-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_6123783-6357845

-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_12-snap.1214-T1
Valid prediction for GeneMark_model.51919_t
Valid prediction for GeneMark_model.51927_t
Valid prediction for GeneMark_model.51923_t
Valid prediction for GeneMark_model.51915_t
Valid prediction for snap_scaffold_12-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_30039-T1
Valid prediction for snap_scaffold_12-snap.1184-T1
Valid prediction for GeneMark_model.51904_t
Valid prediction for GeneMark_model.51954_t
Valid prediction for GeneMark_model.51921_t
Valid prediction for Augustus_model.g19994.t1
Valid prediction for snap_scaffold_12-snap.1216-T1
Valid prediction for GeneMark_model.51925_t
Valid prediction for GeneMark_model.51950_t
Valid prediction for snap_scaffold_12-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_30043-T1
Valid prediction for GlimmerHMM_glimmerT_30051-T1
Valid prediction for GeneMark_model.51952_t
Valid prediction for snap_scaffold_12-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_30050-T1
Valid prediction for snap_scaffold_12-snap.1194-T1
Valid prediction for Augustus_model.g19996.t1
Valid prediction for GeneMark_model.51918_t
Valid prediction for snap_scaffold_12-snap.1189-T1
Valid prediction for snap_scaffold_12-snap.1207-T1
Valid prediction for GeneMark_model.51916_t
Valid prediction for GeneMark_model.51946_t
Valid prediction for Augustus_model.g19992.t1
Valid prediction for snap_scaffold_12-snap.1182-T1
Valid prediction for snap_scaffold_12-snap.1222-T1
Valid prediction for snap_scaffold_12-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_30038-T1
Valid prediction for GeneMark_model.51939_t
Valid prediction for GeneMark_model.51929_t
Valid prediction for Augustus_model.g19995.t1
Valid prediction for snap_scaffold_12-snap.1213-T1
Valid prediction for Augustus_model.g19991.t1
Valid prediction for snap_scaffold_12-snap.1183-T1
Valid prediction for GeneMark_model.51932_t
Valid prediction for GlimmerHMM_glimmerT_30054-T1
Valid prediction for GeneMark_model.51934_t
Valid prediction for snap_scaffold_12-snap.1204-T1
Valid prediction for GlimmerHMM_glimmerT_30056-T1
Valid prediction for snap_scaffold_12-snap.1220-T1
Valid prediction for GeneMark_model.51906_t
Valid prediction for GeneMark_model.51951_t
Valid prediction for snap_scaffold_12-snap.1196-T1
Valid prediction for GeneMark_model.51944_t
Valid prediction for GeneMark_model.51928_t
Valid prediction for Augustus_model.g19990.t1
Valid prediction for GlimmerHMM_glimmerT_30049-T1
Valid prediction for Augustus_model.g19993.t1
Valid prediction for GlimmerHMM_glimmerT_30052-T1
Couldn't classify 73310, 73336
Couldn't classify 77077, 77249
Sorry, prediction pasa_asmbl_8627.p1 fails validation.
(GAG)	 AC	73310-73336	GT	CTG
(GTG)	 AG	74014-74085	GT	AGG
(TTT)	 AG	74300-74448	GT	ATG
(GTG)	 AG	74840-74933	GT	TGG
(TCG)	 AG	75064-75180	GT	AGG
(AGT)	 AG	75331-75501	GT	AGG
(GAC)	 AG	75770-75848	GT	GGG
(GGA)	 AG	76071-76183	GT	AGG
(GGC)	 AG	76477-76563	GT	AGG
(GAA)	 AG	76673-76892	GT	AGG
(GCA)	 AG	77077-77249	GG	GGG
-recovered pasa_asmbl_8627.p1, internal, 74014, 74085
-recovered pasa_asmbl_8627.p1, internal, 74300, 74448
-recovered pasa_asmbl_8627.p1, internal, 74840, 74933
-recovered pasa_asmbl_8627.p1, internal, 75064, 75180
-recovered pasa_asmbl_8627.p1, internal, 75331, 75501
-recovered pasa_asmbl_8627.p1, internal, 75770, 75848
-recovered pasa_asmbl_8627.p1, internal, 76071, 76183
-recovered pasa_asmbl_8627.p1, internal, 76477, 76563
-recovered pasa_asmbl_8627.p1, internal, 76673, 76892
Valid prediction for GeneMark_model.51937_t
Valid prediction for snap_scaffold_12-snap.1210-T1
Valid prediction for snap_scaffold_12-snap.1200-T1
Valid prediction for GeneMark_model.51902_t
Valid prediction for GlimmerHMM_glimmerT_30035-T1
Valid prediction for GlimmerHMM_glimmerT_30045-T1
Valid prediction for GeneMark_model.51910_t
Valid prediction for GeneMark_model.51908_t
Valid prediction for Augustus_model.g19987.t1
Valid prediction for GlimmerHMM_glimmerT_30032-T1
Valid prediction for snap_scaffold_12-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_30040-T1
Valid prediction for GeneMark_model.51948_t
Valid prediction for snap_scaffold_12-snap.1219-T1
Valid prediction for GeneMark_model.51942_t
Valid prediction for snap_scaffold_12-snap.1202-T1
Valid prediction for snap_scaffold_12-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_30055-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 GeneMark_model.51900_t
Valid prediction for GlimmerHMM_glimmerT_30044-T1
Valid prediction for snap_scaffold_12-snap.1218-T1
Valid prediction for GeneMark_model.51901_t
Valid prediction for GlimmerHMM_glimmerT_30041-T1
Valid prediction for Augustus_model.g19989.t1
Valid prediction for GlimmerHMM_glimmerT_30036-T1
Valid prediction for snap_scaffold_12-snap.1209-T1
Valid prediction for GeneMark_model.51945_t
Valid prediction for GeneMark_model.51947_t
Valid prediction for snap_scaffold_12-snap.1223-T1
Valid prediction for GeneMark_model.51922_t
Valid prediction for GeneMark_model.51953_t
Valid prediction for snap_scaffold_12-snap.1195-T1
Valid prediction for GlimmerHMM_glimmerT_30047-T1
Valid prediction for GeneMark_model.51938_t
Valid prediction for GlimmerHMM_glimmerT_30037-T1
Valid prediction for GeneMark_model.51931_t
Valid prediction for GeneMark_model.51933_t
Valid prediction for GeneMark_model.51943_t
Valid prediction for GlimmerHMM_glimmerT_30034-T1
Valid prediction for GlimmerHMM_glimmerT_30046-T1
Valid prediction for GeneMark_model.51917_t
Valid prediction for GeneMark_model.51907_t
Valid prediction for snap_scaffold_12-snap.1208-T1
Valid prediction for GlimmerHMM_glimmerT_30053-T1
Valid prediction for snap_scaffold_12-snap.1215-T1
Valid prediction for snap_scaffold_12-snap.1181-T1
Valid prediction for GeneMark_model.51926_t
Valid prediction for GeneMark_model.51903_t
Valid prediction for GeneMark_model.51949_t
Valid prediction for snap_scaffold_12-snap.1187-T1
Valid prediction for snap_scaffold_12-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_30048-T1
Valid prediction for snap_scaffold_12-snap.1191-T1
Valid prediction for snap_scaffold_12-snap.1212-T1
Valid prediction for snap_scaffold_12-snap.1211-T1
Valid prediction for GeneMark_model.51940_t
Valid prediction for snap_scaffold_12-snap.1201-T1
Valid prediction for snap_scaffold_12-snap.1205-T1
Valid prediction for GeneMark_model.51905_t
Valid prediction for GeneMark_model.51913_t
Valid prediction for GeneMark_model.51911_t
Valid prediction for GeneMark_model.51924_t
Valid prediction for GeneMark_model.51912_t
Valid prediction for Augustus_model.g19986.t1
Valid prediction for GeneMark_model.51909_t
Valid prediction for snap_scaffold_12-snap.1217-T1
Valid prediction for GeneMark_model.51930_t
Valid prediction for GlimmerHMM_glimmerT_30033-T1
Valid prediction for snap_scaffold_12-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_30042-T1
Valid prediction for Augustus_model.g19988.t1
Valid prediction for GeneMark_model.51936_t
Valid prediction for snap_scaffold_12-snap.1188-T1
Valid prediction for snap_scaffold_12-snap.1197-T1
Couldn't classify 54026, 54044
Sorry, prediction GeneMark_model.51941_t fails validation.
(GCA)	 AG	54026-54044	GT	GAG
(GCT)	 AG	55359-55384	GT	AGG
(TCT)	 AG	55469-55522	GT	CAG
(ACC)	 AG	55793-55995	GT	CTG
(GCA)	 AG	56244-56255	GT	CGG
(CTG)	 AG	56755-56870	GA	GAG
-recovered GeneMark_model.51941_t, terminal, 56755, 56870
-recovered GeneMark_model.51941_t, internal, 54026, 54044
-recovered GeneMark_model.51941_t, internal, 55359, 55384
-recovered GeneMark_model.51941_t, internal, 55469, 55522
-recovered GeneMark_model.51941_t, internal, 55793, 55995
-recovered GeneMark_model.51941_t, internal, 56244, 56255
Valid prediction for GeneMark_model.51914_t
Valid prediction for snap_scaffold_12-snap.1198-T1
Valid prediction for snap_scaffold_12-snap.1203-T1
Valid prediction for GeneMark_model.51920_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 94498, rend_intergenic: 92190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101931, rend_intergenic: 100274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104417, rend_intergenic: 102370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115729, rend_intergenic: 112434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116935, rend_intergenic: 116045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131499, rend_intergenic: 121344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141062, rend_intergenic: 132855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144081, rend_intergenic: 141340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147692, rend_intergenic: 144773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157355, rend_intergenic: 149597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162790, rend_intergenic: 158071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170365, rend_intergenic: 163614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182335, rend_intergenic: 171111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185852, rend_intergenic: 183011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193004, rend_intergenic: 186340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202036, rend_intergenic: 194348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234063
-exon list size: 597


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 94498, rend_intergenic: 92190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101931, rend_intergenic: 100274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104417, rend_intergenic: 102370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115729, rend_intergenic: 112434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116935, rend_intergenic: 116045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131499, rend_intergenic: 121344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141062, rend_intergenic: 132855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144081, rend_intergenic: 141340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147692, rend_intergenic: 144773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157355, rend_intergenic: 149597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162790, rend_intergenic: 158071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170365, rend_intergenic: 163614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182335, rend_intergenic: 171111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185852, rend_intergenic: 183011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193004, rend_intergenic: 186340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202036, rend_intergenic: 194348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 41073
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-found 2 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 - 37180
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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

-building DP trellis

-building trellis in range 1 - 35221
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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

-building DP trellis

-building trellis in range 1 - 24774
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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

-building DP trellis

-building trellis in range 1 - 21847
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 1 - 13289

-building DP trellis

-building trellis in range 24782 - 35221
-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

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