-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_4605731-4775984

-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_13-snap.862-T1
Valid prediction for GeneMark_model.55197_t
Valid prediction for GeneMark_model.55194_t
Valid prediction for Augustus_model.g21617.t1
Valid prediction for GlimmerHMM_glimmerT_32271-T1
Valid prediction for GlimmerHMM_glimmerT_32281-T1
Valid prediction for snap_scaffold_13-snap.872-T1
Valid prediction for GeneMark_model.55219_t
Valid prediction for GlimmerHMM_glimmerT_32272-T1
Valid prediction for CodingQuarry_transcript_12974-T1
Valid prediction for GeneMark_model.55233_t
Valid prediction for CodingQuarry_transcript_12975-T1
Valid prediction for GeneMark_model.55201_t
Valid prediction for snap_scaffold_13-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_32280-T1
Valid prediction for GlimmerHMM_glimmerT_32274-T1
Valid prediction for GeneMark_model.55226_t
Valid prediction for GeneMark_model.55211_t
Valid prediction for Augustus_model.g21620.t1
Valid prediction for Augustus_model.g21622.t1
Valid prediction for snap_scaffold_13-snap.887-T1
Valid prediction for GeneMark_model.55230_t
Valid prediction for GlimmerHMM_glimmerT_32290-T1
Couldn't classify 46117, 46231
Sorry, prediction pasa_asmbl_11652.p1 fails validation.
(ATG)	 TC	40497-40560	GT	AAG
(AGA)	 AG	42910-43103	GT	AAG
(GTG)	 AG	44149-44262	GT	TGG
(GAC)	 AG	45730-45890	GT	AGG
(GGG)	 AG	46117-46231	GT	AGG
-recovered pasa_asmbl_11652.p1, initial, 40497, 40560
-recovered pasa_asmbl_11652.p1, internal, 42910, 43103
-recovered pasa_asmbl_11652.p1, internal, 44149, 44262
-recovered pasa_asmbl_11652.p1, internal, 45730, 45890
-recovered pasa_asmbl_11652.p1, internal, 46117, 46231
Valid prediction for GeneMark_model.55189_t
Valid prediction for snap_scaffold_13-snap.885-T1
Valid prediction for snap_scaffold_13-snap.870-T1
Valid prediction for GeneMark_model.55223_t
Valid prediction for GeneMark_model.55199_t
Valid prediction for Augustus_model.g21615.t1
Couldn't classify 8648, 8983
Sorry, prediction pasa_asmbl_9614.p2 fails validation.
(CCT)	 TT	8648-8983	TG	AAT
Valid prediction for pasa_asmbl_10800.p1
Valid prediction for GlimmerHMM_glimmerT_32276-T1
Valid prediction for snap_scaffold_13-snap.879-T1
Valid prediction for snap_scaffold_13-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_32267-T1
Valid prediction for GlimmerHMM_glimmerT_32284-T1
Valid prediction for snap_scaffold_13-snap.859-T1
Valid prediction for Augustus_model.g21610.t1
Valid prediction for GlimmerHMM_glimmerT_32282-T1
Valid prediction for GlimmerHMM_glimmerT_32285-T1
Valid prediction for Augustus_model.g21619.t1
Valid prediction for GlimmerHMM_glimmerT_32277-T1
Valid prediction for GlimmerHMM_glimmerT_32270-T1
Valid prediction for snap_scaffold_13-snap.866-T1
Valid prediction for GeneMark_model.55215_t
Valid prediction for snap_scaffold_13-snap.863-T1
Valid prediction for GeneMark_model.55203_t
Valid prediction for GeneMark_model.55217_t
Valid prediction for snap_scaffold_13-snap.874-T1
Valid prediction for GeneMark_model.55228_t
Valid prediction for GeneMark_model.55213_t
Valid prediction for GeneMark_model.55192_t
Valid prediction for GlimmerHMM_glimmerT_32288-T1
Valid prediction for GeneMark_model.55209_t
Valid prediction for snap_scaffold_13-snap.882-T1
Valid prediction for Augustus_model.g21616.t1
Valid prediction for GeneMark_model.55193_t
Valid prediction for Augustus_model.g21608.t1
Valid prediction for Augustus_model.g21607.t1
Valid prediction for snap_scaffold_13-snap.876-T1
Valid prediction for GeneMark_model.55234_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 GeneMark_model.55188_t
Valid prediction for Augustus_model.g21614.t1
Couldn't classify 153329, 153640
Sorry, prediction pasa_asmbl_9616.p2 fails validation.
(ATG)	 AC	153329-153640	CA	GAC
Valid prediction for GeneMark_model.55190_t
Valid prediction for Augustus_model.g21612.t1
Valid prediction for snap_scaffold_13-snap.889-T1
Valid prediction for GeneMark_model.55227_t
Valid prediction for Augustus_model.g21623.t1
Valid prediction for GeneMark_model.55220_t
Valid prediction for GeneMark_model.55198_t
Valid prediction for snap_scaffold_13-snap.868-T1
Valid prediction for GeneMark_model.55212_t
Valid prediction for Augustus_model.g21611.t1
Valid prediction for snap_scaffold_13-snap.890-T1
Valid prediction for GeneMark_model.55218_t
Couldn't classify 97610, 97999
Sorry, prediction pasa_asmbl_9623.p1 fails validation.
(ACA)	 AC	97610-97999	AT	GAA
Valid prediction for GlimmerHMM_glimmerT_32269-T1
Valid prediction for snap_scaffold_13-snap.883-T1
Couldn't classify 117789, 117878
Sorry, prediction pasa_asmbl_9621.p1 fails validation.
(ATG)	 CA	115755-115810	GT	AGG
(GAG)	 AG	116388-116521	GT	AGG
(GAG)	 AG	116650-116732	GT	CGG
(GAA)	 AG	116827-116922	GT	TGG
(ATC)	 AG	117077-117158	GT	GGG
(GTG)	 AG	117350-117411	GT	TGG
(ATC)	 AG	117515-117619	GT	AGG
(AGA)	 AG	117789-117878	GG	CAG
-recovered pasa_asmbl_9621.p1, initial, 115755, 115810
-recovered pasa_asmbl_9621.p1, internal, 116388, 116521
-recovered pasa_asmbl_9621.p1, internal, 116650, 116732
-recovered pasa_asmbl_9621.p1, internal, 116827, 116922
-recovered pasa_asmbl_9621.p1, internal, 117077, 117158
-recovered pasa_asmbl_9621.p1, internal, 117350, 117411
-recovered pasa_asmbl_9621.p1, internal, 117515, 117619
Valid prediction for GeneMark_model.55225_t
Valid prediction for GeneMark_model.55222_t
Valid prediction for GlimmerHMM_glimmerT_32279-T1
Valid prediction for GeneMark_model.55206_t
Valid prediction for Augustus_model.g21613.t1
Valid prediction for GeneMark_model.55208_t
Valid prediction for snap_scaffold_13-snap.860-T1
Valid prediction for GeneMark_model.55216_t
Valid prediction for snap_scaffold_13-snap.861-T1
Valid prediction for snap_scaffold_13-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_32286-T1
Valid prediction for Augustus_model.g21606.t1
Valid prediction for GeneMark_model.55200_t
Valid prediction for snap_scaffold_13-snap.865-T1
Valid prediction for snap_scaffold_13-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_32273-T1
Valid prediction for snap_scaffold_13-snap.875-T1
Valid prediction for snap_scaffold_13-snap.873-T1
Valid prediction for GeneMark_model.55229_t
Valid prediction for GeneMark_model.55202_t
Valid prediction for GeneMark_model.55207_t
Valid prediction for GeneMark_model.55235_t
Valid prediction for Augustus_model.g21618.t1
Valid prediction for snap_scaffold_13-snap.877-T1
Couldn't classify 96267, 96339
Couldn't classify 97060, 97183
Sorry, prediction pasa_asmbl_9624.p1 fails validation.
(TGG)	 TT	96267-96339	GT	GGG
(GAG)	 AG	96560-96751	GT	CGG
(ACC)	 AG	96849-96963	GT	AGG
(TGA)	 AG	97060-97183	GT	AGG
-recovered pasa_asmbl_9624.p1, internal, 96560, 96751
-recovered pasa_asmbl_9624.p1, internal, 96849, 96963
-recovered pasa_asmbl_9624.p1, internal, 97060, 97183
Valid prediction for GeneMark_model.55196_t
Valid prediction for GeneMark_model.55231_t
Valid prediction for GlimmerHMM_glimmerT_32278-T1
Valid prediction for GlimmerHMM_glimmerT_32289-T1
Valid prediction for GeneMark_model.55232_t
Valid prediction for Augustus_model.g21605.t1
Valid prediction for snap_scaffold_13-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_32268-T1
Valid prediction for Augustus_model.g21604.t1
Valid prediction for Augustus_model.g21609.t1
Valid prediction for GlimmerHMM_glimmerT_32283-T1
Valid prediction for snap_scaffold_13-snap.858-T1
Valid prediction for snap_scaffold_13-snap.884-T1
Valid prediction for snap_scaffold_13-snap.878-T1
Valid prediction for GeneMark_model.55191_t
Valid prediction for GlimmerHMM_glimmerT_32275-T1
Valid prediction for GeneMark_model.55195_t
Valid prediction for GeneMark_model.55204_t
Valid prediction for snap_scaffold_13-snap.871-T1
Valid prediction for Augustus_model.g21621.t1
Valid prediction for snap_scaffold_13-snap.864-T1
Valid prediction for GeneMark_model.55214_t
Valid prediction for GlimmerHMM_glimmerT_32287-T1
Valid prediction for GeneMark_model.55210_t
Valid prediction for snap_scaffold_13-snap.888-T1
Valid prediction for GeneMark_model.55224_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16926, rend_intergenic: 2316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27160, rend_intergenic: 20162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50756, rend_intergenic: 42836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58240, rend_intergenic: 57382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69274, rend_intergenic: 65702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79751, rend_intergenic: 72262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102586, rend_intergenic: 99826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113020, rend_intergenic: 103295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141287, rend_intergenic: 138128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170254
-exon list size: 665


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 16926, rend_intergenic: 2316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27160, rend_intergenic: 20162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50756, rend_intergenic: 42836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58240, rend_intergenic: 57382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69274, rend_intergenic: 65702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79751, rend_intergenic: 72262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102586, rend_intergenic: 99826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113020, rend_intergenic: 103295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141287, rend_intergenic: 138128  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