-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_9288351-9486530

-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_7-snap.1827-T1
Valid prediction for HiQ_model.g11997.t1
Valid prediction for snap_scaffold_7-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_17871-T1
Valid prediction for snap_scaffold_7-snap.1839-T1
Valid prediction for Augustus_model.g12001.t1
Valid prediction for Augustus_model.g11994.t1
Valid prediction for snap_scaffold_7-snap.1823-T1
Valid prediction for GlimmerHMM_glimmerT_17891-T1
Valid prediction for GlimmerHMM_glimmerT_17876-T1
Valid prediction for GlimmerHMM_glimmerT_17884-T1
Valid prediction for GlimmerHMM_glimmerT_17875-T1
Valid prediction for Augustus_model.g11992.t1
Valid prediction for snap_scaffold_7-snap.1819-T1
Valid prediction for snap_scaffold_7-snap.1830-T1
Valid prediction for snap_scaffold_7-snap.1833-T1
Valid prediction for snap_scaffold_7-snap.1828-T1
Valid prediction for GlimmerHMM_glimmerT_17873-T1
Couldn't classify 104130, 104174
Couldn't classify 105470, 105507
Sorry, prediction pasa_asmbl_50080.p1 fails validation.
(GCT)	 CC	104130-104174	GT	AGG
(GAG)	 AG	104448-104619	GT	AGG
(TGG)	 AG	104862-105047	GT	AAG
(TTA)	 AG	105470-105507	CA	CCC
-recovered pasa_asmbl_50080.p1, internal, 104448, 104619
-recovered pasa_asmbl_50080.p1, internal, 104862, 105047
Valid prediction for Augustus_model.g11999.t1
Valid prediction for snap_scaffold_7-snap.1832-T1
Valid prediction for GlimmerHMM_glimmerT_17877-T1
Valid prediction for GlimmerHMM_glimmerT_17887-T1
Valid prediction for HiQ_model.g11995.t1
Valid prediction for snap_scaffold_7-snap.1815-T1
Valid prediction for CodingQuarry_transcript_57586-T1
Valid prediction for snap_scaffold_7-snap.1817-T1
Valid prediction for pasa_asmbl_50074.p1
Valid prediction for GlimmerHMM_glimmerT_17881-T1
Valid prediction for snap_scaffold_7-snap.1826-T1
Valid prediction for GlimmerHMM_glimmerT_17883-T1
Valid prediction for Augustus_model.g12008.t1
Valid prediction for snap_scaffold_7-snap.1818-T1
Valid prediction for Augustus_model.g12007.t1
Valid prediction for Augustus_model.g12004.t1
Valid prediction for snap_scaffold_7-snap.1841-T1
Valid prediction for GlimmerHMM_glimmerT_17889-T1
Valid prediction for snap_scaffold_7-snap.1821-T1
Valid prediction for snap_scaffold_7-snap.1824-T1
Valid prediction for Augustus_model.g12000.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 Augustus_model.g12005.t1
Valid prediction for Augustus_model.g12002.t1
Valid prediction for snap_scaffold_7-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_17893-T1
Valid prediction for GlimmerHMM_glimmerT_17886-T1
Valid prediction for GlimmerHMM_glimmerT_17882-T1
Valid prediction for Augustus_model.g12009.t1
Valid prediction for CodingQuarry_transcript_57585-T1
Valid prediction for snap_scaffold_7-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_17880-T1
Valid prediction for snap_scaffold_7-snap.1840-T1
Valid prediction for CodingQuarry_transcript_57588-T1
Valid prediction for GlimmerHMM_glimmerT_17885-T1
Valid prediction for pasa_asmbl_51046.p1
Valid prediction for snap_scaffold_7-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_17874-T1
Valid prediction for GlimmerHMM_glimmerT_17879-T1
Valid prediction for GlimmerHMM_glimmerT_17890-T1
Valid prediction for Augustus_model.g11996.t1
Valid prediction for Augustus_model.g11998.t1
Valid prediction for snap_scaffold_7-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_17878-T1
Valid prediction for Augustus_model.g12006.t1
Valid prediction for CodingQuarry_transcript_57587-T1
Valid prediction for GlimmerHMM_glimmerT_17892-T1
Valid prediction for snap_scaffold_7-snap.1834-T1
Valid prediction for snap_scaffold_7-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_17872-T1
Valid prediction for snap_scaffold_7-snap.1836-T1
Valid prediction for HiQ_model.g11993.t1
Valid prediction for pasa_asmbl_51048.p1
Valid prediction for snap_scaffold_7-snap.1838-T1
Valid prediction for snap_scaffold_7-snap.1822-T1
Valid prediction for GlimmerHMM_glimmerT_17888-T1
Valid prediction for Augustus_model.g12003.t1
Valid prediction for snap_scaffold_7-snap.1837-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 180772, rend_intergenic: 180769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68642, rend_intergenic: 62863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183565, rend_intergenic: 178763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198180
-exon list size: 224


building trellis

0.4    
0.9    
1.3    
1.8    
2.2    
2.7    
3.1    
3.5    
4.0    
4.4    
4.9    
5.3    
5.8    
6.2    
6.6    
7.1    
7.5    
8.0    
8.4    
8.8    
9.3    
9.7    
10.2    
10.6    
11.1    
11.5    
11.9    
12.4    
12.8    
13.3    
13.7    
14.2    
14.6    
15.0    
15.5    
15.9    
16.4    
16.8    
17.3    
17.7    
18.1    
18.6    
19.0    
19.5    
19.9    
20.4    
20.8    
21.2    
21.7    
22.1    
22.6    
23.0    
23.5    
23.9    
24.3    
24.8    
25.2    
25.7    
26.1    
26.5    
27.0    
27.4    
27.9    
28.3    
28.8    
29.2    
29.6    
30.1    
30.5    
31.0    
31.4    
31.9    
32.3    
32.7    
33.2    
33.6    
34.1    
34.5    
35.0    
35.4    
35.8    
36.3    
36.7    
37.2    
37.6    
38.1    
38.5    
38.9    
39.4    
39.8    
40.3    
40.7    
41.2    
41.6    
42.0    
42.5    
42.9    
43.4    
43.8    
44.2    
44.7    
45.1    
45.6    
46.0    
46.5    
46.9    
47.3    
47.8    
48.2    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.8    
52.2    
52.7    
53.1    
53.5    
54.0    
54.4    
54.9    
55.3    
55.8    
56.2    
56.6    
57.1    
57.5    
58.0    
58.4    
58.8    
59.3    
59.7    
60.2    
60.6    
61.1    
61.5    
61.9    
62.4    
62.8    
63.3    
63.7    
64.2    
64.6    
65.0    
65.5    
65.9    
66.4    
66.8    
67.3    
67.7    
68.1    
68.6    
69.0    
69.5    
69.9    
70.4    
70.8    
71.2    
71.7    
72.1    
72.6    
73.0    
73.5    
73.9    
74.3    
74.8    
75.2    
75.7    
76.1    
76.5    
77.0    
77.4    
77.9    
78.3    
78.8    
79.2    
79.6    
80.1    
80.5    
81.0    
81.4    
81.9    
82.3    
82.7    
83.2    
83.6    
84.1    
84.5    
85.0    
85.4    
85.8    
86.3    
86.7    
87.2    
87.6    
88.1    
88.5    
88.9    
89.4    
89.8    
90.3    
90.7    
91.2    
91.6    
92.0    
92.5    
92.9    
93.4    
93.8    
94.2    
94.7    
95.1    
95.6    
96.0    
96.5    
96.9    
97.3    
97.8    
98.2    
98.7    
99.1    
99.6    
-found 24 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 180772, rend_intergenic: 180769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68642, rend_intergenic: 62863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183565, rend_intergenic: 178763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support