
Valid prediction for GeneMark_model.90316_t
Valid prediction for GlimmerHMM_glimmerT_52002-T1
Valid prediction for GeneMark_model.90293_t
Valid prediction for GlimmerHMM_glimmerT_51999-T1
Valid prediction for GeneMark_model.90296_t
Valid prediction for GeneMark_model.90284_t
Valid prediction for HiQ_model.g34939.t1
Valid prediction for snap_scaffold_23-snap.648-T1
Valid prediction for GeneMark_model.90321_t
Valid prediction for Augustus_model.g34948.t1
Valid prediction for GlimmerHMM_glimmerT_51988-T1
Valid prediction for GlimmerHMM_glimmerT_52004-T1
Valid prediction for GlimmerHMM_glimmerT_52003-T1
Valid prediction for GeneMark_model.90317_t
Valid prediction for snap_scaffold_23-snap.652-T1
Valid prediction for snap_scaffold_23-snap.632-T1
Valid prediction for GlimmerHMM_glimmerT_51995-T1
Valid prediction for Augustus_model.g34956.t1
Valid prediction for GeneMark_model.90290_t
Valid prediction for snap_scaffold_23-snap.646-T1
Valid prediction for Augustus_model.g34955.t1
Valid prediction for GlimmerHMM_glimmerT_51994-T1
Valid prediction for Augustus_model.g34947.t1
Valid prediction for Augustus_model.g34945.t1
Valid prediction for GeneMark_model.90291_t
Valid prediction for GeneMark_model.90319_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 80941, rend_intergenic: 75892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88469, rend_intergenic: 86855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93005, rend_intergenic: 91684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94890, rend_intergenic: 93111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103354, rend_intergenic: 97617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108642, rend_intergenic: 106935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119259, rend_intergenic: 111748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131269, rend_intergenic: 121216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134146
-exon list size: 505


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 80941, rend_intergenic: 75892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88469, rend_intergenic: 86855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93005, rend_intergenic: 91684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94890, rend_intergenic: 93111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103354, rend_intergenic: 97617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108642, rend_intergenic: 106935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119259, rend_intergenic: 111748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131269, rend_intergenic: 121216  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