-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_4361824-4540767

-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 GlimmerHMM_glimmerT_36801-T1
Valid prediction for GlimmerHMM_glimmerT_36795-T1
Valid prediction for GeneMark_model.63342_t
Valid prediction for snap_scaffold_15-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_36788-T1
Valid prediction for GeneMark_model.63351_t
Valid prediction for CodingQuarry_transcript_17939-T1
Valid prediction for HiQ_model.g24711.t1
Valid prediction for snap_scaffold_15-snap.966-T1
Valid prediction for snap_scaffold_15-snap.969-T1
Valid prediction for snap_scaffold_15-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_36800-T1
Valid prediction for Augustus_model.g24703.t1
Valid prediction for snap_scaffold_15-snap.964-T1
Valid prediction for snap_scaffold_15-snap.949-T1
Valid prediction for GeneMark_model.63346_t
Valid prediction for Augustus_model.g24709.t1
Valid prediction for GeneMark_model.63335_t
Valid prediction for GeneMark_model.63334_t
Valid prediction for snap_scaffold_15-snap.965-T1
Valid prediction for snap_scaffold_15-snap.973-T1
Couldn't classify 150218, 150451
Couldn't classify 152942, 153073
Sorry, prediction pasa_asmbl_14095.p1 fails validation.
(TGT)	 TG	150218-150451	GT	TGG
(TTT)	 AG	152395-152505	GT	AGG
(CTC)	 AG	152623-152715	GT	AGG
(CTG)	 AG	152942-153073	TG	GGT
-recovered pasa_asmbl_14095.p1, internal, 152395, 152505
-recovered pasa_asmbl_14095.p1, internal, 152623, 152715
Valid prediction for Augustus_model.g24704.t1
Valid prediction for GlimmerHMM_glimmerT_36798-T1
Valid prediction for GeneMark_model.63319_t
Valid prediction for snap_scaffold_15-snap.945-T1
Valid prediction for GeneMark_model.63348_t
Valid prediction for snap_scaffold_15-snap.968-T1
Valid prediction for GeneMark_model.63332_t
Valid prediction for snap_scaffold_15-snap.952-T1
Valid prediction for pasa_asmbl_14090.p1
Valid prediction for GeneMark_model.63324_t
Valid prediction for GeneMark_model.63327_t
Valid prediction for GeneMark_model.63339_t
Valid prediction for snap_scaffold_15-snap.971-T1
Valid prediction for Augustus_model.g24713.t1
Valid prediction for GeneMark_model.63320_t
Valid prediction for snap_scaffold_15-snap.960-T1
Valid prediction for snap_scaffold_15-snap.953-T1
Valid prediction for Augustus_model.g24714.t1
Valid prediction for snap_scaffold_15-snap.947-T1
Valid prediction for GeneMark_model.63330_t
Valid prediction for GeneMark_model.63318_t
Valid prediction for GlimmerHMM_glimmerT_36782-T1
Valid prediction for snap_scaffold_15-snap.954-T1
Valid prediction for GlimmerHMM_glimmerT_36796-T1
Valid prediction for snap_scaffold_15-snap.946-T1
Valid prediction for snap_scaffold_15-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_36780-T1
Valid prediction for snap_scaffold_15-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_36783-T1
Valid prediction for CodingQuarry_transcript_17938-T1
Valid prediction for GlimmerHMM_glimmerT_36786-T1
Valid prediction for snap_scaffold_15-snap.948-T1
Valid prediction for GeneMark_model.63323_t
Valid prediction for GlimmerHMM_glimmerT_36802-T1
Couldn't classify 153406, 153420
Sorry, prediction pasa_asmbl_14097.p1 fails validation.
(GTT)	 GT	153406-153420	GT	AGG
(CTG)	 AG	153646-153699	GT	CAG
(ACA)	 AG	153902-154072	GT	AGG
(GTG)	 AG	154250-154377	GT	AAG
(AAC)	 AG	154734-154835	GT	AAG
(AGA)	 AG	154942-155014	GT	AGG
(TTC)	 AG	155139-155255	GT	AGG
(ATC)	 AG	155865-155999	AC	AGA
-recovered pasa_asmbl_14097.p1, terminal, 155865, 155999
-recovered pasa_asmbl_14097.p1, internal, 153646, 153699
-recovered pasa_asmbl_14097.p1, internal, 153902, 154072
-recovered pasa_asmbl_14097.p1, internal, 154250, 154377
-recovered pasa_asmbl_14097.p1, internal, 154734, 154835
-recovered pasa_asmbl_14097.p1, internal, 154942, 155014
-recovered pasa_asmbl_14097.p1, internal, 155139, 155255
Valid prediction for snap_scaffold_15-snap.970-T1
Valid prediction for GeneMark_model.63344_t
Valid prediction for GlimmerHMM_glimmerT_36791-T1
Valid prediction for GeneMark_model.63345_t
Valid prediction for CodingQuarry_transcript_17935-T1
Valid prediction for GlimmerHMM_glimmerT_36787-T1
Valid prediction for GlimmerHMM_glimmerT_36785-T1
Valid prediction for pasa_asmbl_14083.p1
Valid prediction for Augustus_model.g24708.t1
Valid prediction for Augustus_model.g24706.t1
Valid prediction for snap_scaffold_15-snap.975-T1
Valid prediction for GeneMark_model.63337_t
Valid prediction for HiQ_model.g24712.t1
Valid prediction for GeneMark_model.63341_t
Valid prediction for GlimmerHMM_glimmerT_36781-T1
Valid prediction for CodingQuarry_transcript_17936-T1
Valid prediction for GeneMark_model.63325_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 Augustus_model.g24707.t1
Valid prediction for snap_scaffold_15-snap.977-T1
Valid prediction for GeneMark_model.63340_t
Valid prediction for snap_scaffold_15-snap.957-T1
Valid prediction for Augustus_model.g24702.t1
Valid prediction for GeneMark_model.63349_t
Valid prediction for GeneMark_model.63336_t
Valid prediction for GlimmerHMM_glimmerT_36789-T1
Valid prediction for GlimmerHMM_glimmerT_36797-T1
Valid prediction for GlimmerHMM_glimmerT_36779-T1
Valid prediction for GlimmerHMM_glimmerT_36790-T1
Valid prediction for HiQ_model.g24710.t1
Valid prediction for GlimmerHMM_glimmerT_36805-T1
Valid prediction for GeneMark_model.63350_t
Valid prediction for GlimmerHMM_glimmerT_36792-T1
Valid prediction for GeneMark_model.63343_t
Valid prediction for GeneMark_model.63322_t
Valid prediction for GeneMark_model.63328_t
Valid prediction for GlimmerHMM_glimmerT_36799-T1
Valid prediction for GeneMark_model.63347_t
Valid prediction for snap_scaffold_15-snap.950-T1
Valid prediction for snap_scaffold_15-snap.972-T1
Valid prediction for snap_scaffold_15-snap.967-T1
Valid prediction for GeneMark_model.63321_t
Valid prediction for GeneMark_model.63331_t
Valid prediction for snap_scaffold_15-snap.956-T1
Valid prediction for Augustus_model.g24701.t1
Valid prediction for snap_scaffold_15-snap.951-T1
Valid prediction for snap_scaffold_15-snap.961-T1
Couldn't classify 10148, 10450
Sorry, prediction pasa_asmbl_15157.p1 fails validation.
(ATG)	 TC	10148-10450	CG	ACC
Valid prediction for pasa_asmbl_15153.p1
Valid prediction for GeneMark_model.63326_t
Valid prediction for snap_scaffold_15-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_36793-T1
Valid prediction for snap_scaffold_15-snap.944-T1
Valid prediction for GeneMark_model.63329_t
Valid prediction for GlimmerHMM_glimmerT_36794-T1
Valid prediction for Augustus_model.g24705.t1
Valid prediction for snap_scaffold_15-snap.955-T1
Valid prediction for GeneMark_model.63338_t
Valid prediction for Augustus_model.g24715.t1
Valid prediction for GeneMark_model.63333_t
Valid prediction for GlimmerHMM_glimmerT_36803-T1
Valid prediction for GlimmerHMM_glimmerT_36784-T1
Valid prediction for GlimmerHMM_glimmerT_36804-T1
Valid prediction for GeneMark_model.63317_t
Valid prediction for snap_scaffold_15-snap.974-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 155999, rend_intergenic: 155996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32599, rend_intergenic: 31846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55798, rend_intergenic: 49663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76522, rend_intergenic: 74450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151057, rend_intergenic: 147333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152786, rend_intergenic: 151390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155999, rend_intergenic: 153829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178944
-exon list size: 462


building trellis

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99.1    
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99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 155999, rend_intergenic: 155996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32599, rend_intergenic: 31846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55798, rend_intergenic: 49663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76522, rend_intergenic: 74450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151057, rend_intergenic: 147333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152786, rend_intergenic: 151390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155999, rend_intergenic: 153829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support