-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_2061122-2212143

-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.509-T1
Valid prediction for GlimmerHMM_glimmerT_16985-T1
Valid prediction for snap_scaffold_7-snap.503-T1
Valid prediction for snap_scaffold_7-snap.487-T1
Valid prediction for snap_scaffold_7-snap.514-T1
Valid prediction for HiQ_model.g11334.t1
Valid prediction for snap_scaffold_7-snap.506-T1
Valid prediction for snap_scaffold_7-snap.490-T1
Valid prediction for snap_scaffold_7-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_16996-T1
Valid prediction for Augustus_model.g11336.t1
Valid prediction for snap_scaffold_7-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_16993-T1
Valid prediction for Augustus_model.g11325.t1
Couldn't classify 94885, 95007
Couldn't classify 97796, 97846
Sorry, prediction pasa_asmbl_49627.p1 fails validation.
(CTG)	 GG	94885-95007	GT	AGG
(GTG)	 AG	95477-95752	GT	ATG
(GTG)	 AG	96301-96381	GT	AGG
(TGC)	 AG	97276-97416	GT	AGG
(GGG)	 AG	97796-97846	AC	ACA
-recovered pasa_asmbl_49627.p1, internal, 95477, 95752
-recovered pasa_asmbl_49627.p1, internal, 96301, 96381
-recovered pasa_asmbl_49627.p1, internal, 97276, 97416
Valid prediction for snap_scaffold_7-snap.507-T1
Valid prediction for Augustus_model.g11335.t1
Valid prediction for GlimmerHMM_glimmerT_16990-T1
Valid prediction for GlimmerHMM_glimmerT_16995-T1
Valid prediction for snap_scaffold_7-snap.492-T1
Valid prediction for Augustus_model.g11327.t1
Valid prediction for snap_scaffold_7-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_16982-T1
Valid prediction for Augustus_model.g11329.t1
Valid prediction for GlimmerHMM_glimmerT_16983-T1
Valid prediction for GlimmerHMM_glimmerT_16978-T1
Valid prediction for snap_scaffold_7-snap.500-T1
Valid prediction for snap_scaffold_7-snap.502-T1
Valid prediction for Augustus_model.g11324.t1
Valid prediction for snap_scaffold_7-snap.496-T1
Valid prediction for snap_scaffold_7-snap.498-T1
Valid prediction for Augustus_model.g11326.t1
Valid prediction for snap_scaffold_7-snap.519-T1
Valid prediction for snap_scaffold_7-snap.495-T1
Valid prediction for snap_scaffold_7-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_16977-T1
Valid prediction for snap_scaffold_7-snap.520-T1
Valid prediction for GlimmerHMM_glimmerT_16987-T1
Valid prediction for Augustus_model.g11337.t1
Valid prediction for GlimmerHMM_glimmerT_16989-T1
Valid prediction for GlimmerHMM_glimmerT_16994-T1
Valid prediction for GlimmerHMM_glimmerT_16992-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.g11331.t1
Valid prediction for Augustus_model.g11333.t1
Valid prediction for snap_scaffold_7-snap.511-T1
Valid prediction for snap_scaffold_7-snap.488-T1
Valid prediction for snap_scaffold_7-snap.521-T1
Valid prediction for snap_scaffold_7-snap.486-T1
Valid prediction for snap_scaffold_7-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_16986-T1
Valid prediction for GlimmerHMM_glimmerT_16979-T1
Valid prediction for snap_scaffold_7-snap.516-T1
Couldn't classify 72242, 72304
Sorry, prediction pasa_asmbl_50750.p1 fails validation.
(ATG)	 AG	69181-69246	GT	TGG
(GTG)	 AG	70463-70639	GT	AGG
(GAT)	 AG	72242-72304	AG	ACA
-recovered pasa_asmbl_50750.p1, initial, 69181, 69246
-recovered pasa_asmbl_50750.p1, internal, 69181, 69246
-recovered pasa_asmbl_50750.p1, internal, 70463, 70639
Valid prediction for GlimmerHMM_glimmerT_16991-T1
Couldn't classify 108345, 108440
Couldn't classify 109871, 109978
Sorry, prediction pasa_asmbl_50749.p2 fails validation.
(CTG)	 CT	108345-108440	GT	AGG
(CTG)	 AG	108707-108856	GT	AGG
(ACG)	 AG	109871-109978	CA	GGC
-recovered pasa_asmbl_50749.p2, internal, 108707, 108856
Valid prediction for snap_scaffold_7-snap.508-T1
Valid prediction for snap_scaffold_7-snap.513-T1
Valid prediction for snap_scaffold_7-snap.518-T1
Valid prediction for GlimmerHMM_glimmerT_16997-T1
Valid prediction for GlimmerHMM_glimmerT_16981-T1
Valid prediction for snap_scaffold_7-snap.505-T1
Valid prediction for Augustus_model.g11328.t1
Valid prediction for snap_scaffold_7-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_16980-T1
Valid prediction for snap_scaffold_7-snap.510-T1
Valid prediction for Augustus_model.g11332.t1
Valid prediction for GlimmerHMM_glimmerT_16988-T1
Valid prediction for snap_scaffold_7-snap.485-T1
Valid prediction for snap_scaffold_7-snap.494-T1
Valid prediction for Augustus_model.g11338.t1
Valid prediction for GlimmerHMM_glimmerT_16984-T1
Valid prediction for snap_scaffold_7-snap.493-T1
Valid prediction for snap_scaffold_7-snap.517-T1
Valid prediction for snap_scaffold_7-snap.515-T1
Valid prediction for snap_scaffold_7-snap.489-T1
Valid prediction for Augustus_model.g11330.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9888, rend_intergenic: 6734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67097, rend_intergenic: 48663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67938, rend_intergenic: 67397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71269, rend_intergenic: 69194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75291, rend_intergenic: 72386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80537, rend_intergenic: 75814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91264, rend_intergenic: 89204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101000, rend_intergenic: 99319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111689, rend_intergenic: 110577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129472, rend_intergenic: 111722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137265, rend_intergenic: 133161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143202, rend_intergenic: 137888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151022
-exon list size: 285


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.3    
6.6    
7.0    
7.3    
7.7    
8.0    
8.4    
8.7    
9.1    
9.4    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.3    
14.6    
15.0    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.8    
19.2    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.8    
27.2    
27.5    
27.9    
28.2    
28.6    
28.9    
29.3    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.9    
36.2    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.5    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.5    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.8    
64.1    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.7    
71.1    
71.4    
71.8    
72.1    
72.5    
72.8    
73.2    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.0    
85.4    
85.7    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.6    
90.9    
91.3    
91.6    
92.0    
92.3    
92.7    
93.0    
93.4    
93.7    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9888, rend_intergenic: 6734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67097, rend_intergenic: 48663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67938, rend_intergenic: 67397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71269, rend_intergenic: 69194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75291, rend_intergenic: 72386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80537, rend_intergenic: 75814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91264, rend_intergenic: 89204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101000, rend_intergenic: 99319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111689, rend_intergenic: 110577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129472, rend_intergenic: 111722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137265, rend_intergenic: 133161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143202, rend_intergenic: 137888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 138140 - 151022
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 138140 - 149692
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support