-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_14304498-14467005

-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 GeneMark_model.36318_t
Valid prediction for GeneMark_model.36349_t
Valid prediction for GeneMark_model.36354_t
Valid prediction for GlimmerHMM_glimmerT_21300-T1
Valid prediction for GeneMark_model.36325_t
Valid prediction for snap_scaffold_8-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_21291-T1
Valid prediction for GeneMark_model.36340_t
Valid prediction for snap_scaffold_8-snap.2637-T1
Valid prediction for snap_scaffold_8-snap.2625-T1
Valid prediction for GeneMark_model.36350_t
Valid prediction for snap_scaffold_8-snap.2635-T1
Valid prediction for snap_scaffold_8-snap.2640-T1
Valid prediction for snap_scaffold_8-snap.2630-T1
Valid prediction for HiQ_model.g14273.t1
Valid prediction for CodingQuarry_transcript_59752-T1
Valid prediction for GeneMark_model.36348_t
Couldn't classify 93125, 93249
Sorry, prediction pasa_asmbl_52359.p1 fails validation.
(TAT)	 TG	93125-93249	GT	AGG
(GTA)	 AG	93386-93475	GT	AAG
(GTG)	 AG	93626-93735	GT	CAG
(AAG)	 AG	94178-94264	GT	TGG
(AGG)	 AG	94533-94660	CG	GAC
-recovered pasa_asmbl_52359.p1, terminal, 94533, 94660
-recovered pasa_asmbl_52359.p1, internal, 93386, 93475
-recovered pasa_asmbl_52359.p1, internal, 93626, 93735
-recovered pasa_asmbl_52359.p1, internal, 94178, 94264
Valid prediction for GeneMark_model.36314_t
Valid prediction for GlimmerHMM_glimmerT_21297-T1
Valid prediction for GlimmerHMM_glimmerT_21284-T1
Valid prediction for GlimmerHMM_glimmerT_21294-T1
Valid prediction for CodingQuarry_transcript_59747-T1
Valid prediction for GlimmerHMM_glimmerT_21285-T1
Valid prediction for GeneMark_model.36335_t
Valid prediction for GeneMark_model.36329_t
Valid prediction for Augustus_model.g14265.t1
Valid prediction for snap_scaffold_8-snap.2617-T1
Valid prediction for snap_scaffold_8-snap.2624-T1
Valid prediction for snap_scaffold_8-snap.2647-T1
Valid prediction for GeneMark_model.36316_t
Valid prediction for GlimmerHMM_glimmerT_21296-T1
Valid prediction for snap_scaffold_8-snap.2622-T1
Valid prediction for GeneMark_model.36338_t
Valid prediction for Augustus_model.g14262.t1
Valid prediction for snap_scaffold_8-snap.2618-T1
Valid prediction for Augustus_model.g14267.t1
Valid prediction for GlimmerHMM_glimmerT_21282-T1
Valid prediction for Augustus_model.g14269.t1
Valid prediction for GeneMark_model.36342_t
Valid prediction for GeneMark_model.36321_t
Valid prediction for GlimmerHMM_glimmerT_21288-T1
Valid prediction for Augustus_model.g14263.t1
Valid prediction for GeneMark_model.36332_t
Valid prediction for pasa_asmbl_52360.p1
Valid prediction for CodingQuarry_transcript_59751-T1
Valid prediction for GeneMark_model.36333_t
Valid prediction for GlimmerHMM_glimmerT_21299-T1
Valid prediction for GeneMark_model.36323_t
Valid prediction for GeneMark_model.36320_t
Valid prediction for snap_scaffold_8-snap.2641-T1
Valid prediction for snap_scaffold_8-snap.2610-T1
Valid prediction for snap_scaffold_8-snap.2608-T1
Valid prediction for snap_scaffold_8-snap.2633-T1
Valid prediction for snap_scaffold_8-snap.2620-T1
Valid prediction for GeneMark_model.36326_t
Valid prediction for snap_scaffold_8-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_21286-T1
Valid prediction for GlimmerHMM_glimmerT_21278-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 GeneMark_model.36330_t
Valid prediction for GeneMark_model.36328_t
Valid prediction for snap_scaffold_8-snap.2616-T1
Valid prediction for snap_scaffold_8-snap.2612-T1
Valid prediction for HiQ_model.g14268.t1
Valid prediction for snap_scaffold_8-snap.2636-T1
Valid prediction for CodingQuarry_transcript_59748-T1
Valid prediction for GeneMark_model.36345_t
Valid prediction for snap_scaffold_8-snap.2628-T1
Valid prediction for Augustus_model.g14266.t1
Valid prediction for snap_scaffold_8-snap.2611-T1
Valid prediction for GeneMark_model.36313_t
Valid prediction for GlimmerHMM_glimmerT_21295-T1
Valid prediction for snap_scaffold_8-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_21281-T1
Valid prediction for pasa_asmbl_53320.p1
Valid prediction for HiQ_model.g14270.t1
Valid prediction for GeneMark_model.36337_t
Valid prediction for GeneMark_model.36351_t
Valid prediction for HiQ_model.g14274.t1
Valid prediction for GeneMark_model.36339_t
Valid prediction for snap_scaffold_8-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_21290-T1
Valid prediction for GeneMark_model.36315_t
Valid prediction for GeneMark_model.36355_t
Valid prediction for GlimmerHMM_glimmerT_21298-T1
Couldn't classify 77517, 77738
Sorry, prediction pasa_asmbl_53313.p1 fails validation.
(CAG)	 TT	77517-77738	GT	TGG
(ATT)	 AG	77891-78013	GT	CTG
(GAT)	 AG	78300-78479	GT	AGG
(GCG)	 AG	78678-78917	GT	AGG
(ATA)	 AG	79525-79668	GT	CGG
(GTC)	 AG	80185-80364	AC	AGA
-recovered pasa_asmbl_53313.p1, terminal, 80185, 80364
-recovered pasa_asmbl_53313.p1, internal, 77891, 78013
-recovered pasa_asmbl_53313.p1, internal, 78300, 78479
-recovered pasa_asmbl_53313.p1, internal, 78678, 78917
-recovered pasa_asmbl_53313.p1, internal, 79525, 79668
Valid prediction for GeneMark_model.36341_t
Valid prediction for CodingQuarry_transcript_59746-T1
Valid prediction for GlimmerHMM_glimmerT_21279-T1
Valid prediction for GlimmerHMM_glimmerT_21287-T1
Valid prediction for snap_scaffold_8-snap.2634-T1
Valid prediction for snap_scaffold_8-snap.2639-T1
Valid prediction for snap_scaffold_8-snap.2638-T1
Valid prediction for Augustus_model.g14276.t1
Valid prediction for GlimmerHMM_glimmerT_21289-T1
Valid prediction for GeneMark_model.36336_t
Valid prediction for GeneMark_model.36317_t
Valid prediction for GlimmerHMM_glimmerT_21301-T1
Valid prediction for GeneMark_model.36319_t
Valid prediction for GlimmerHMM_glimmerT_21303-T1
Valid prediction for GeneMark_model.36346_t
Valid prediction for GlimmerHMM_glimmerT_21293-T1
Valid prediction for HiQ_model.g14272.t1
Valid prediction for Augustus_model.g14275.t1
Valid prediction for Augustus_model.g14271.t1
Valid prediction for snap_scaffold_8-snap.2644-T1
Valid prediction for snap_scaffold_8-snap.2632-T1
Valid prediction for GeneMark_model.36327_t
Valid prediction for GeneMark_model.36334_t
Valid prediction for snap_scaffold_8-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_21283-T1
Valid prediction for GeneMark_model.36347_t
Valid prediction for snap_scaffold_8-snap.2609-T1
Valid prediction for GeneMark_model.36352_t
Valid prediction for snap_scaffold_8-snap.2626-T1
Valid prediction for GeneMark_model.36353_t
Valid prediction for Augustus_model.g14264.t1
Valid prediction for snap_scaffold_8-snap.2645-T1
Valid prediction for GlimmerHMM_glimmerT_21302-T1
Valid prediction for snap_scaffold_8-snap.2642-T1
Valid prediction for CodingQuarry_transcript_59750-T1
Valid prediction for snap_scaffold_8-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_21280-T1
Couldn't classify 22616, 22834
Sorry, prediction pasa_asmbl_53322.p1 fails validation.
(CCA)	 CT	22616-22834	GT	AGG
(GCA)	 AG	24114-24173	GT	AGG
(TTC)	 AG	24349-24575	GT	AAG
(GGT)	 AG	25072-25152	GT	GGG
(CCA)	 AG	25576-25709	GT	AGG
(GGG)	 AG	25929-26125	GT	AGG
(ACT)	 AG	27684-27828	GT	AGG
(GCT)	 AG	28006-28133	GT	CGG
(GAG)	 AG	28424-28615	CA	AAC
-recovered pasa_asmbl_53322.p1, terminal, 28424, 28615
-recovered pasa_asmbl_53322.p1, internal, 24114, 24173
-recovered pasa_asmbl_53322.p1, internal, 24349, 24575
-recovered pasa_asmbl_53322.p1, internal, 25072, 25152
-recovered pasa_asmbl_53322.p1, internal, 25576, 25709
-recovered pasa_asmbl_53322.p1, internal, 25929, 26125
-recovered pasa_asmbl_53322.p1, internal, 27684, 27828
-recovered pasa_asmbl_53322.p1, internal, 28006, 28133
Valid prediction for GeneMark_model.36343_t
Valid prediction for CodingQuarry_transcript_59749-T1
Valid prediction for snap_scaffold_8-snap.2627-T1
Valid prediction for snap_scaffold_8-snap.2615-T1
Valid prediction for GeneMark_model.36324_t
Valid prediction for pasa_asmbl_53318.p1
Valid prediction for snap_scaffold_8-snap.2643-T1
Valid prediction for snap_scaffold_8-snap.2621-T1
Valid prediction for GeneMark_model.36344_t
Valid prediction for GeneMark_model.36331_t
Valid prediction for GlimmerHMM_glimmerT_21292-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8423, rend_intergenic: 5074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14956, rend_intergenic: 12802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22373, rend_intergenic: 18536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35520, rend_intergenic: 33176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45434, rend_intergenic: 41065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51672, rend_intergenic: 46176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53173, rend_intergenic: 52644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63303, rend_intergenic: 60770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75947, rend_intergenic: 71066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102647, rend_intergenic: 97889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162508
-exon list size: 516


building trellis

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99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 8423, rend_intergenic: 5074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14956, rend_intergenic: 12802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22373, rend_intergenic: 18536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35520, rend_intergenic: 33176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45434, rend_intergenic: 41065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51672, rend_intergenic: 46176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53173, rend_intergenic: 52644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63303, rend_intergenic: 60770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75947, rend_intergenic: 71066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102647, rend_intergenic: 97889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support