-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_13579442-13719484

-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.2547-T1
Valid prediction for GeneMark_model.22320_t
Valid prediction for snap_scaffold_5-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_13251-T1
Valid prediction for GlimmerHMM_glimmerT_13246-T1
Couldn't classify 93343, 93440
Couldn't classify 95492, 95690
Sorry, prediction pasa_asmbl_44556.p1 fails validation.
(CAC)	 AC	93343-93440	GT	AGG
(CGC)	 AG	94383-94449	GT	AGG
(CGG)	 AG	94537-94614	GT	AGG
(GAA)	 AG	94867-94932	GT	AGG
(GTG)	 AG	95235-95353	GT	AGG
(CTA)	 AG	95492-95690	AG	GGA
-recovered pasa_asmbl_44556.p1, internal, 94383, 94449
-recovered pasa_asmbl_44556.p1, internal, 94537, 94614
-recovered pasa_asmbl_44556.p1, internal, 94867, 94932
-recovered pasa_asmbl_44556.p1, internal, 95235, 95353
Valid prediction for snap_scaffold_5-snap.2529-T1
Valid prediction for Augustus_model.g8847.t1
Valid prediction for pasa_asmbl_44557.p1
Valid prediction for Augustus_model.g8858.t1
Valid prediction for snap_scaffold_5-snap.2536-T1
Valid prediction for snap_scaffold_5-snap.2541-T1
Valid prediction for GeneMark_model.22308_t
Valid prediction for GeneMark_model.22319_t
Valid prediction for GeneMark_model.22311_t
Valid prediction for GlimmerHMM_glimmerT_13239-T1
Valid prediction for GeneMark_model.22318_t
Valid prediction for Augustus_model.g8853.t1
Valid prediction for GlimmerHMM_glimmerT_13250-T1
Valid prediction for Augustus_model.g8846.t1
Valid prediction for GeneMark_model.22327_t
Valid prediction for snap_scaffold_5-snap.2545-T1
Valid prediction for GeneMark_model.22336_t
Valid prediction for GlimmerHMM_glimmerT_13247-T1
Valid prediction for Augustus_model.g8845.t1
Valid prediction for GeneMark_model.22313_t
Valid prediction for GeneMark_model.22306_t
Valid prediction for GlimmerHMM_glimmerT_13240-T1
Valid prediction for GeneMark_model.22304_t
Valid prediction for snap_scaffold_5-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_13237-T1
Valid prediction for GlimmerHMM_glimmerT_13252-T1
Valid prediction for snap_scaffold_5-snap.2542-T1
Valid prediction for Augustus_model.g8852.t1
Valid prediction for GeneMark_model.22339_t
Valid prediction for GlimmerHMM_glimmerT_13242-T1
Valid prediction for GeneMark_model.22317_t
Valid prediction for GeneMark_model.22330_t
Valid prediction for GeneMark_model.22312_t
Valid prediction for CodingQuarry_transcript_52203-T1
Valid prediction for snap_scaffold_5-snap.2527-T1
Valid prediction for GeneMark_model.22334_t
Valid prediction for snap_scaffold_5-snap.2532-T1
Valid prediction for snap_scaffold_5-snap.2522-T1
Valid prediction for snap_scaffold_5-snap.2525-T1
Valid prediction for Augustus_model.g8843.t1
Valid prediction for GeneMark_model.22299_t
Valid prediction for GlimmerHMM_glimmerT_13256-T1
Valid prediction for GeneMark_model.22302_t
Valid prediction for GlimmerHMM_glimmerT_13241-T1
Valid prediction for GeneMark_model.22300_t
Valid prediction for GeneMark_model.22322_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.22314_t
Valid prediction for GlimmerHMM_glimmerT_13253-T1
Valid prediction for Augustus_model.g8863.t1
Valid prediction for Augustus_model.g8860.t1
Valid prediction for GeneMark_model.22335_t
Valid prediction for GlimmerHMM_glimmerT_13260-T1
Valid prediction for snap_scaffold_5-snap.2544-T1
Valid prediction for Augustus_model.g8857.t1
Valid prediction for GlimmerHMM_glimmerT_13236-T1
Valid prediction for Augustus_model.g8862.t1
Valid prediction for Augustus_model.g8848.t1
Valid prediction for GlimmerHMM_glimmerT_13238-T1
Valid prediction for snap_scaffold_5-snap.2519-T1
Valid prediction for GeneMark_model.22307_t
Valid prediction for Augustus_model.g8856.t1
Valid prediction for GeneMark_model.22333_t
Valid prediction for GlimmerHMM_glimmerT_13245-T1
Valid prediction for snap_scaffold_5-snap.2523-T1
Valid prediction for GeneMark_model.22323_t
Couldn't classify 24766, 24919
Couldn't classify 27047, 27084
Sorry, prediction pasa_asmbl_45932.p1 fails validation.
(GAG)	 AG	24766-24919	GT	GCG
(CCC)	 AG	25027-25121	GT	CTG
(GTC)	 AG	25219-25411	GT	TGG
(AGG)	 AG	26225-26419	GT	AGG
(TCA)	 AG	27047-27084	CC	GCC
-recovered pasa_asmbl_45932.p1, internal, 24766, 24919
-recovered pasa_asmbl_45932.p1, internal, 25027, 25121
-recovered pasa_asmbl_45932.p1, internal, 25219, 25411
-recovered pasa_asmbl_45932.p1, internal, 26225, 26419
Valid prediction for snap_scaffold_5-snap.2537-T1
Valid prediction for GeneMark_model.22331_t
Valid prediction for snap_scaffold_5-snap.2548-T1
Valid prediction for snap_scaffold_5-snap.2533-T1
Valid prediction for GeneMark_model.22309_t
Valid prediction for GlimmerHMM_glimmerT_13259-T1
Valid prediction for GeneMark_model.22338_t
Valid prediction for GeneMark_model.22305_t
Valid prediction for GeneMark_model.22325_t
Valid prediction for snap_scaffold_5-snap.2549-T1
Valid prediction for GlimmerHMM_glimmerT_13243-T1
Valid prediction for pasa_asmbl_45925.p1
Valid prediction for snap_scaffold_5-snap.2526-T1
Valid prediction for CodingQuarry_transcript_52202-T1
Valid prediction for GeneMark_model.22321_t
Valid prediction for snap_scaffold_5-snap.2528-T1
Valid prediction for GeneMark_model.22324_t
Valid prediction for snap_scaffold_5-snap.2524-T1
Valid prediction for GlimmerHMM_glimmerT_13258-T1
Valid prediction for snap_scaffold_5-snap.2540-T1
Valid prediction for GeneMark_model.22328_t
Valid prediction for snap_scaffold_5-snap.2530-T1
Valid prediction for snap_scaffold_5-snap.2521-T1
Valid prediction for GeneMark_model.22326_t
Valid prediction for GlimmerHMM_glimmerT_13257-T1
Valid prediction for Augustus_model.g8850.t1
Valid prediction for GeneMark_model.22298_t
Valid prediction for Augustus_model.g8855.t1
Valid prediction for GeneMark_model.22337_t
Couldn't classify 37810, 38358
Sorry, prediction pasa_asmbl_45929.p1 fails validation.
(GAT)	 AT	37810-38358	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_13255-T1
Valid prediction for snap_scaffold_5-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_13254-T1
Valid prediction for Augustus_model.g8861.t1
Valid prediction for GeneMark_model.22303_t
Valid prediction for GeneMark_model.22315_t
Valid prediction for GlimmerHMM_glimmerT_13244-T1
Valid prediction for GlimmerHMM_glimmerT_13248-T1
Valid prediction for GeneMark_model.22310_t
Valid prediction for snap_scaffold_5-snap.2539-T1
Valid prediction for Augustus_model.g8854.t1
Valid prediction for snap_scaffold_5-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_13249-T1
Valid prediction for GeneMark_model.22301_t
Valid prediction for snap_scaffold_5-snap.2535-T1
Valid prediction for Augustus_model.g8849.t1
Couldn't classify 27223, 27232
Sorry, prediction pasa_asmbl_45930.p1 fails validation.
(CCC)	 TC	27223-27232	GT	TGG
(AGA)	 AG	27454-27550	GT	AGG
(AAA)	 AG	28519-28621	GT	AGG
(GGG)	 AG	28864-29001	GT	AGG
(GTG)	 AG	29196-29334	GT	CAG
(GTA)	 AG	30546-31606	CG	GAC
-recovered pasa_asmbl_45930.p1, terminal, 30546, 31606
-recovered pasa_asmbl_45930.p1, internal, 27454, 27550
-recovered pasa_asmbl_45930.p1, internal, 28519, 28621
-recovered pasa_asmbl_45930.p1, internal, 28864, 29001
-recovered pasa_asmbl_45930.p1, internal, 29196, 29334
Valid prediction for Augustus_model.g8851.t1
Valid prediction for Augustus_model.g8844.t1
Valid prediction for Augustus_model.g8859.t1
Valid prediction for GeneMark_model.22316_t
Valid prediction for snap_scaffold_5-snap.2538-T1
Valid prediction for snap_scaffold_5-snap.2543-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12159, rend_intergenic: 4708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14142, rend_intergenic: 12711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27640, rend_intergenic: 15129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32949, rend_intergenic: 28933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42564, rend_intergenic: 37843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44455, rend_intergenic: 43482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47905, rend_intergenic: 44786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56999, rend_intergenic: 53067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61557, rend_intergenic: 61366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67214, rend_intergenic: 61651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111561, rend_intergenic: 108438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123796, rend_intergenic: 119438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138486, rend_intergenic: 124108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140043
-exon list size: 640


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12159, rend_intergenic: 4708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14142, rend_intergenic: 12711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27640, rend_intergenic: 15129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32949, rend_intergenic: 28933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42564, rend_intergenic: 37843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44455, rend_intergenic: 43482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47905, rend_intergenic: 44786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56999, rend_intergenic: 53067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61557, rend_intergenic: 61366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67214, rend_intergenic: 61651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111561, rend_intergenic: 108438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123796, rend_intergenic: 119438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138486, rend_intergenic: 124108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support