-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_4801037-5112074

-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.g11605.t1
Valid prediction for snap_scaffold_7-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_17358-T1
Valid prediction for CodingQuarry_transcript_57496-T1
Valid prediction for CodingQuarry_transcript_57497-T1
Valid prediction for GlimmerHMM_glimmerT_17359-T1
Valid prediction for snap_scaffold_7-snap.1092-T1
Valid prediction for snap_scaffold_7-snap.1065-T1
Couldn't classify 303578, 303612
Sorry, prediction pasa_asmbl_49784.p1 fails validation.
(ATG)	 AT	301104-301287	GT	AGG
(GCA)	 AG	302876-302951	GT	AGG
(TAT)	 AG	303426-303493	GT	AGG
(TTG)	 AG	303578-303612	CT	ACC
-recovered pasa_asmbl_49784.p1, initial, 301104, 301287
-recovered pasa_asmbl_49784.p1, internal, 302876, 302951
-recovered pasa_asmbl_49784.p1, internal, 303426, 303493
Valid prediction for pasa_asmbl_49782.p1
Valid prediction for pasa_asmbl_49785.p1
Valid prediction for snap_scaffold_7-snap.1078-T1
Valid prediction for snap_scaffold_7-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_17375-T1
Valid prediction for snap_scaffold_7-snap.1081-T1
Valid prediction for snap_scaffold_7-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_17354-T1
Valid prediction for snap_scaffold_7-snap.1057-T1
Valid prediction for CodingQuarry_transcript_57499-T1
Valid prediction for HiQ_model.g11618.t1
Valid prediction for GlimmerHMM_glimmerT_17349-T1
Valid prediction for GlimmerHMM_glimmerT_17371-T1
Valid prediction for GlimmerHMM_glimmerT_17346-T1
Couldn't classify 108121, 108271
Sorry, prediction pasa_asmbl_49756.p1 fails validation.
(ATG)	 AC	99518-99558	GT	AGG
(GCT)	 AG	101313-107078	GT	AGG
(AGC)	 AG	108121-108271	TA	GGT
-recovered pasa_asmbl_49756.p1, initial, 99518, 99558
-recovered pasa_asmbl_49756.p1, internal, 101313, 107078
Valid prediction for GlimmerHMM_glimmerT_17355-T1
Valid prediction for snap_scaffold_7-snap.1073-T1
Valid prediction for snap_scaffold_7-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_17374-T1
Valid prediction for pasa_asmbl_49772.p1
Valid prediction for Augustus_model.g11615.t1
Valid prediction for Augustus_model.g11602.t1
Couldn't classify 114091, 115050
Sorry, prediction pasa_asmbl_49759.p1 fails validation.
(TGC)	 GG	114091-115050	TA	GGT
Valid prediction for Augustus_model.g11620.t1
Valid prediction for snap_scaffold_7-snap.1058-T1
Couldn't classify 284569, 284654
Sorry, prediction pasa_asmbl_49780.p1 fails validation.
(CTG)	 CT	284569-284654	GT	CTG
(AGA)	 AG	284771-284858	GT	AGG
(TAT)	 AG	285126-285302	GT	TGG
(CTA)	 AG	285480-285574	GT	ACG
(GCA)	 AG	285728-285815	GT	AGG
(TTG)	 AG	285919-286050	GT	AGG
(GCC)	 AG	286175-286252	GT	AGG
(AAC)	 AG	286351-286437	GT	AGG
(GTG)	 AG	286545-286613	GT	AGG
(GGT)	 AG	286702-287184	TT	AGT
-recovered pasa_asmbl_49780.p1, terminal, 286702, 287184
-recovered pasa_asmbl_49780.p1, internal, 284771, 284858
-recovered pasa_asmbl_49780.p1, internal, 285126, 285302
-recovered pasa_asmbl_49780.p1, internal, 285480, 285574
-recovered pasa_asmbl_49780.p1, internal, 285728, 285815
-recovered pasa_asmbl_49780.p1, internal, 285919, 286050
-recovered pasa_asmbl_49780.p1, internal, 286175, 286252
-recovered pasa_asmbl_49780.p1, internal, 286351, 286437
-recovered pasa_asmbl_49780.p1, internal, 286545, 286613
Valid prediction for snap_scaffold_7-snap.1076-T1
Valid prediction for Augustus_model.g11622.t1
Valid prediction for CodingQuarry_transcript_57498-T1
Valid prediction for GlimmerHMM_glimmerT_17368-T1
Valid prediction for pasa_asmbl_49749.p1
Valid prediction for snap_scaffold_7-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_17361-T1
Valid prediction for snap_scaffold_7-snap.1069-T1
Valid prediction for snap_scaffold_7-snap.1084-T1
Valid prediction for HiQ_model.g11604.t1
Valid prediction for HiQ_model.g11621.t1
Valid prediction for pasa_asmbl_49752.p1
Valid prediction for Augustus_model.g11612.t1
Valid prediction for snap_scaffold_7-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_17369-T1
Valid prediction for Augustus_model.g11609.t1
Couldn't classify 282614, 283258
Couldn't classify 283860, 284028
Sorry, prediction pasa_asmbl_50612.p1 fails validation.
(GCT)	 CA	282614-283258	GT	TTG
(CTA)	 AG	283457-283539	GT	AGG
(GTT)	 AG	283658-283771	GT	AAG
(AGA)	 AG	283860-284028	TA	GGT
-recovered pasa_asmbl_50612.p1, internal, 283457, 283539
-recovered pasa_asmbl_50612.p1, internal, 283658, 283771
Valid prediction for snap_scaffold_7-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_17360-T1
Valid prediction for snap_scaffold_7-snap.1052-T1
Valid prediction for snap_scaffold_7-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_17373-T1
Valid prediction for GlimmerHMM_glimmerT_17362-T1
Valid prediction for snap_scaffold_7-snap.1075-T1
Valid prediction for CodingQuarry_transcript_57501-T1
Valid prediction for Augustus_model.g11607.t1
Valid prediction for Augustus_model.g11616.t1
Valid prediction for GlimmerHMM_glimmerT_17356-T1
Valid prediction for GlimmerHMM_glimmerT_17352-T1
Valid prediction for GlimmerHMM_glimmerT_17348-T1
Valid prediction for Augustus_model.g11608.t1
Valid prediction for CodingQuarry_transcript_57502-T1
Valid prediction for snap_scaffold_7-snap.1087-T1
Valid prediction for snap_scaffold_7-snap.1061-T1
Valid prediction for CodingQuarry_transcript_57495-T1
Valid prediction for snap_scaffold_7-snap.1064-T1
Valid prediction for snap_scaffold_7-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_17366-T1
Valid prediction for snap_scaffold_7-snap.1094-T1
Valid prediction for snap_scaffold_7-snap.1072-T1
Valid prediction for snap_scaffold_7-snap.1060-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.g11613.t1
Valid prediction for snap_scaffold_7-snap.1055-T1
Valid prediction for Augustus_model.g11619.t1
Valid prediction for CodingQuarry_transcript_57500-T1
Valid prediction for snap_scaffold_7-snap.1067-T1
Valid prediction for CodingQuarry_transcript_57494-T1
Valid prediction for snap_scaffold_7-snap.1083-T1
Valid prediction for snap_scaffold_7-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_17357-T1
Valid prediction for snap_scaffold_7-snap.1056-T1
Valid prediction for snap_scaffold_7-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_17353-T1
Valid prediction for GlimmerHMM_glimmerT_17363-T1
Valid prediction for Augustus_model.g11606.t1
Valid prediction for pasa_asmbl_50870.p1
Valid prediction for Augustus_model.g11611.t1
Valid prediction for Augustus_model.g11598.t1
Valid prediction for snap_scaffold_7-snap.1079-T1
Valid prediction for Augustus_model.g11610.t1
Valid prediction for pasa_asmbl_50869.p1
Valid prediction for snap_scaffold_7-snap.1070-T1
Valid prediction for GlimmerHMM_glimmerT_17365-T1
Valid prediction for snap_scaffold_7-snap.1054-T1
Valid prediction for snap_scaffold_7-snap.1090-T1
Valid prediction for HiQ_model.g11617.t1
Valid prediction for CodingQuarry_transcript_57493-T1
Valid prediction for GlimmerHMM_glimmerT_17350-T1
Valid prediction for snap_scaffold_7-snap.1063-T1
Couldn't classify 197460, 197795
Sorry, prediction pasa_asmbl_49758.p1 fails validation.
(TTC)	 GT	197460-197795	TC	CCT
Valid prediction for GlimmerHMM_glimmerT_17347-T1
Valid prediction for Augustus_model.g11600.t1
Valid prediction for GlimmerHMM_glimmerT_17370-T1
Valid prediction for Augustus_model.g11603.t1
Valid prediction for GlimmerHMM_glimmerT_17372-T1
Valid prediction for snap_scaffold_7-snap.1077-T1
Valid prediction for GlimmerHMM_glimmerT_17351-T1
Valid prediction for Augustus_model.g11599.t1
Valid prediction for snap_scaffold_7-snap.1085-T1
Valid prediction for pasa_asmbl_50868.p1
Valid prediction for snap_scaffold_7-snap.1071-T1
Valid prediction for snap_scaffold_7-snap.1053-T1
Valid prediction for Augustus_model.g11614.t1
Valid prediction for HiQ_model.g11601.t1
Valid prediction for GlimmerHMM_glimmerT_17364-T1
Valid prediction for GlimmerHMM_glimmerT_17367-T1
Valid prediction for snap_scaffold_7-snap.1086-T1
Valid prediction for Augustus_model.g11597.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 123271, rend_intergenic: 122757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245906, rend_intergenic: 235352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250847, rend_intergenic: 246528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 311038
-exon list size: 376


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.6    
2.9    
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3.7    
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4.5    
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5.6    
5.8    
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6.3    
6.6    
6.9    
7.1    
7.4    
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7.9    
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9.0    
9.3    
9.5    
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10.1    
10.3    
10.6    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
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14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
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16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
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21.4    
21.7    
22.0    
22.2    
22.5    
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23.3    
23.5    
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24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 123271, rend_intergenic: 122757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245906, rend_intergenic: 235352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250847, rend_intergenic: 246528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 48324
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 1 - 12982
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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
	-no exons in range 1 - 10956

-building DP trellis

-building trellis in range 13020 - 48324
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 13020 - 40828