-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_9843700-10161135

-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.g3011.t1
Valid prediction for CodingQuarry_transcript_28601-T1
Valid prediction for GlimmerHMM_glimmerT_4489-T1
Valid prediction for CodingQuarry_transcript_28603-T1
Valid prediction for GeneMark_model.7186_t
Valid prediction for GlimmerHMM_glimmerT_4468-T1
Valid prediction for Augustus_model.g3006.t1
Valid prediction for GeneMark_model.7179_t
Valid prediction for snap_scaffold_2-snap.1994-T1
Valid prediction for GeneMark_model.7173_t
Valid prediction for snap_scaffold_2-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_4470-T1
Valid prediction for snap_scaffold_2-snap.1983-T1
Valid prediction for snap_scaffold_2-snap.2016-T1
Valid prediction for snap_scaffold_2-snap.2004-T1
Valid prediction for GlimmerHMM_glimmerT_4488-T1
Valid prediction for CodingQuarry_transcript_28602-T1
Valid prediction for snap_scaffold_2-snap.2020-T1
Valid prediction for GeneMark_model.7184_t
Valid prediction for snap_scaffold_2-snap.1992-T1
Valid prediction for snap_scaffold_2-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_4476-T1
Valid prediction for snap_scaffold_2-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_4492-T1
Valid prediction for pasa_asmbl_24733.p1
Valid prediction for GeneMark_model.7185_t
Valid prediction for GlimmerHMM_glimmerT_4462-T1
Valid prediction for snap_scaffold_2-snap.1988-T1
Valid prediction for snap_scaffold_2-snap.1993-T1
Valid prediction for GeneMark_model.7168_t
Valid prediction for snap_scaffold_2-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_4486-T1
Valid prediction for snap_scaffold_2-snap.2015-T1
Valid prediction for GeneMark_model.7180_t
Valid prediction for GeneMark_model.7172_t
Valid prediction for Augustus_model.g3009.t1
Valid prediction for pasa_asmbl_24731.p1
Valid prediction for GeneMark_model.7169_t
Valid prediction for Augustus_model.g3008.t1
Valid prediction for GeneMark_model.7175_t
Valid prediction for snap_scaffold_2-snap.2005-T1
Valid prediction for CodingQuarry_transcript_28600-T1
Valid prediction for Augustus_model.g3012.t1
Valid prediction for GlimmerHMM_glimmerT_4487-T1
Valid prediction for snap_scaffold_2-snap.2003-T1
Couldn't classify 60658, 60814
Couldn't classify 61651, 61710
Sorry, prediction pasa_asmbl_24728.p1 fails validation.
(GCC)	 AC	60658-60814	GT	AGG
(GTG)	 AG	60909-61036	GT	AAG
(GCG)	 AG	61155-61373	GT	AGG
(ATG)	 AG	61651-61710	AG	GGA
-recovered pasa_asmbl_24728.p1, internal, 60909, 61036
-recovered pasa_asmbl_24728.p1, internal, 61155, 61373
Valid prediction for snap_scaffold_2-snap.1982-T1
Valid prediction for Augustus_model.g3003.t1
Valid prediction for GlimmerHMM_glimmerT_4490-T1
Valid prediction for snap_scaffold_2-snap.1989-T1
Valid prediction for Augustus_model.g3013.t1
Valid prediction for Augustus_model.g3004.t1
Valid prediction for HiQ_model.g3010.t1
Valid prediction for GeneMark_model.7164_t
Valid prediction for Augustus_model.g2999.t1
Valid prediction for snap_scaffold_2-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_4482-T1
Valid prediction for GeneMark_model.7182_t
Valid prediction for GeneMark_model.7166_t
Valid prediction for snap_scaffold_2-snap.2017-T1
Valid prediction for snap_scaffold_2-snap.2009-T1
Valid prediction for snap_scaffold_2-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_4481-T1
Valid prediction for GlimmerHMM_glimmerT_4478-T1
Valid prediction for GlimmerHMM_glimmerT_4471-T1
Valid prediction for GeneMark_model.7183_t
Valid prediction for snap_scaffold_2-snap.2006-T1
Couldn't classify 65363, 65438
Sorry, prediction pasa_asmbl_24729.p1 fails validation.
(TGC)	 CG	65363-65438	GT	AGG
(ACC)	 AG	65677-65777	GT	AGG
(GTG)	 AG	65891-66094	GT	AGG
(TTT)	 AG	66671-66867	GT	AAG
(CAA)	 AG	66991-67057	GT	AGG
(GAG)	 AG	67240-67430	GT	CAG
(TTT)	 AG	67630-67782	GT	AGG
(CTC)	 AG	68122-68327	GT	AGG
(AGA)	 AG	68761-68829	GT	CGG
(AAG)	 AG	68936-69060	GT	GAG
add_exon() Sorry, pasa_asmbl_24729.p1 68122-68327-terminal-2 is invalid.
-recovered pasa_asmbl_24729.p1, terminal, 68122, 68327
-recovered pasa_asmbl_24729.p1, terminal, 68936, 69060
-recovered pasa_asmbl_24729.p1, internal, 65677, 65777
-recovered pasa_asmbl_24729.p1, internal, 65891, 66094
-recovered pasa_asmbl_24729.p1, internal, 66671, 66867
-recovered pasa_asmbl_24729.p1, internal, 66991, 67057
-recovered pasa_asmbl_24729.p1, internal, 67240, 67430
-recovered pasa_asmbl_24729.p1, internal, 67630, 67782
-recovered pasa_asmbl_24729.p1, internal, 68122, 68327
-recovered pasa_asmbl_24729.p1, internal, 68761, 68829
-recovered pasa_asmbl_24729.p1, internal, 68936, 69060
Valid prediction for snap_scaffold_2-snap.2018-T1
Valid prediction for GeneMark_model.7177_t
Valid prediction for GlimmerHMM_glimmerT_4466-T1
Valid prediction for GlimmerHMM_glimmerT_4469-T1
Valid prediction for GlimmerHMM_glimmerT_4474-T1
Valid prediction for GlimmerHMM_glimmerT_4484-T1
Valid prediction for Augustus_model.g3002.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 GlimmerHMM_glimmerT_4467-T1
Valid prediction for GlimmerHMM_glimmerT_4483-T1
Valid prediction for GeneMark_model.7171_t
Valid prediction for GlimmerHMM_glimmerT_4465-T1
Valid prediction for snap_scaffold_2-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_4473-T1
Valid prediction for GlimmerHMM_glimmerT_4464-T1
Valid prediction for snap_scaffold_2-snap.1995-T1
Valid prediction for GeneMark_model.7163_t
Valid prediction for GlimmerHMM_glimmerT_4480-T1
Valid prediction for snap_scaffold_2-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_4475-T1
Valid prediction for snap_scaffold_2-snap.2011-T1
Valid prediction for GeneMark_model.7167_t
Valid prediction for GeneMark_model.7165_t
Valid prediction for snap_scaffold_2-snap.1987-T1
Valid prediction for snap_scaffold_2-snap.2014-T1
Valid prediction for snap_scaffold_2-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_4477-T1
Valid prediction for GlimmerHMM_glimmerT_4463-T1
Valid prediction for HiQ_model.g2998.t1
Valid prediction for snap_scaffold_2-snap.2008-T1
Valid prediction for snap_scaffold_2-snap.1986-T1
Valid prediction for snap_scaffold_2-snap.2007-T1
Valid prediction for GeneMark_model.7174_t
Valid prediction for pasa_asmbl_23414.p1
Valid prediction for GlimmerHMM_glimmerT_4461-T1
Valid prediction for Augustus_model.g3000.t1
Valid prediction for GeneMark_model.7178_t
Valid prediction for GeneMark_model.7176_t
Couldn't classify 295165, 295206
Couldn't classify 300437, 300572
Sorry, prediction pasa_asmbl_23409.p1 fails validation.
(CGC)	 CT	295165-295206	GT	AAG
(GGT)	 AG	295502-295667	GT	AGG
(AGA)	 AG	297320-297377	GT	AAG
(CTC)	 AG	297683-297737	GT	AGG
(GCT)	 AG	297829-298028	GT	ATG
(TTC)	 AG	298793-298900	GT	CAG
(AGG)	 AG	300437-300572	GG	AAG
-recovered pasa_asmbl_23409.p1, internal, 295502, 295667
-recovered pasa_asmbl_23409.p1, internal, 297320, 297377
-recovered pasa_asmbl_23409.p1, internal, 297683, 297737
-recovered pasa_asmbl_23409.p1, internal, 297829, 298028
-recovered pasa_asmbl_23409.p1, internal, 298793, 298900
Valid prediction for snap_scaffold_2-snap.2021-T1
Valid prediction for GeneMark_model.7187_t
Valid prediction for snap_scaffold_2-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_4472-T1
Valid prediction for CodingQuarry_transcript_28599-T1
Valid prediction for GlimmerHMM_glimmerT_4479-T1
Valid prediction for GeneMark_model.7181_t
Valid prediction for snap_scaffold_2-snap.1984-T1
Couldn't classify 300775, 300938
Sorry, prediction pasa_asmbl_23408.p1 fails validation.
(AAG)	 GC	300775-300938	GT	TCG
(GTC)	 AG	301156-301320	GT	AGG
(GTT)	 AG	301612-301729	GT	AGG
(ATG)	 AG	301928-302098	GT	AGG
(CAA)	 AG	302553-302752	GT	GAG
(TGA)	 AG	303026-303113	AA	GAA
-recovered pasa_asmbl_23408.p1, initial, 301928, 302098
-recovered pasa_asmbl_23408.p1, terminal, 303026, 303113
-recovered pasa_asmbl_23408.p1, internal, 301156, 301320
-recovered pasa_asmbl_23408.p1, internal, 301612, 301729
-recovered pasa_asmbl_23408.p1, internal, 301928, 302098
-recovered pasa_asmbl_23408.p1, internal, 302553, 302752
Valid prediction for Augustus_model.g3001.t1
Couldn't classify 285718, 285897
Couldn't classify 294420, 294516
Sorry, prediction pasa_asmbl_23412.p1 fails validation.
(GGC)	 CG	285718-285897	GT	AGG
(CTG)	 AG	287179-287328	GT	AGG
(ATG)	 AG	287571-287702	GT	ATG
(CAA)	 AG	288060-288230	GT	TGG
(CTT)	 AG	288674-288789	GT	AGG
(CCA)	 AG	288903-289098	GT	CGG
(GGC)	 AG	289456-289645	GT	TGG
(GAG)	 AG	289859-289922	GT	AGG
(GGC)	 AG	290147-290350	GT	AGG
(TAG)	 AG	292047-292137	GT	CGG
(GAG)	 AG	292224-292338	GT	AGG
(AGA)	 AG	292569-292757	GT	GGG
(GCT)	 AG	292999-293198	GT	AGG
(GTG)	 AG	293483-293590	GT	AGG
(CAC)	 AG	293840-293908	GT	AGG
(GTG)	 AG	294028-294176	GT	AGG
(GCA)	 AG	294420-294516	AG	AGA
-recovered pasa_asmbl_23412.p1, initial, 287571, 287702
-recovered pasa_asmbl_23412.p1, internal, 287179, 287328
-recovered pasa_asmbl_23412.p1, internal, 287571, 287702
-recovered pasa_asmbl_23412.p1, internal, 288060, 288230
-recovered pasa_asmbl_23412.p1, internal, 288674, 288789
-recovered pasa_asmbl_23412.p1, internal, 288903, 289098
-recovered pasa_asmbl_23412.p1, internal, 289456, 289645
-recovered pasa_asmbl_23412.p1, internal, 289859, 289922
-recovered pasa_asmbl_23412.p1, internal, 290147, 290350
-recovered pasa_asmbl_23412.p1, internal, 292047, 292137
-recovered pasa_asmbl_23412.p1, internal, 292224, 292338
-recovered pasa_asmbl_23412.p1, internal, 292569, 292757
-recovered pasa_asmbl_23412.p1, internal, 292999, 293198
-recovered pasa_asmbl_23412.p1, internal, 293483, 293590
-recovered pasa_asmbl_23412.p1, internal, 293840, 293908
-recovered pasa_asmbl_23412.p1, internal, 294028, 294176
Valid prediction for snap_scaffold_2-snap.1997-T1
Couldn't classify 166471, 166773
Sorry, prediction pasa_asmbl_23419.p1 fails validation.
(GTT)	 AT	166471-166773	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_4485-T1
Valid prediction for Augustus_model.g2997.t1
Valid prediction for Augustus_model.g3005.t1
Valid prediction for Augustus_model.g3007.t1
Valid prediction for snap_scaffold_2-snap.1998-T1
Valid prediction for snap_scaffold_2-snap.1991-T1
Valid prediction for snap_scaffold_2-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_4491-T1
Valid prediction for snap_scaffold_2-snap.2001-T1
Valid prediction for GeneMark_model.7170_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30394, rend_intergenic: 26110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33805, rend_intergenic: 31492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83862, rend_intergenic: 81112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95452, rend_intergenic: 93474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276477, rend_intergenic: 270077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307617, rend_intergenic: 303344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 311590, rend_intergenic: 309301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315137, rend_intergenic: 312018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 317436
-exon list size: 588


building trellis

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89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 30394, rend_intergenic: 26110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33805, rend_intergenic: 31492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83862, rend_intergenic: 81112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95452, rend_intergenic: 93474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276477, rend_intergenic: 270077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307617, rend_intergenic: 303344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 311590, rend_intergenic: 309301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315137, rend_intergenic: 312018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support