-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_4729992-4901687

-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_18-snap.956-T1
Valid prediction for pasa_asmbl_20585.p1
Valid prediction for snap_scaffold_18-snap.980-T1
Valid prediction for GeneMark_model.74652_t
Valid prediction for GlimmerHMM_glimmerT_43226-T1
Valid prediction for GlimmerHMM_glimmerT_43234-T1
Couldn't classify 18474, 19574
Sorry, prediction pasa_asmbl_20582.p1 fails validation.
(TTT)	 AG	18474-19574	AA	GCA
Valid prediction for GeneMark_model.74642_t
Valid prediction for GeneMark_model.74646_t
Valid prediction for snap_scaffold_18-snap.957-T1
Valid prediction for HiQ_model.g28924.t1
Valid prediction for GeneMark_model.74638_t
Valid prediction for GeneMark_model.74627_t
Valid prediction for GeneMark_model.74634_t
Valid prediction for Augustus_model.g28909.t1
Valid prediction for Augustus_model.g28915.t1
Valid prediction for HiQ_model.g28910.t1
Valid prediction for snap_scaffold_18-snap.966-T1
Valid prediction for Augustus_model.g28914.t1
Valid prediction for snap_scaffold_18-snap.990-T1
Valid prediction for snap_scaffold_18-snap.992-T1
Valid prediction for GlimmerHMM_glimmerT_43230-T1
Valid prediction for GlimmerHMM_glimmerT_43229-T1
Valid prediction for GlimmerHMM_glimmerT_43241-T1
Valid prediction for Augustus_model.g28917.t1
Valid prediction for GeneMark_model.74640_t
Valid prediction for CodingQuarry_transcript_23706-T1
Valid prediction for GeneMark_model.74648_t
Valid prediction for CodingQuarry_transcript_23701-T1
Couldn't classify 23699, 23737
Sorry, prediction pasa_asmbl_20583.p1 fails validation.
(AAG)	 TT	23699-23737	GT	ATG
(ACT)	 AG	23991-24060	GT	AGG
(GTG)	 AG	24314-24390	GT	GGG
(GCT)	 AG	24611-24690	GT	CGG
(GCT)	 AG	24819-24964	GT	AGG
(TGG)	 AG	25205-25306	GT	CGG
(ATG)	 AG	25433-25535	GT	AGG
(GAT)	 AG	25640-25812	GT	AGG
(CTT)	 AG	25981-26062	GT	ATG
(GGA)	 AG	26232-26337	GT	AGG
(GGC)	 AG	26683-26761	GT	CGG
(GGA)	 AG	26988-27145	GA	GAG
add_exon() Sorry, pasa_asmbl_20583.p1 25433-25535-initial-1 is invalid.
-recovered pasa_asmbl_20583.p1, initial, 25433, 25535
-recovered pasa_asmbl_20583.p1, terminal, 26988, 27145
-recovered pasa_asmbl_20583.p1, internal, 23991, 24060
-recovered pasa_asmbl_20583.p1, internal, 24314, 24390
-recovered pasa_asmbl_20583.p1, internal, 24611, 24690
-recovered pasa_asmbl_20583.p1, internal, 24819, 24964
-recovered pasa_asmbl_20583.p1, internal, 25205, 25306
-recovered pasa_asmbl_20583.p1, internal, 25433, 25535
-recovered pasa_asmbl_20583.p1, internal, 25640, 25812
-recovered pasa_asmbl_20583.p1, internal, 25981, 26062
-recovered pasa_asmbl_20583.p1, internal, 26232, 26337
-recovered pasa_asmbl_20583.p1, internal, 26683, 26761
Valid prediction for GlimmerHMM_glimmerT_43235-T1
Valid prediction for CodingQuarry_transcript_23704-T1
Valid prediction for Augustus_model.g28926.t1
Valid prediction for GlimmerHMM_glimmerT_43225-T1
Valid prediction for GeneMark_model.74657_t
Valid prediction for snap_scaffold_18-snap.977-T1
Valid prediction for GeneMark_model.74655_t
Valid prediction for snap_scaffold_18-snap.979-T1
Valid prediction for CodingQuarry_transcript_23702-T1
Valid prediction for snap_scaffold_18-snap.984-T1
Valid prediction for GeneMark_model.74639_t
Valid prediction for GlimmerHMM_glimmerT_43219-T1
Valid prediction for GlimmerHMM_glimmerT_43232-T1
Valid prediction for CodingQuarry_transcript_23705-T1
Valid prediction for GeneMark_model.74629_t
Valid prediction for GlimmerHMM_glimmerT_43223-T1
Couldn't classify 119929, 120129
Couldn't classify 122182, 122227
Sorry, prediction CodingQuarry_transcript_23708-T1 fails validation.
(ATG)	 TC	119533-119649	GT	AGG
(GCA)	 AG	119766-119860	GT	AGG
(GTG)	 AG	119929-120129	CT	ACC
(CTT)	 AC	122182-122227	AG	AGA
-recovered CodingQuarry_transcript_23708-T1, initial, 119533, 119649
-recovered CodingQuarry_transcript_23708-T1, internal, 119766, 119860
Valid prediction for GlimmerHMM_glimmerT_43227-T1
Valid prediction for snap_scaffold_18-snap.965-T1
Valid prediction for snap_scaffold_18-snap.986-T1
Valid prediction for snap_scaffold_18-snap.962-T1
Valid prediction for GeneMark_model.74650_t
Valid prediction for CodingQuarry_transcript_23707-T1
Valid prediction for GeneMark_model.74632_t
Valid prediction for snap_scaffold_18-snap.968-T1
Valid prediction for snap_scaffold_18-snap.970-T1
Valid prediction for GeneMark_model.74643_t
Valid prediction for GeneMark_model.74653_t
Valid prediction for pasa_asmbl_21082.p1
Valid prediction for GeneMark_model.74636_t
Valid prediction for HiQ_model.g28911.t1
Valid prediction for GlimmerHMM_glimmerT_43236-T1
Valid prediction for GeneMark_model.74625_t
Valid prediction for snap_scaffold_18-snap.958-T1
Valid prediction for GeneMark_model.74637_t
Valid prediction for GeneMark_model.74635_t
Valid prediction for GlimmerHMM_glimmerT_43224-T1
Valid prediction for snap_scaffold_18-snap.961-T1
Valid prediction for HiQ_model.g28925.t1
Valid prediction for snap_scaffold_18-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_43243-T1
Valid prediction for snap_scaffold_18-snap.989-T1
Valid prediction for snap_scaffold_18-snap.971-T1
Valid prediction for HiQ_model.g28912.t1
Valid prediction for GlimmerHMM_glimmerT_43242-T1
Valid prediction for HiQ_model.g28923.t1
Valid prediction for GlimmerHMM_glimmerT_43246-T1
Valid prediction for pasa_asmbl_20604.p1
Valid prediction for pasa_asmbl_20600.p1
Valid prediction for Augustus_model.g28920.t1
Valid prediction for CodingQuarry_transcript_23703-T1
Valid prediction for snap_scaffold_18-snap.985-T1
Valid prediction for GeneMark_model.74661_t
Valid prediction for GeneMark_model.74649_t
Valid prediction for GlimmerHMM_glimmerT_43240-T1
Valid prediction for Augustus_model.g28913.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.954-T1
Valid prediction for GeneMark_model.74647_t
Valid prediction for Augustus_model.g28921.t1
Valid prediction for GeneMark_model.74658_t
Valid prediction for snap_scaffold_18-snap.955-T1
Valid prediction for Augustus_model.g28928.t1
Valid prediction for snap_scaffold_18-snap.967-T1
Valid prediction for snap_scaffold_18-snap.960-T1
Valid prediction for Augustus_model.g28922.t1
Valid prediction for GlimmerHMM_glimmerT_43239-T1
Valid prediction for GeneMark_model.74633_t
Valid prediction for GeneMark_model.74626_t
Valid prediction for Augustus_model.g28908.t1
Valid prediction for GeneMark_model.74656_t
Valid prediction for GeneMark_model.74651_t
Valid prediction for GeneMark_model.74624_t
Valid prediction for snap_scaffold_18-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_43221-T1
Valid prediction for Augustus_model.g28930.t1
Valid prediction for snap_scaffold_18-snap.974-T1
Valid prediction for snap_scaffold_18-snap.963-T1
Valid prediction for snap_scaffold_18-snap.991-T1
Valid prediction for snap_scaffold_18-snap.976-T1
Valid prediction for GeneMark_model.74630_t
Valid prediction for GlimmerHMM_glimmerT_43233-T1
Valid prediction for snap_scaffold_18-snap.981-T1
Valid prediction for snap_scaffold_18-snap.964-T1
Valid prediction for snap_scaffold_18-snap.969-T1
Valid prediction for snap_scaffold_18-snap.972-T1
Valid prediction for GeneMark_model.74660_t
Valid prediction for GeneMark_model.74644_t
Valid prediction for snap_scaffold_18-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_43245-T1
Valid prediction for snap_scaffold_18-snap.987-T1
Valid prediction for GeneMark_model.74641_t
Couldn't classify 129202, 129567
Sorry, prediction pasa_asmbl_20596.p1 fails validation.
(GAG)	 GA	129202-129567	GC	AAG
Valid prediction for snap_scaffold_18-snap.993-T1
Valid prediction for snap_scaffold_18-snap.983-T1
Valid prediction for snap_scaffold_18-snap.973-T1
Valid prediction for snap_scaffold_18-snap.988-T1
Valid prediction for GeneMark_model.74645_t
Valid prediction for Augustus_model.g28918.t1
Valid prediction for Augustus_model.g28927.t1
Valid prediction for GlimmerHMM_glimmerT_43231-T1
Valid prediction for GlimmerHMM_glimmerT_43220-T1
Valid prediction for GeneMark_model.74631_t
Valid prediction for Augustus_model.g28916.t1
Valid prediction for GlimmerHMM_glimmerT_43228-T1
Valid prediction for snap_scaffold_18-snap.982-T1
Valid prediction for GeneMark_model.74659_t
Valid prediction for Augustus_model.g28929.t1
Valid prediction for Augustus_model.g28919.t1
Valid prediction for GlimmerHMM_glimmerT_43244-T1
Valid prediction for snap_scaffold_18-snap.978-T1
Valid prediction for GeneMark_model.74662_t
Valid prediction for GeneMark_model.74654_t
Valid prediction for GeneMark_model.74628_t
Valid prediction for GlimmerHMM_glimmerT_43238-T1
Valid prediction for GlimmerHMM_glimmerT_43222-T1
Valid prediction for GlimmerHMM_glimmerT_43237-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56901, rend_intergenic: 56617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73380, rend_intergenic: 70056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76602, rend_intergenic: 73804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79437, rend_intergenic: 78371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115977, rend_intergenic: 115094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132347, rend_intergenic: 129654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165576, rend_intergenic: 164395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168230, rend_intergenic: 166095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171696
-exon list size: 523


building trellis

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99.2    
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99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 56901, rend_intergenic: 56617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73380, rend_intergenic: 70056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76602, rend_intergenic: 73804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79437, rend_intergenic: 78371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115977, rend_intergenic: 115094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132347, rend_intergenic: 129654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165576, rend_intergenic: 164395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168230, rend_intergenic: 166095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support