-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_15267555-15475695

-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_6-snap.3218-T1
Valid prediction for GlimmerHMM_glimmerT_16112-T1
Valid prediction for snap_scaffold_6-snap.3245-T1
Valid prediction for GlimmerHMM_glimmerT_16080-T1
Valid prediction for snap_scaffold_6-snap.3216-T1
Valid prediction for snap_scaffold_6-snap.3232-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3241-T1
Valid prediction for snap_scaffold_6-snap.3231-T1
Valid prediction for GlimmerHMM_glimmerT_16093-T1
Valid prediction for GlimmerHMM_glimmerT_16103-T1
Valid prediction for snap_scaffold_6-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_16084-T1
Valid prediction for snap_scaffold_6-snap.3225-T1
Valid prediction for Augustus_model.g10806.t1
Valid prediction for GlimmerHMM_glimmerT_16087-T1
Valid prediction for Augustus_model.g10805.t1
Valid prediction for Augustus_model.g10822.t1
Valid prediction for snap_scaffold_6-snap.3219-T1
Valid prediction for snap_scaffold_6-snap.3221-T1
Valid prediction for snap_scaffold_6-snap.3238-T1
Valid prediction for Augustus_model.g10816.t1
Valid prediction for GlimmerHMM_glimmerT_16086-T1
Valid prediction for Augustus_model.g10807.t1
Valid prediction for snap_scaffold_6-snap.3235-T1
Valid prediction for snap_scaffold_6-snap.3229-T1
Valid prediction for Augustus_model.g10818.t1
Valid prediction for snap_scaffold_6-snap.3248-T1
Valid prediction for GlimmerHMM_glimmerT_16082-T1
Valid prediction for snap_scaffold_6-snap.3251-T1
Valid prediction for pasa_asmbl_47659.p1
Valid prediction for snap_scaffold_6-snap.3237-T1
Couldn't classify 82047, 82346
Sorry, prediction pasa_asmbl_47658.p1 fails validation.
(TTC)	 GG	82047-82346	AC	AGA
Valid prediction for snap_scaffold_6-snap.3253-T1
Valid prediction for CodingQuarry_transcript_55360-T1
Valid prediction for GlimmerHMM_glimmerT_16090-T1
Valid prediction for HiQ_model.g10810.t1
Valid prediction for GlimmerHMM_glimmerT_16092-T1
Valid prediction for snap_scaffold_6-snap.3230-T1
Valid prediction for Augustus_model.g10827.t1
Valid prediction for Augustus_model.g10809.t1
Valid prediction for GlimmerHMM_glimmerT_16088-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_6-snap.3233-T1
Valid prediction for snap_scaffold_6-snap.3255-T1
Valid prediction for Augustus_model.g10811.t1
Valid prediction for snap_scaffold_6-snap.3220-T1
Valid prediction for snap_scaffold_6-snap.3239-T1
Valid prediction for GlimmerHMM_glimmerT_16095-T1
Valid prediction for GlimmerHMM_glimmerT_16083-T1
Valid prediction for snap_scaffold_6-snap.3227-T1
Valid prediction for Augustus_model.g10804.t1
Valid prediction for pasa_asmbl_49070.p1
Valid prediction for Augustus_model.g10826.t1
Valid prediction for GlimmerHMM_glimmerT_16108-T1
Valid prediction for Augustus_model.g10824.t1
Valid prediction for GlimmerHMM_glimmerT_16099-T1
Valid prediction for GlimmerHMM_glimmerT_16081-T1
Couldn't classify 60501, 61331
Sorry, prediction pasa_asmbl_49065.p1 fails validation.
(TGC)	 AG	60501-61331	GA	GCG
Valid prediction for Augustus_model.g10823.t1
Valid prediction for GlimmerHMM_glimmerT_16100-T1
Valid prediction for Augustus_model.g10821.t1
Couldn't classify 58195, 58202
Couldn't classify 59984, 60452
Sorry, prediction pasa_asmbl_49066.p1 fails validation.
(TCC)	 TG	58195-58202	GT	CGG
(AGT)	 AG	58531-58690	GT	AGG
(TTC)	 AG	59288-59430	GT	AGG
(TGT)	 AG	59756-59779	GT	TGG
(GTC)	 AG	59984-60452	AC	AGA
-recovered pasa_asmbl_49066.p1, internal, 58531, 58690
-recovered pasa_asmbl_49066.p1, internal, 59288, 59430
-recovered pasa_asmbl_49066.p1, internal, 59756, 59779
Valid prediction for GlimmerHMM_glimmerT_16102-T1
Valid prediction for Augustus_model.g10820.t1
Couldn't classify 21937, 22473
Sorry, prediction pasa_asmbl_49069.p1 fails validation.
(ATG)	 AC	21937-22473	TG	GCT
Valid prediction for GlimmerHMM_glimmerT_16085-T1
Valid prediction for snap_scaffold_6-snap.3228-T1
Valid prediction for Augustus_model.g10825.t1
Couldn't classify 92439, 92678
Sorry, prediction pasa_asmbl_49063.p2 fails validation.
(ATG)	 AA	91566-91571	GT	AGG
(GAT)	 AG	91766-91991	GT	AAG
(TCT)	 AG	92103-92221	GT	CGG
(GAC)	 AG	92439-92678	GT	AGG
-recovered pasa_asmbl_49063.p2, initial, 91566, 91571
-recovered pasa_asmbl_49063.p2, internal, 91766, 91991
-recovered pasa_asmbl_49063.p2, internal, 92103, 92221
-recovered pasa_asmbl_49063.p2, internal, 92439, 92678
Valid prediction for snap_scaffold_6-snap.3222-T1
Valid prediction for GlimmerHMM_glimmerT_16105-T1
Couldn't classify 105068, 105242
Couldn't classify 108722, 108795
Sorry, prediction pasa_asmbl_49059.p1 fails validation.
(GCG)	 TC	105068-105242	GT	AGG
(ACG)	 AG	105531-105692	GT	AGG
(GCT)	 AG	105778-105860	GT	AGG
(GTG)	 AG	106155-106295	GT	AGG
(GAC)	 AG	106738-106809	GT	AGG
(GCG)	 AG	108057-108217	GT	GGG
(GTC)	 AG	108379-108488	GT	AGG
(AGG)	 AG	108722-108795	GT	AGG
-recovered pasa_asmbl_49059.p1, internal, 105531, 105692
-recovered pasa_asmbl_49059.p1, internal, 105778, 105860
-recovered pasa_asmbl_49059.p1, internal, 106155, 106295
-recovered pasa_asmbl_49059.p1, internal, 106738, 106809
-recovered pasa_asmbl_49059.p1, internal, 108057, 108217
-recovered pasa_asmbl_49059.p1, internal, 108379, 108488
-recovered pasa_asmbl_49059.p1, internal, 108722, 108795
Valid prediction for GlimmerHMM_glimmerT_16109-T1
Valid prediction for GlimmerHMM_glimmerT_16101-T1
Valid prediction for GlimmerHMM_glimmerT_16107-T1
Valid prediction for GlimmerHMM_glimmerT_16111-T1
Valid prediction for snap_scaffold_6-snap.3236-T1
Valid prediction for snap_scaffold_6-snap.3242-T1
Valid prediction for snap_scaffold_6-snap.3249-T1
Couldn't classify 23413, 23742
Sorry, prediction pasa_asmbl_49068.p1 fails validation.
(CGC)	 CC	23413-23742	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_16104-T1
Valid prediction for Augustus_model.g10814.t1
Valid prediction for snap_scaffold_6-snap.3247-T1
Valid prediction for Augustus_model.g10817.t1
Valid prediction for snap_scaffold_6-snap.3240-T1
Valid prediction for GlimmerHMM_glimmerT_16098-T1
Valid prediction for snap_scaffold_6-snap.3224-T1
Valid prediction for snap_scaffold_6-snap.3252-T1
Valid prediction for GlimmerHMM_glimmerT_16106-T1
Valid prediction for Augustus_model.g10808.t1
Valid prediction for Augustus_model.g10815.t1
Valid prediction for CodingQuarry_transcript_55361-T1
Couldn't classify 96176, 96260
Sorry, prediction pasa_asmbl_49062.p1 fails validation.
(ATG)	 GG	94701-94756	GT	CCG
(GTT)	 AG	95027-95104	GT	GGG
(CTT)	 AG	95500-95567	GT	GAG
(GGT)	 AG	95753-95903	GT	AGG
(GTT)	 AG	96176-96260	GT	ATG
-recovered pasa_asmbl_49062.p1, initial, 94701, 94756
-recovered pasa_asmbl_49062.p1, internal, 95027, 95104
-recovered pasa_asmbl_49062.p1, internal, 95500, 95567
-recovered pasa_asmbl_49062.p1, internal, 95753, 95903
-recovered pasa_asmbl_49062.p1, internal, 96176, 96260
Valid prediction for GlimmerHMM_glimmerT_16097-T1
Valid prediction for GlimmerHMM_glimmerT_16096-T1
Valid prediction for Augustus_model.g10813.t1
Valid prediction for snap_scaffold_6-snap.3244-T1
Valid prediction for GlimmerHMM_glimmerT_16089-T1
Valid prediction for GlimmerHMM_glimmerT_16091-T1
Valid prediction for snap_scaffold_6-snap.3234-T1
Couldn't classify 57066, 57202
Couldn't classify 57982, 58071
Sorry, prediction pasa_asmbl_49067.p2 fails validation.
(GAG)	 GC	57066-57202	GT	AGG
(TCT)	 AG	57497-57599	GT	AGG
(GTG)	 AG	57982-58071	CT	CGC
-recovered pasa_asmbl_49067.p2, internal, 57497, 57599
Valid prediction for snap_scaffold_6-snap.3243-T1
Valid prediction for GlimmerHMM_glimmerT_16110-T1
Valid prediction for GlimmerHMM_glimmerT_16094-T1
Valid prediction for snap_scaffold_6-snap.3254-T1
Valid prediction for snap_scaffold_6-snap.3217-T1
Valid prediction for snap_scaffold_6-snap.3246-T1
Valid prediction for snap_scaffold_6-snap.3250-T1
Valid prediction for Augustus_model.g10803.t1
Valid prediction for Augustus_model.g10819.t1
Valid prediction for Augustus_model.g10812.t1
Valid prediction for snap_scaffold_6-snap.3226-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21120, rend_intergenic: 11506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40540, rend_intergenic: 21909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52951, rend_intergenic: 49343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60513, rend_intergenic: 56092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61947, rend_intergenic: 61505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82346, rend_intergenic: 61951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101991, rend_intergenic: 97475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106702, rend_intergenic: 106105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113472, rend_intergenic: 108423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121187, rend_intergenic: 113673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134799, rend_intergenic: 128866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165397, rend_intergenic: 148616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174198, rend_intergenic: 165756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180669, rend_intergenic: 174522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193644, rend_intergenic: 190083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199549, rend_intergenic: 198973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200938, rend_intergenic: 200715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 80794, rend_intergenic: 80791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 85889, rend_intergenic: 85886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208141
-exon list size: 502


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 21120, rend_intergenic: 11506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40540, rend_intergenic: 21909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52951, rend_intergenic: 49343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60513, rend_intergenic: 56092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61947, rend_intergenic: 61505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82346, rend_intergenic: 61951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101991, rend_intergenic: 97475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106702, rend_intergenic: 106105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113472, rend_intergenic: 108423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121187, rend_intergenic: 113673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134799, rend_intergenic: 128866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165397, rend_intergenic: 148616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174198, rend_intergenic: 165756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180669, rend_intergenic: 174522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193644, rend_intergenic: 190083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199549, rend_intergenic: 198973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200938, rend_intergenic: 200715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 80794, rend_intergenic: 80791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 85889, rend_intergenic: 85886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18571
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18538
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11505
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 11474