-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_3546578-3729594

-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 HiQ_model.g28790.t1
Valid prediction for snap_scaffold_18-snap.723-T1
Valid prediction for HiQ_model.g28789.t1
Valid prediction for snap_scaffold_18-snap.752-T1
Valid prediction for snap_scaffold_18-snap.727-T1
Valid prediction for HiQ_model.g28796.t1
Valid prediction for snap_scaffold_18-snap.751-T1
Valid prediction for GeneMark_model.74362_t
Valid prediction for Augustus_model.g28795.t1
Valid prediction for GlimmerHMM_glimmerT_43030-T1
Valid prediction for GlimmerHMM_glimmerT_43057-T1
Valid prediction for snap_scaffold_18-snap.740-T1
Valid prediction for snap_scaffold_18-snap.738-T1
Valid prediction for GlimmerHMM_glimmerT_43047-T1
Valid prediction for snap_scaffold_18-snap.753-T1
Valid prediction for Augustus_model.g28788.t1
Valid prediction for snap_scaffold_18-snap.716-T1
Valid prediction for snap_scaffold_18-snap.721-T1
Valid prediction for pasa_asmbl_20501.p1
Valid prediction for GeneMark_model.74330_t
Valid prediction for GeneMark_model.74361_t
Valid prediction for GeneMark_model.74344_t
Valid prediction for HiQ_model.g28798.t1
Valid prediction for GlimmerHMM_glimmerT_43036-T1
Valid prediction for GeneMark_model.74358_t
Valid prediction for GeneMark_model.74338_t
Valid prediction for snap_scaffold_18-snap.748-T1
Valid prediction for snap_scaffold_18-snap.747-T1
Valid prediction for snap_scaffold_18-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_43042-T1
Valid prediction for GlimmerHMM_glimmerT_43037-T1
Couldn't classify 48878, 48916
Sorry, prediction pasa_asmbl_20489.p1 fails validation.
(CTG)	 CG	48878-48916	GT	AGG
(TCG)	 AG	50525-50605	GT	AGG
(GTG)	 AG	51273-51374	GT	AGG
(ATC)	 AG	51557-51760	GT	AGG
(GGT)	 AG	52455-52539	GT	TGG
(GGC)	 AG	52772-52931	GT	CAG
(GTT)	 AG	53604-53829	GT	AGG
(GCT)	 AG	54858-55042	GT	GAG
(GTC)	 AG	55263-55344	GT	AGG
(GGA)	 AG	55514-55612	GT	AGG
(GTG)	 AG	55736-55832	GT	CGG
(GAA)	 AG	55918-56016	GT	AGG
(GTA)	 AG	56169-56266	GT	AGG
(CCG)	 AG	56405-56494	GT	GGG
(GAC)	 AG	57355-57491	GT	AGG
(GCT)	 AG	58190-58375	GT	GAG
(CAC)	 AG	59191-59344	GT	AGG
(GTG)	 AG	60216-60321	GT	ACG
(GAC)	 AG	60911-61016	GT	AGG
(GAG)	 AG	61150-61255	GT	AGG
(GAG)	 AG	61621-61677	AC	GAA
-recovered pasa_asmbl_20489.p1, terminal, 61621, 61677
-recovered pasa_asmbl_20489.p1, internal, 50525, 50605
-recovered pasa_asmbl_20489.p1, internal, 51273, 51374
-recovered pasa_asmbl_20489.p1, internal, 51557, 51760
-recovered pasa_asmbl_20489.p1, internal, 52455, 52539
-recovered pasa_asmbl_20489.p1, internal, 52772, 52931
-recovered pasa_asmbl_20489.p1, internal, 53604, 53829
-recovered pasa_asmbl_20489.p1, internal, 54858, 55042
-recovered pasa_asmbl_20489.p1, internal, 55263, 55344
-recovered pasa_asmbl_20489.p1, internal, 55514, 55612
-recovered pasa_asmbl_20489.p1, internal, 55736, 55832
-recovered pasa_asmbl_20489.p1, internal, 55918, 56016
-recovered pasa_asmbl_20489.p1, internal, 56169, 56266
-recovered pasa_asmbl_20489.p1, internal, 56405, 56494
-recovered pasa_asmbl_20489.p1, internal, 57355, 57491
-recovered pasa_asmbl_20489.p1, internal, 58190, 58375
-recovered pasa_asmbl_20489.p1, internal, 59191, 59344
-recovered pasa_asmbl_20489.p1, internal, 60216, 60321
-recovered pasa_asmbl_20489.p1, internal, 60911, 61016
-recovered pasa_asmbl_20489.p1, internal, 61150, 61255
Valid prediction for snap_scaffold_18-snap.724-T1
Valid prediction for GlimmerHMM_glimmerT_43043-T1
Valid prediction for GlimmerHMM_glimmerT_43031-T1
Valid prediction for snap_scaffold_18-snap.733-T1
Valid prediction for GlimmerHMM_glimmerT_43026-T1
Valid prediction for snap_scaffold_18-snap.718-T1
Valid prediction for GeneMark_model.74331_t
Valid prediction for GeneMark_model.74355_t
Valid prediction for GlimmerHMM_glimmerT_43052-T1
Valid prediction for CodingQuarry_transcript_23666-T1
Valid prediction for GeneMark_model.74326_t
Valid prediction for snap_scaffold_18-snap.736-T1
Valid prediction for GeneMark_model.74328_t
Couldn't classify 147484, 147574
Sorry, prediction pasa_asmbl_20500.p1 fails validation.
(TCT)	 AT	147484-147574	GT	GGG
(TGG)	 AG	147949-148124	GT	CGG
(CAC)	 AG	148252-148386	GT	AGG
(GCT)	 AG	148528-148653	GT	AGG
(GCT)	 AG	148849-148932	GT	AGG
(GTA)	 AG	149033-149089	GT	AGG
(ACC)	 AG	149830-150000	GT	AGG
(ATT)	 AG	150224-150301	GT	AGG
(GTA)	 AG	150422-150518	GT	AGG
(CTC)	 AG	150650-150789	TT	AGT
-recovered pasa_asmbl_20500.p1, terminal, 150650, 150789
-recovered pasa_asmbl_20500.p1, internal, 147949, 148124
-recovered pasa_asmbl_20500.p1, internal, 148252, 148386
-recovered pasa_asmbl_20500.p1, internal, 148528, 148653
-recovered pasa_asmbl_20500.p1, internal, 148849, 148932
-recovered pasa_asmbl_20500.p1, internal, 149033, 149089
-recovered pasa_asmbl_20500.p1, internal, 149830, 150000
-recovered pasa_asmbl_20500.p1, internal, 150224, 150301
-recovered pasa_asmbl_20500.p1, internal, 150422, 150518
Valid prediction for snap_scaffold_18-snap.746-T1
Valid prediction for Augustus_model.g28782.t1
Valid prediction for Augustus_model.g28791.t1
Valid prediction for GlimmerHMM_glimmerT_43049-T1
Couldn't classify 82578, 82618
Sorry, prediction pasa_asmbl_20492.p1 fails validation.
(AGC)	 AC	82578-82618	GT	AAG
(TAA)	 AG	84076-84164	GT	AGG
(CTC)	 AG	85338-85440	GT	AGG
(CTT)	 AG	87030-87171	GT	AGG
(AGG)	 AG	88005-88085	GT	CAG
(GAG)	 AG	88400-88528	GT	AGG
(GAG)	 AG	88876-88947	GT	TGG
(AGC)	 AG	89064-89203	GT	GGG
(TTG)	 AG	89324-89469	GT	GGG
(TTC)	 AG	89568-89587	GT	TGG
(GAT)	 AG	89875-89997	GT	ACG
(TAC)	 AG	90082-90114	GT	AGG
(GAG)	 AG	90208-90258	GT	AGG
(AAG)	 AG	91839-91877	AG	GAA
-recovered pasa_asmbl_20492.p1, terminal, 91839, 91877
-recovered pasa_asmbl_20492.p1, internal, 84076, 84164
-recovered pasa_asmbl_20492.p1, internal, 85338, 85440
-recovered pasa_asmbl_20492.p1, internal, 87030, 87171
-recovered pasa_asmbl_20492.p1, internal, 88005, 88085
-recovered pasa_asmbl_20492.p1, internal, 88400, 88528
-recovered pasa_asmbl_20492.p1, internal, 88876, 88947
-recovered pasa_asmbl_20492.p1, internal, 89064, 89203
-recovered pasa_asmbl_20492.p1, internal, 89324, 89469
-recovered pasa_asmbl_20492.p1, internal, 89568, 89587
-recovered pasa_asmbl_20492.p1, internal, 89875, 89997
-recovered pasa_asmbl_20492.p1, internal, 90082, 90114
-recovered pasa_asmbl_20492.p1, internal, 90208, 90258
Valid prediction for GeneMark_model.74340_t
Valid prediction for Augustus_model.g28799.t1
Valid prediction for snap_scaffold_18-snap.722-T1
Valid prediction for CodingQuarry_transcript_23664-T1
Valid prediction for Augustus_model.g28785.t1
Valid prediction for GlimmerHMM_glimmerT_43034-T1
Valid prediction for GeneMark_model.74352_t
Valid prediction for snap_scaffold_18-snap.755-T1
Valid prediction for GeneMark_model.74363_t
Valid prediction for GeneMark_model.74357_t
Valid prediction for snap_scaffold_18-snap.737-T1
Valid prediction for GeneMark_model.74360_t
Valid prediction for GlimmerHMM_glimmerT_43054-T1
Valid prediction for GlimmerHMM_glimmerT_43053-T1
Valid prediction for Augustus_model.g28784.t1
Valid prediction for snap_scaffold_18-snap.742-T1
Valid prediction for snap_scaffold_18-snap.749-T1
Valid prediction for snap_scaffold_18-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_43029-T1
Valid prediction for GlimmerHMM_glimmerT_43050-T1
Valid prediction for GeneMark_model.74334_t
Valid prediction for snap_scaffold_18-snap.719-T1
Valid prediction for Augustus_model.g28792.t1
Valid prediction for GlimmerHMM_glimmerT_43041-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_18-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_43048-T1
Valid prediction for GlimmerHMM_glimmerT_43032-T1
Valid prediction for snap_scaffold_18-snap.734-T1
Valid prediction for GeneMark_model.74349_t
Valid prediction for snap_scaffold_18-snap.717-T1
Valid prediction for GeneMark_model.74346_t
Valid prediction for GeneMark_model.74336_t
Valid prediction for snap_scaffold_18-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_43056-T1
Valid prediction for snap_scaffold_18-snap.735-T1
Valid prediction for snap_scaffold_18-snap.730-T1
Valid prediction for GeneMark_model.74347_t
Valid prediction for GlimmerHMM_glimmerT_43033-T1
Valid prediction for GeneMark_model.74335_t
Valid prediction for snap_scaffold_18-snap.754-T1
Valid prediction for Augustus_model.g28794.t1
Valid prediction for GlimmerHMM_glimmerT_43044-T1
Valid prediction for GeneMark_model.74342_t
Valid prediction for GeneMark_model.74359_t
Valid prediction for snap_scaffold_18-snap.750-T1
Valid prediction for GeneMark_model.74339_t
Valid prediction for GlimmerHMM_glimmerT_43045-T1
Valid prediction for GeneMark_model.74327_t
Valid prediction for GeneMark_model.74356_t
Valid prediction for GeneMark_model.74333_t
Valid prediction for GlimmerHMM_glimmerT_43039-T1
Valid prediction for GeneMark_model.74354_t
Valid prediction for GlimmerHMM_glimmerT_43038-T1
Valid prediction for snap_scaffold_18-snap.743-T1
Valid prediction for GeneMark_model.74332_t
Valid prediction for snap_scaffold_18-snap.732-T1
Valid prediction for GlimmerHMM_glimmerT_43051-T1
Valid prediction for GlimmerHMM_glimmerT_43028-T1
Valid prediction for snap_scaffold_18-snap.725-T1
Valid prediction for Augustus_model.g28783.t1
Valid prediction for GlimmerHMM_glimmerT_43035-T1
Valid prediction for Augustus_model.g28787.t1
Valid prediction for Augustus_model.g28786.t1
Valid prediction for snap_scaffold_18-snap.744-T1
Valid prediction for GeneMark_model.74329_t
Valid prediction for Augustus_model.g28793.t1
Valid prediction for GlimmerHMM_glimmerT_43046-T1
Valid prediction for GlimmerHMM_glimmerT_43027-T1
Valid prediction for GeneMark_model.74353_t
Valid prediction for snap_scaffold_18-snap.741-T1
Valid prediction for snap_scaffold_18-snap.720-T1
Valid prediction for Augustus_model.g28797.t1
Valid prediction for GlimmerHMM_glimmerT_43040-T1
Valid prediction for snap_scaffold_18-snap.739-T1
Valid prediction for GeneMark_model.74351_t
Valid prediction for GeneMark_model.74343_t
Valid prediction for GlimmerHMM_glimmerT_43055-T1
Valid prediction for GeneMark_model.74341_t
Valid prediction for Augustus_model.g28800.t1
Valid prediction for snap_scaffold_18-snap.731-T1
Valid prediction for GeneMark_model.74337_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14606, rend_intergenic: 9099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24276, rend_intergenic: 22421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41932, rend_intergenic: 40974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61282, rend_intergenic: 48285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70322, rend_intergenic: 66462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101054, rend_intergenic: 98289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109635, rend_intergenic: 105768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139886, rend_intergenic: 133702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174226, rend_intergenic: 170708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183017
-exon list size: 599


building trellis

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88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 14606, rend_intergenic: 9099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24276, rend_intergenic: 22421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41932, rend_intergenic: 40974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61282, rend_intergenic: 48285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70322, rend_intergenic: 66462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101054, rend_intergenic: 98289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109635, rend_intergenic: 105768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139886, rend_intergenic: 133702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174226, rend_intergenic: 170708  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