-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_10264687-10485187

-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_22771-T1
Valid prediction for snap_scaffold_9-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_22798-T1
Valid prediction for snap_scaffold_9-snap.2028-T1
Valid prediction for snap_scaffold_9-snap.2027-T1
Couldn't classify 15889, 16009
Couldn't classify 16132, 16457
Sorry, prediction pasa_asmbl_54286.p1 fails validation.
(AGT)	 AG	15889-16009	GT	AGG
(GAA)	 AG	16132-16457	GG	CAG
-recovered pasa_asmbl_54286.p1, internal, 15889, 16009
Valid prediction for snap_scaffold_9-snap.2050-T1
Valid prediction for snap_scaffold_9-snap.2043-T1
Valid prediction for snap_scaffold_9-snap.2032-T1
Valid prediction for snap_scaffold_9-snap.2025-T1
Valid prediction for Augustus_model.g15165.t1
Valid prediction for snap_scaffold_9-snap.2062-T1
Valid prediction for HiQ_model.g15155.t1
Valid prediction for CodingQuarry_transcript_62291-T1
Valid prediction for Augustus_model.g15157.t1
Valid prediction for HiQ_model.g15156.t1
Valid prediction for CodingQuarry_transcript_62292-T1
Valid prediction for GlimmerHMM_glimmerT_22789-T1
Valid prediction for GlimmerHMM_glimmerT_22791-T1
Valid prediction for GlimmerHMM_glimmerT_22782-T1
Valid prediction for GlimmerHMM_glimmerT_22777-T1
Valid prediction for Augustus_model.g15164.t1
Valid prediction for GlimmerHMM_glimmerT_22772-T1
Valid prediction for snap_scaffold_9-snap.2055-T1
Valid prediction for snap_scaffold_9-snap.2058-T1
Couldn't classify 12907, 13038
Sorry, prediction pasa_asmbl_54284.p1 fails validation.
(GTC)	 AT	12907-13038	GT	TGG
(AGT)	 AG	13343-13613	GT	TGG
(GAC)	 AG	13690-14123	GA	AGG
-recovered pasa_asmbl_54284.p1, terminal, 13690, 14123
-recovered pasa_asmbl_54284.p1, internal, 13343, 13613
Valid prediction for GlimmerHMM_glimmerT_22788-T1
Valid prediction for snap_scaffold_9-snap.2051-T1
Valid prediction for snap_scaffold_9-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_22778-T1
Valid prediction for snap_scaffold_9-snap.2064-T1
Valid prediction for snap_scaffold_9-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_22770-T1
Valid prediction for Augustus_model.g15163.t1
Valid prediction for snap_scaffold_9-snap.2047-T1
Valid prediction for snap_scaffold_9-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_22780-T1
Valid prediction for snap_scaffold_9-snap.2034-T1
Valid prediction for snap_scaffold_9-snap.2059-T1
Valid prediction for GlimmerHMM_glimmerT_22774-T1
Valid prediction for GlimmerHMM_glimmerT_22768-T1
Valid prediction for Augustus_model.g15159.t1
Valid prediction for pasa_asmbl_54280.p1
Valid prediction for GlimmerHMM_glimmerT_22796-T1
Valid prediction for GlimmerHMM_glimmerT_22785-T1
Valid prediction for GlimmerHMM_glimmerT_22769-T1
Valid prediction for snap_scaffold_9-snap.2056-T1
Valid prediction for pasa_asmbl_54282.p1
Valid prediction for snap_scaffold_9-snap.2039-T1
Valid prediction for snap_scaffold_9-snap.2037-T1
Valid prediction for Augustus_model.g15160.t1
Valid prediction for snap_scaffold_9-snap.2026-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_22794-T1
Valid prediction for Augustus_model.g15162.t1
Valid prediction for snap_scaffold_9-snap.2042-T1
Valid prediction for snap_scaffold_9-snap.2030-T1
Valid prediction for snap_scaffold_9-snap.2048-T1
Valid prediction for snap_scaffold_9-snap.2054-T1
Valid prediction for GlimmerHMM_glimmerT_22767-T1
Valid prediction for GlimmerHMM_glimmerT_22786-T1
Valid prediction for Augustus_model.g15161.t1
Valid prediction for GlimmerHMM_glimmerT_22790-T1
Valid prediction for snap_scaffold_9-snap.2053-T1
Valid prediction for snap_scaffold_9-snap.2044-T1
Valid prediction for snap_scaffold_9-snap.2052-T1
Valid prediction for HiQ_model.g15154.t1
Valid prediction for snap_scaffold_9-snap.2024-T1
Valid prediction for snap_scaffold_9-snap.2063-T1
Valid prediction for pasa_asmbl_55252.p1
Valid prediction for GlimmerHMM_glimmerT_22787-T1
Valid prediction for GlimmerHMM_glimmerT_22781-T1
Valid prediction for snap_scaffold_9-snap.2033-T1
Valid prediction for snap_scaffold_9-snap.2029-T1
Valid prediction for GlimmerHMM_glimmerT_22792-T1
Valid prediction for snap_scaffold_9-snap.2045-T1
Valid prediction for snap_scaffold_9-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_22783-T1
Valid prediction for GlimmerHMM_glimmerT_22784-T1
Valid prediction for GlimmerHMM_glimmerT_22775-T1
Valid prediction for GlimmerHMM_glimmerT_22779-T1
Valid prediction for snap_scaffold_9-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_22797-T1
Valid prediction for GlimmerHMM_glimmerT_22793-T1
Valid prediction for snap_scaffold_9-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_22776-T1
Valid prediction for GlimmerHMM_glimmerT_22773-T1
Valid prediction for Augustus_model.g15158.t1
Valid prediction for CodingQuarry_transcript_62290-T1
Valid prediction for snap_scaffold_9-snap.2065-T1
Valid prediction for snap_scaffold_9-snap.2061-T1
Valid prediction for snap_scaffold_9-snap.2049-T1
Valid prediction for GlimmerHMM_glimmerT_22795-T1
Valid prediction for snap_scaffold_9-snap.2057-T1
Valid prediction for snap_scaffold_9-snap.2040-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46853, rend_intergenic: 37497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89401, rend_intergenic: 80305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95429, rend_intergenic: 93630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95908, rend_intergenic: 95770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100250, rend_intergenic: 97732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106157, rend_intergenic: 100965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111810, rend_intergenic: 109078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135728, rend_intergenic: 133293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143678, rend_intergenic: 139657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156354, rend_intergenic: 144601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161726, rend_intergenic: 156358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165568, rend_intergenic: 161813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208325, rend_intergenic: 198118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213868, rend_intergenic: 208910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216918, rend_intergenic: 216829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220501
-exon list size: 280


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.2    
8.5    
8.9    
9.2    
9.6    
9.9    
10.3    
10.6    
11.0    
11.3    
11.7    
12.1    
12.4    
12.8    
13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.2    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.7    
23.0    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
27.0    
27.3    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.8    
30.1    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.8    
35.1    
35.5    
35.8    
36.2    
36.5    
36.9    
37.2    
37.6    
37.9    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.6    
42.9    
43.3    
43.6    
44.0    
44.3    
44.7    
45.0    
45.4    
45.7    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.3    
54.6    
55.0    
55.3    
55.7    
56.0    
56.4    
56.7    
57.1    
57.4    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.1    
62.4    
62.8    
63.1    
63.5    
63.8    
64.2    
64.5    
64.9    
65.2    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.9    
70.2    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.7    
73.0    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
77.0    
77.3    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.8    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.2    
87.6    
87.9    
88.3    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.5    
91.8    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 46853, rend_intergenic: 37497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89401, rend_intergenic: 80305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95429, rend_intergenic: 93630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95908, rend_intergenic: 95770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100250, rend_intergenic: 97732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106157, rend_intergenic: 100965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111810, rend_intergenic: 109078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135728, rend_intergenic: 133293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143678, rend_intergenic: 139657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156354, rend_intergenic: 144601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161726, rend_intergenic: 156358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165568, rend_intergenic: 161813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208325, rend_intergenic: 198118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213868, rend_intergenic: 208910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216918, rend_intergenic: 216829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support