-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_7153186-7286930

-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_27357-T1
Valid prediction for snap_scaffold_11-snap.1679-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27350-T1
Valid prediction for snap_scaffold_11-snap.1684-T1
Valid prediction for snap_scaffold_11-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_27353-T1
Valid prediction for GlimmerHMM_glimmerT_27355-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.1671-T1
Valid prediction for snap_scaffold_11-snap.1678-T1
Valid prediction for snap_scaffold_11-snap.1690-T1
Valid prediction for snap_scaffold_11-snap.1685-T1
Valid prediction for snap_scaffold_11-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_27352-T1
Valid prediction for snap_scaffold_11-snap.1688-T1
Valid prediction for snap_scaffold_11-snap.1669-T1
Valid prediction for snap_scaffold_11-snap.1665-T1
Valid prediction for snap_scaffold_11-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_27345-T1
Valid prediction for snap_scaffold_11-snap.1676-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_11-snap.1670-T1
Couldn't classify 66451, 66507
Sorry, prediction pasa_asmbl_6765.p1 fails validation.
(TCA)	 TA	66451-66507	GT	AGG
(AGC)	 AG	68047-68080	GT	CGG
(GTG)	 AG	69184-69276	GT	AGG
(CAA)	 AG	69720-69936	GT	CCG
(GCC)	 AG	70095-70172	GT	CAG
(GAA)	 AG	70306-70438	AA	AGA
add_exon() Sorry, pasa_asmbl_6765.p1 69184-69276-terminal-1 is invalid.
-recovered pasa_asmbl_6765.p1, terminal, 69184, 69276
-recovered pasa_asmbl_6765.p1, terminal, 70306, 70438
-recovered pasa_asmbl_6765.p1, internal, 68047, 68080
-recovered pasa_asmbl_6765.p1, internal, 69184, 69276
-recovered pasa_asmbl_6765.p1, internal, 69720, 69936
-recovered pasa_asmbl_6765.p1, internal, 70095, 70172
Valid prediction for GlimmerHMM_glimmerT_27349-T1
Valid prediction for snap_scaffold_11-snap.1682-T1
Valid prediction for snap_scaffold_11-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_27358-T1
Valid prediction for GlimmerHMM_glimmerT_27347-T1
Valid prediction for GlimmerHMM_glimmerT_27354-T1
Valid prediction for Augustus_model.g18099.t1
Valid prediction for Augustus_model.g18101.t1
Valid prediction for snap_scaffold_11-snap.1666-T1
Valid prediction for Augustus_model.g18100.t1
Valid prediction for GlimmerHMM_glimmerT_27359-T1
Valid prediction for Augustus_model.g18105.t1
Valid prediction for snap_scaffold_11-snap.1673-T1
Valid prediction for GlimmerHMM_glimmerT_27356-T1
Valid prediction for snap_scaffold_11-snap.1689-T1
Valid prediction for Augustus_model.g18102.t1
Valid prediction for pasa_asmbl_6762.p1
Valid prediction for Augustus_model.g18107.t1
Valid prediction for GlimmerHMM_glimmerT_27351-T1
Valid prediction for snap_scaffold_11-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_27348-T1
Couldn't classify 47142, 47257
Couldn't classify 47690, 47892
Sorry, prediction pasa_asmbl_6770.p1 fails validation.
(TCT)	 AG	47142-47257	GT	AGG
(GCT)	 AG	47367-47437	GT	AGG
(GTG)	 AG	47690-47892	GC	AGG
-recovered pasa_asmbl_6770.p1, internal, 47142, 47257
-recovered pasa_asmbl_6770.p1, internal, 47367, 47437
-recovered pasa_asmbl_6770.p1, internal, 47690, 47892
Valid prediction for snap_scaffold_11-snap.1677-T1
Valid prediction for Augustus_model.g18103.t1
Valid prediction for Augustus_model.g18106.t1
Valid prediction for snap_scaffold_11-snap.1681-T1
Valid prediction for snap_scaffold_11-snap.1691-T1
Valid prediction for Augustus_model.g18104.t1
Valid prediction for GlimmerHMM_glimmerT_27360-T1
Valid prediction for snap_scaffold_11-snap.1672-T1
Couldn't classify 63043, 63103
Couldn't classify 65533, 65694
Sorry, prediction pasa_asmbl_6767.p1 fails validation.
(AGG)	 AG	63043-63103	GT	AGG
(CCA)	 AG	63257-63429	GT	AGG
(GCC)	 AG	63876-64022	GT	TGG
(CGG)	 AG	64385-64573	GT	AGG
(ATC)	 AG	64887-64997	GT	TGG
(TCT)	 AG	65533-65694	AT	CCA
-recovered pasa_asmbl_6767.p1, internal, 63043, 63103
-recovered pasa_asmbl_6767.p1, internal, 63257, 63429
-recovered pasa_asmbl_6767.p1, internal, 63876, 64022
-recovered pasa_asmbl_6767.p1, internal, 64385, 64573
-recovered pasa_asmbl_6767.p1, internal, 64887, 64997
Valid prediction for GlimmerHMM_glimmerT_27346-T1
Valid prediction for snap_scaffold_11-snap.1686-T1
Valid prediction for snap_scaffold_11-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_27361-T1
Valid prediction for snap_scaffold_11-snap.1687-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9534, rend_intergenic: 5046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18719, rend_intergenic: 13392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29976, rend_intergenic: 19369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38955, rend_intergenic: 31343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42203, rend_intergenic: 40184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49607, rend_intergenic: 46378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56157, rend_intergenic: 53419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70932, rend_intergenic: 67682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94964, rend_intergenic: 85416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112638, rend_intergenic: 109075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128992, rend_intergenic: 118946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131892, rend_intergenic: 129303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133745
-exon list size: 239


building trellis

0.4    
0.8    
1.2    
1.7    
2.1    
2.5    
2.9    
3.3    
3.7    
4.1    
4.6    
5.0    
5.4    
5.8    
6.2    
6.6    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.5    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.3    
18.7    
19.1    
19.5    
19.9    
20.3    
20.7    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
46.1    
46.5    
46.9    
47.3    
47.7    
48.1    
48.5    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.5    
51.9    
52.3    
52.7    
53.1    
53.5    
53.9    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.3    
79.7    
80.1    
80.5    
80.9    
81.3    
81.7    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.4    
93.8    
94.2    
94.6    
95.0    
95.4    
95.9    
96.3    
96.7    
97.1    
97.5    
97.9    
98.3    
98.8    
99.2    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 9534, rend_intergenic: 5046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18719, rend_intergenic: 13392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29976, rend_intergenic: 19369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38955, rend_intergenic: 31343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42203, rend_intergenic: 40184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49607, rend_intergenic: 46378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56157, rend_intergenic: 53419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70932, rend_intergenic: 67682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94964, rend_intergenic: 85416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112638, rend_intergenic: 109075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128992, rend_intergenic: 118946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131892, rend_intergenic: 129303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support