-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_2784174-2926940

-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 GlimmerHMM_glimmerT_53475-T1
Valid prediction for GeneMark_model.93233_t
Valid prediction for GlimmerHMM_glimmerT_53465-T1
Valid prediction for GlimmerHMM_glimmerT_53466-T1
Valid prediction for GlimmerHMM_glimmerT_53477-T1
Valid prediction for GlimmerHMM_glimmerT_53467-T1
Valid prediction for snap_scaffold_24-snap.639-T1
Valid prediction for GeneMark_model.93218_t
Valid prediction for GlimmerHMM_glimmerT_53470-T1
Valid prediction for GeneMark_model.93214_t
Valid prediction for GeneMark_model.93229_t
Valid prediction for Augustus_model.g35812.t1
Valid prediction for GlimmerHMM_glimmerT_53472-T1
Valid prediction for Augustus_model.g35813.t1
Couldn't classify 138459, 138592
Couldn't classify 139651, 139978
Sorry, prediction pasa_asmbl_32124.p1 fails validation.
(TTG)	 CC	138459-138592	GT	AGG
(GCT)	 AG	138795-138942	GT	TGG
(GTG)	 AG	139066-139273	GT	GGG
(GTT)	 AG	139374-139446	GT	AGG
(GTA)	 AG	139651-139978	GC	CGG
-recovered pasa_asmbl_32124.p1, internal, 138795, 138942
-recovered pasa_asmbl_32124.p1, internal, 139066, 139273
-recovered pasa_asmbl_32124.p1, internal, 139374, 139446
-recovered pasa_asmbl_32124.p1, internal, 139651, 139978
Valid prediction for GeneMark_model.93224_t
Valid prediction for GeneMark_model.93228_t
Valid prediction for GeneMark_model.93222_t
Valid prediction for GeneMark_model.93198_t
Valid prediction for GeneMark_model.93210_t
Valid prediction for GeneMark_model.93231_t
Valid prediction for snap_scaffold_24-snap.641-T1
Valid prediction for GeneMark_model.93208_t
Valid prediction for GeneMark_model.93226_t
Valid prediction for GeneMark_model.93194_t
Valid prediction for GlimmerHMM_glimmerT_53474-T1
Valid prediction for snap_scaffold_24-snap.653-T1
Valid prediction for GeneMark_model.93201_t
Valid prediction for snap_scaffold_24-snap.646-T1
Valid prediction for GeneMark_model.93211_t
Valid prediction for GeneMark_model.93223_t
Valid prediction for GlimmerHMM_glimmerT_53469-T1
Valid prediction for GlimmerHMM_glimmerT_53476-T1
Valid prediction for Augustus_model.g35814.t1
Valid prediction for GeneMark_model.93206_t
Valid prediction for snap_scaffold_24-snap.644-T1
Valid prediction for snap_scaffold_24-snap.650-T1
Valid prediction for GeneMark_model.93235_t
Valid prediction for Augustus_model.g35811.t1
Valid prediction for GeneMark_model.93220_t
Valid prediction for snap_scaffold_24-snap.655-T1
Valid prediction for GeneMark_model.93204_t
Valid prediction for snap_scaffold_24-snap.634-T1
Valid prediction for GlimmerHMM_glimmerT_53473-T1
Valid prediction for snap_scaffold_24-snap.651-T1
Valid prediction for GlimmerHMM_glimmerT_53468-T1
Valid prediction for snap_scaffold_24-snap.636-T1
Valid prediction for GeneMark_model.93215_t
Couldn't classify 137646, 137719
Sorry, prediction pasa_asmbl_32123.p1 fails validation.
(ATG)	 AG	135846-135977	GT	AGG
(GAG)	 AG	136114-136302	GT	AGG
(ACC)	 AG	136552-136717	GT	TGG
(GAA)	 AG	137646-137719	GT	GGG
-recovered pasa_asmbl_32123.p1, initial, 135846, 135977
-recovered pasa_asmbl_32123.p1, internal, 135846, 135977
-recovered pasa_asmbl_32123.p1, internal, 136114, 136302
-recovered pasa_asmbl_32123.p1, internal, 136552, 136717
-recovered pasa_asmbl_32123.p1, internal, 137646, 137719
Valid prediction for snap_scaffold_24-snap.647-T1
Valid prediction for GeneMark_model.93202_t
Valid prediction for GeneMark_model.93196_t

-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_24-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_53463-T1
Valid prediction for snap_scaffold_24-snap.654-T1
Valid prediction for GeneMark_model.93199_t
Valid prediction for snap_scaffold_24-snap.640-T1
Valid prediction for GeneMark_model.93203_t
Valid prediction for GeneMark_model.93205_t
Valid prediction for GeneMark_model.93216_t
Valid prediction for GeneMark_model.93219_t
Valid prediction for GeneMark_model.93197_t
Valid prediction for snap_scaffold_24-snap.632-T1
Valid prediction for snap_scaffold_24-snap.652-T1
Valid prediction for GeneMark_model.93193_t
Valid prediction for GlimmerHMM_glimmerT_53464-T1
Valid prediction for GeneMark_model.93207_t
Valid prediction for GeneMark_model.93209_t
Valid prediction for HiQ_model.g35806.t1
Valid prediction for snap_scaffold_24-snap.645-T1
Valid prediction for GeneMark_model.93217_t
Valid prediction for GeneMark_model.93190_t
Valid prediction for snap_scaffold_24-snap.649-T1
Valid prediction for GeneMark_model.93227_t
Valid prediction for HiQ_model.g35810.t1
Valid prediction for GeneMark_model.93230_t
Valid prediction for Augustus_model.g35808.t1
Valid prediction for GeneMark_model.93221_t
Valid prediction for GeneMark_model.93200_t
Valid prediction for snap_scaffold_24-snap.642-T1
Couldn't classify 140689, 141113
Sorry, prediction pasa_asmbl_32792.p1 fails validation.
(ATG)	 TG	139480-139546	GT	GGG
(AAG)	 AG	139711-139751	GT	TTG
(GCA)	 AG	139861-139935	GT	AGG
(CAG)	 AG	140260-140443	GT	CGG
(GTA)	 AG	140689-141113	GG	GAG
-recovered pasa_asmbl_32792.p1, initial, 139480, 139546
-recovered pasa_asmbl_32792.p1, internal, 139711, 139751
-recovered pasa_asmbl_32792.p1, internal, 139861, 139935
-recovered pasa_asmbl_32792.p1, internal, 140260, 140443
Valid prediction for GlimmerHMM_glimmerT_53471-T1
Valid prediction for snap_scaffold_24-snap.648-T1
Valid prediction for GeneMark_model.93212_t
Valid prediction for GeneMark_model.93192_t
Valid prediction for GeneMark_model.93225_t
Valid prediction for Augustus_model.g35809.t1
Valid prediction for snap_scaffold_24-snap.631-T1
Valid prediction for snap_scaffold_24-snap.635-T1
Valid prediction for GeneMark_model.93191_t
Valid prediction for GeneMark_model.93232_t
Valid prediction for GeneMark_model.93234_t
Valid prediction for snap_scaffold_24-snap.633-T1
Valid prediction for snap_scaffold_24-snap.637-T1
Valid prediction for GeneMark_model.93195_t
Valid prediction for Augustus_model.g35807.t1
Valid prediction for snap_scaffold_24-snap.638-T1
Couldn't classify 33773, 33985
Couldn't classify 34437, 34583
Sorry, prediction pasa_asmbl_33241.p1 fails validation.
(CTC)	 GT	33773-33985	GT	ACG
(GAT)	 AG	34112-34258	GT	GTG
(GTG)	 AG	34437-34583	GT	AGG
-recovered pasa_asmbl_33241.p1, internal, 34112, 34258
-recovered pasa_asmbl_33241.p1, internal, 34437, 34583

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21324, rend_intergenic: 14128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36178, rend_intergenic: 21788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57995, rend_intergenic: 36265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79550, rend_intergenic: 61819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82232, rend_intergenic: 79660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101134, rend_intergenic: 82653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106075, rend_intergenic: 101402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107043, rend_intergenic: 106856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113105, rend_intergenic: 108100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119178, rend_intergenic: 115007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121089, rend_intergenic: 119512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129215, rend_intergenic: 124353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134252, rend_intergenic: 131870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142767
-exon list size: 609


building trellis

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98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 21324, rend_intergenic: 14128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36178, rend_intergenic: 21788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57995, rend_intergenic: 36265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79550, rend_intergenic: 61819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82232, rend_intergenic: 79660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101134, rend_intergenic: 82653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106075, rend_intergenic: 101402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107043, rend_intergenic: 106856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113105, rend_intergenic: 108100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119178, rend_intergenic: 115007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121089, rend_intergenic: 119512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129215, rend_intergenic: 124353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134252, rend_intergenic: 131870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support