-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_3480213-3676472

-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_5-snap.716-T1
Valid prediction for Augustus_model.g7865.t1
Valid prediction for CodingQuarry_transcript_51884-T1
Valid prediction for GlimmerHMM_glimmerT_11974-T1
Valid prediction for snap_scaffold_5-snap.681-T1
Valid prediction for GeneMark_model.20143_t
Valid prediction for GlimmerHMM_glimmerT_11952-T1
Valid prediction for snap_scaffold_5-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_11956-T1
Valid prediction for GeneMark_model.20155_t
Valid prediction for snap_scaffold_5-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_11959-T1
Valid prediction for GeneMark_model.20151_t
Valid prediction for GeneMark_model.20190_t
Valid prediction for GlimmerHMM_glimmerT_11958-T1
Valid prediction for GeneMark_model.20175_t
Valid prediction for Augustus_model.g7868.t1
Valid prediction for snap_scaffold_5-snap.710-T1
Valid prediction for Augustus_model.g7854.t1
Valid prediction for snap_scaffold_5-snap.680-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.20157_t
Valid prediction for snap_scaffold_5-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_11967-T1
Valid prediction for GlimmerHMM_glimmerT_11946-T1
Valid prediction for HiQ_model.g7856.t1
Valid prediction for snap_scaffold_5-snap.687-T1
Valid prediction for snap_scaffold_5-snap.718-T1
Valid prediction for snap_scaffold_5-snap.705-T1
Valid prediction for GeneMark_model.20148_t
Valid prediction for snap_scaffold_5-snap.723-T1
Valid prediction for snap_scaffold_5-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_11950-T1
Valid prediction for snap_scaffold_5-snap.700-T1
Valid prediction for snap_scaffold_5-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_11947-T1
Valid prediction for Augustus_model.g7864.t1
Valid prediction for snap_scaffold_5-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_11969-T1
Valid prediction for HiQ_model.g7851.t1
Valid prediction for snap_scaffold_5-snap.688-T1
Valid prediction for GeneMark_model.20173_t
Couldn't classify 139380, 139827
Sorry, prediction pasa_asmbl_43891.p1 fails validation.
(ACC)	 GT	139380-139827	GT	GGG
(CTG)	 AG	140105-140216	GT	TCG
(CCC)	 AG	142314-142320	GG	GAG
-recovered pasa_asmbl_43891.p1, terminal, 142314, 142320
-recovered pasa_asmbl_43891.p1, internal, 140105, 140216
Valid prediction for GeneMark_model.20145_t
Valid prediction for Augustus_model.g7870.t1
Valid prediction for snap_scaffold_5-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_11971-T1
Valid prediction for snap_scaffold_5-snap.693-T1
Valid prediction for GeneMark_model.20185_t
Valid prediction for GeneMark_model.20153_t
Valid prediction for GeneMark_model.20181_t
Valid prediction for GeneMark_model.20179_t
Valid prediction for GeneMark_model.20162_t
Valid prediction for GlimmerHMM_glimmerT_11968-T1
Valid prediction for Augustus_model.g7871.t1
Valid prediction for GeneMark_model.20167_t
Valid prediction for GlimmerHMM_glimmerT_11965-T1
Valid prediction for GlimmerHMM_glimmerT_11966-T1
Valid prediction for GeneMark_model.20178_t
Valid prediction for CodingQuarry_transcript_51883-T1
Valid prediction for pasa_asmbl_43883.p1
Valid prediction for GeneMark_model.20182_t
Valid prediction for snap_scaffold_5-snap.698-T1
Valid prediction for Augustus_model.g7860.t1
Valid prediction for Augustus_model.g7866.t1
Valid prediction for GeneMark_model.20188_t
Valid prediction for GeneMark_model.20171_t
Valid prediction for GlimmerHMM_glimmerT_11973-T1
Couldn't classify 156614, 157942
Sorry, prediction pasa_asmbl_43898.p1 fails validation.
(AAG)	 CC	156614-157942	AG	GAA
Valid prediction for snap_scaffold_5-snap.685-T1
Couldn't classify 154226, 154789
Sorry, prediction pasa_asmbl_43896.p1 fails validation.
(CAT)	 GA	154226-154789	CC	CGC
Valid prediction for snap_scaffold_5-snap.721-T1
Valid prediction for Augustus_model.g7863.t1
Valid prediction for GlimmerHMM_glimmerT_11960-T1
Valid prediction for GeneMark_model.20161_t
Valid prediction for GlimmerHMM_glimmerT_11964-T1
Valid prediction for snap_scaffold_5-snap.706-T1
Valid prediction for snap_scaffold_5-snap.722-T1
Valid prediction for GeneMark_model.20183_t
Valid prediction for pasa_asmbl_43887.p1
Valid prediction for GlimmerHMM_glimmerT_11953-T1
Valid prediction for GeneMark_model.20165_t
Valid prediction for GlimmerHMM_glimmerT_11954-T1
Valid prediction for CodingQuarry_transcript_51882-T1
Valid prediction for snap_scaffold_5-snap.692-T1
Valid prediction for snap_scaffold_5-snap.696-T1
Valid prediction for Augustus_model.g7872.t1
Valid prediction for snap_scaffold_5-snap.725-T1
Valid prediction for snap_scaffold_5-snap.701-T1
Valid prediction for snap_scaffold_5-snap.711-T1
Valid prediction for GeneMark_model.20160_t
Valid prediction for Augustus_model.g7857.t1
Valid prediction for GlimmerHMM_glimmerT_11961-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 snap_scaffold_5-snap.689-T1
Valid prediction for GeneMark_model.20187_t
Valid prediction for snap_scaffold_5-snap.686-T1
Valid prediction for snap_scaffold_5-snap.678-T1
Valid prediction for GeneMark_model.20159_t
Valid prediction for snap_scaffold_5-snap.708-T1
Valid prediction for snap_scaffold_5-snap.717-T1
Valid prediction for GeneMark_model.20156_t
Valid prediction for snap_scaffold_5-snap.702-T1
Valid prediction for GeneMark_model.20150_t
Valid prediction for Augustus_model.g7859.t1
Valid prediction for snap_scaffold_5-snap.695-T1
Valid prediction for GeneMark_model.20149_t
Valid prediction for GlimmerHMM_glimmerT_11948-T1
Valid prediction for Augustus_model.g7867.t1
Valid prediction for GeneMark_model.20152_t
Valid prediction for snap_scaffold_5-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_11963-T1
Valid prediction for GlimmerHMM_glimmerT_11949-T1
Valid prediction for GlimmerHMM_glimmerT_11951-T1
Valid prediction for GeneMark_model.20154_t
Valid prediction for snap_scaffold_5-snap.724-T1
Valid prediction for snap_scaffold_5-snap.704-T1
Valid prediction for Augustus_model.g7869.t1
Valid prediction for snap_scaffold_5-snap.697-T1
Valid prediction for snap_scaffold_5-snap.709-T1
Valid prediction for Augustus_model.g7855.t1
Valid prediction for GeneMark_model.20164_t
Valid prediction for snap_scaffold_5-snap.715-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.694-T1
Valid prediction for GeneMark_model.20189_t
Valid prediction for GeneMark_model.20176_t
Valid prediction for GlimmerHMM_glimmerT_11955-T1
Valid prediction for snap_scaffold_5-snap.683-T1
Couldn't classify 149997, 150164
Couldn't classify 152096, 152210
Sorry, prediction pasa_asmbl_46348.p1 fails validation.
(AGG)	 GC	149997-150164	GT	AGG
(CAG)	 AG	150353-150474	GT	AGG
(GAA)	 AG	151017-151158	GT	AGG
(GAG)	 AG	151467-151603	GT	AGG
(GGT)	 AG	152096-152210	GA	TGG
-recovered pasa_asmbl_46348.p1, internal, 150353, 150474
-recovered pasa_asmbl_46348.p1, internal, 151017, 151158
-recovered pasa_asmbl_46348.p1, internal, 151467, 151603
Valid prediction for GeneMark_model.20144_t
Valid prediction for GeneMark_model.20147_t
Valid prediction for GeneMark_model.20166_t
Valid prediction for GeneMark_model.20142_t
Valid prediction for GeneMark_model.20170_t
Valid prediction for GeneMark_model.20146_t
Valid prediction for snap_scaffold_5-snap.712-T1
Valid prediction for snap_scaffold_5-snap.690-T1
Valid prediction for GeneMark_model.20172_t
Valid prediction for GeneMark_model.20177_t
Valid prediction for Augustus_model.g7861.t1
Valid prediction for GlimmerHMM_glimmerT_11972-T1
Valid prediction for snap_scaffold_5-snap.682-T1
Valid prediction for Augustus_model.g7853.t1
Valid prediction for GeneMark_model.20163_t
Valid prediction for GlimmerHMM_glimmerT_11970-T1
Valid prediction for GeneMark_model.20174_t
Valid prediction for Augustus_model.g7862.t1
Couldn't classify 141710, 141748
Couldn't classify 144807, 144987
Sorry, prediction pasa_asmbl_45303.p1 fails validation.
(CAG)	 CC	141710-141748	GT	AGG
(GAG)	 AG	141960-142049	GT	AGG
(GTG)	 AG	143357-143510	GT	CGG
(GAT)	 AG	143732-143803	GT	TGG
(ACC)	 AG	144045-144160	GT	AGG
(GTG)	 AG	144346-144428	GT	AGG
(GTG)	 AG	144807-144987	CT	GAC
-recovered pasa_asmbl_45303.p1, internal, 141960, 142049
-recovered pasa_asmbl_45303.p1, internal, 143357, 143510
-recovered pasa_asmbl_45303.p1, internal, 143732, 143803
-recovered pasa_asmbl_45303.p1, internal, 144045, 144160
-recovered pasa_asmbl_45303.p1, internal, 144346, 144428
Valid prediction for snap_scaffold_5-snap.719-T1
Valid prediction for Augustus_model.g7858.t1
Valid prediction for GlimmerHMM_glimmerT_11944-T1
Valid prediction for GeneMark_model.20186_t
Valid prediction for GlimmerHMM_glimmerT_11957-T1
Valid prediction for GeneMark_model.20184_t
Valid prediction for GlimmerHMM_glimmerT_11962-T1
Valid prediction for Augustus_model.g7852.t1
Valid prediction for Augustus_model.g7850.t1
Valid prediction for GeneMark_model.20169_t
Valid prediction for snap_scaffold_5-snap.713-T1
Valid prediction for GeneMark_model.20168_t
Valid prediction for snap_scaffold_5-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_11945-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52917, rend_intergenic: 44062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77482, rend_intergenic: 74677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83736, rend_intergenic: 80091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102489, rend_intergenic: 100790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107603, rend_intergenic: 104025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111617, rend_intergenic: 107714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127834, rend_intergenic: 116272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137450, rend_intergenic: 133607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142370, rend_intergenic: 139395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150350, rend_intergenic: 144453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196260
-exon list size: 702


building trellis

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92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 52917, rend_intergenic: 44062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77482, rend_intergenic: 74677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83736, rend_intergenic: 80091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102489, rend_intergenic: 100790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107603, rend_intergenic: 104025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111617, rend_intergenic: 107714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127834, rend_intergenic: 116272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137450, rend_intergenic: 133607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142370, rend_intergenic: 139395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150350, rend_intergenic: 144453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support