-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_12285699-12455000

-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.g3110.t1
Valid prediction for snap_scaffold_2-snap.2334-T1
Valid prediction for snap_scaffold_2-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_4619-T1
Valid prediction for GlimmerHMM_glimmerT_4622-T1
Valid prediction for snap_scaffold_2-snap.2321-T1
Valid prediction for snap_scaffold_2-snap.2318-T1
Valid prediction for snap_scaffold_2-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_4626-T1
Valid prediction for snap_scaffold_2-snap.2316-T1
Valid prediction for snap_scaffold_2-snap.2330-T1
Valid prediction for GlimmerHMM_glimmerT_4624-T1
Valid prediction for Augustus_model.g3103.t1
Valid prediction for snap_scaffold_2-snap.2326-T1
Valid prediction for snap_scaffold_2-snap.2354-T1
Valid prediction for snap_scaffold_2-snap.2343-T1
Valid prediction for Augustus_model.g3101.t1
Valid prediction for Augustus_model.g3106.t1
Valid prediction for snap_scaffold_2-snap.2351-T1
Couldn't classify 86327, 86496
Couldn't classify 92670, 92877
Sorry, prediction pasa_asmbl_24790.p1 fails validation.
(GGG)	 CA	86327-86496	GT	AGG
(GTA)	 AG	86900-87039	GT	AGG
(CCG)	 AG	87264-87362	GT	AGG
(ACG)	 AG	89033-89659	GT	AGG
(CTC)	 AG	91953-92030	GT	AAG
(ATT)	 AG	92267-92345	GT	AGG
(CTT)	 AG	92670-92877	GC	TGG
-recovered pasa_asmbl_24790.p1, internal, 86900, 87039
-recovered pasa_asmbl_24790.p1, internal, 87264, 87362
-recovered pasa_asmbl_24790.p1, internal, 89033, 89659
-recovered pasa_asmbl_24790.p1, internal, 91953, 92030
-recovered pasa_asmbl_24790.p1, internal, 92267, 92345
-recovered pasa_asmbl_24790.p1, internal, 92670, 92877
Valid prediction for GlimmerHMM_glimmerT_4627-T1
Valid prediction for Augustus_model.g3105.t1
Valid prediction for snap_scaffold_2-snap.2328-T1
Valid prediction for snap_scaffold_2-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_4634-T1
Valid prediction for pasa_asmbl_24787.p1
Valid prediction for Augustus_model.g3108.t1
Valid prediction for snap_scaffold_2-snap.2348-T1
Valid prediction for snap_scaffold_2-snap.2339-T1
Couldn't classify 43351, 43451
Sorry, prediction pasa_asmbl_24785.p1 fails validation.
(ATG)	 TC	37430-37565	GT	CGG
(GGG)	 AG	40376-40459	GT	AGG
(GTG)	 AG	43351-43451	GT	TGG
-recovered pasa_asmbl_24785.p1, initial, 37430, 37565
-recovered pasa_asmbl_24785.p1, internal, 40376, 40459
-recovered pasa_asmbl_24785.p1, internal, 43351, 43451
Valid prediction for GlimmerHMM_glimmerT_4618-T1
Valid prediction for snap_scaffold_2-snap.2336-T1
Valid prediction for snap_scaffold_2-snap.2346-T1
Valid prediction for snap_scaffold_2-snap.2317-T1
Valid prediction for GlimmerHMM_glimmerT_4621-T1
Valid prediction for snap_scaffold_2-snap.2352-T1
Valid prediction for Augustus_model.g3113.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_2-snap.2323-T1
Valid prediction for snap_scaffold_2-snap.2327-T1
Valid prediction for Augustus_model.g3115.t1
Valid prediction for GlimmerHMM_glimmerT_4632-T1
Valid prediction for snap_scaffold_2-snap.2347-T1
Valid prediction for snap_scaffold_2-snap.2340-T1
Valid prediction for GlimmerHMM_glimmerT_4633-T1
Valid prediction for Augustus_model.g3112.t1
Valid prediction for snap_scaffold_2-snap.2341-T1
Valid prediction for snap_scaffold_2-snap.2344-T1
Couldn't classify 17465, 17639
Couldn't classify 19774, 19868
Sorry, prediction pasa_asmbl_23466.p1 fails validation.
(GAC)	 CA	17465-17639	GT	AGG
(GTT)	 AG	19090-19215	GT	AAG
(AAT)	 AG	19774-19868	CT	AAC
-recovered pasa_asmbl_23466.p1, terminal, 19090, 19215
-recovered pasa_asmbl_23466.p1, internal, 19090, 19215
Couldn't classify 26708, 26879
Sorry, prediction pasa_asmbl_23465.p1 fails validation.
(GTG)	 CA	26708-26879	GT	CGG
(TGC)	 AG	27204-27395	GT	AGG
(TTA)	 AG	27635-28549	GT	TGG
(ATA)	 AG	28735-28911	GT	AGG
(CCT)	 AG	29196-29262	GT	AGG
(GAA)	 AG	29692-29921	GT	AGG
(TAT)	 AG	30185-30564	GT	GGG
(GTG)	 AG	31276-31851	GA	GAG
-recovered pasa_asmbl_23465.p1, terminal, 31276, 31851
-recovered pasa_asmbl_23465.p1, internal, 27204, 27395
-recovered pasa_asmbl_23465.p1, internal, 27635, 28549
-recovered pasa_asmbl_23465.p1, internal, 28735, 28911
-recovered pasa_asmbl_23465.p1, internal, 29196, 29262
-recovered pasa_asmbl_23465.p1, internal, 29692, 29921
-recovered pasa_asmbl_23465.p1, internal, 30185, 30564
Valid prediction for snap_scaffold_2-snap.2353-T1
Valid prediction for GlimmerHMM_glimmerT_4623-T1
Valid prediction for snap_scaffold_2-snap.2331-T1
Valid prediction for snap_scaffold_2-snap.2325-T1
Valid prediction for snap_scaffold_2-snap.2332-T1
Valid prediction for snap_scaffold_2-snap.2315-T1
Valid prediction for snap_scaffold_2-snap.2349-T1
Valid prediction for Augustus_model.g3100.t1
Valid prediction for Augustus_model.g3111.t1
Valid prediction for GlimmerHMM_glimmerT_4630-T1
Valid prediction for Augustus_model.g3114.t1
Valid prediction for snap_scaffold_2-snap.2337-T1
Valid prediction for snap_scaffold_2-snap.2320-T1
Valid prediction for Augustus_model.g3104.t1
Valid prediction for GlimmerHMM_glimmerT_4631-T1
Valid prediction for snap_scaffold_2-snap.2314-T1
Valid prediction for GlimmerHMM_glimmerT_4616-T1
Valid prediction for GlimmerHMM_glimmerT_4615-T1
Valid prediction for Augustus_model.g3109.t1
Valid prediction for snap_scaffold_2-snap.2338-T1
Valid prediction for GlimmerHMM_glimmerT_4620-T1
Valid prediction for snap_scaffold_2-snap.2350-T1
Valid prediction for snap_scaffold_2-snap.2319-T1
Valid prediction for GlimmerHMM_glimmerT_4617-T1
Valid prediction for GlimmerHMM_glimmerT_4625-T1
Valid prediction for snap_scaffold_2-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_4628-T1
Valid prediction for Augustus_model.g3107.t1
Valid prediction for Augustus_model.g3102.t1
Couldn't classify 73074, 73457
Sorry, prediction pasa_asmbl_23464.p1 fails validation.
(AAC)	 CA	73074-73457	GG	TCG
Valid prediction for snap_scaffold_2-snap.2335-T1
Valid prediction for snap_scaffold_2-snap.2345-T1
Valid prediction for snap_scaffold_2-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_4629-T1
Valid prediction for GlimmerHMM_glimmerT_4635-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9842, rend_intergenic: 8698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24250, rend_intergenic: 21569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51047, rend_intergenic: 41795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57930, rend_intergenic: 54142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68728, rend_intergenic: 63625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83375, rend_intergenic: 71446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86110, rend_intergenic: 84806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93706, rend_intergenic: 92941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114521, rend_intergenic: 113081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122270, rend_intergenic: 118353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126569, rend_intergenic: 123830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135816, rend_intergenic: 134947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137701, rend_intergenic: 137452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139655, rend_intergenic: 139398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145265, rend_intergenic: 140034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165259, rend_intergenic: 164584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167898, rend_intergenic: 165418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169302
-exon list size: 336


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 9842, rend_intergenic: 8698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24250, rend_intergenic: 21569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51047, rend_intergenic: 41795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57930, rend_intergenic: 54142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68728, rend_intergenic: 63625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83375, rend_intergenic: 71446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86110, rend_intergenic: 84806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93706, rend_intergenic: 92941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114521, rend_intergenic: 113081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122270, rend_intergenic: 118353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126569, rend_intergenic: 123830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135816, rend_intergenic: 134947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137701, rend_intergenic: 137452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139655, rend_intergenic: 139398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145265, rend_intergenic: 140034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165259, rend_intergenic: 164584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167898, rend_intergenic: 165418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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