-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_15682148-15878022

-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.41226_t
Valid prediction for GlimmerHMM_glimmerT_24042-T1
Valid prediction for GlimmerHMM_glimmerT_24031-T1
Valid prediction for snap_scaffold_9-snap.3203-T1
Valid prediction for GeneMark_model.41210_t
Valid prediction for GlimmerHMM_glimmerT_24032-T1
Valid prediction for snap_scaffold_9-snap.3215-T1
Valid prediction for GeneMark_model.41247_t
Valid prediction for pasa_asmbl_54562.p1
Valid prediction for GlimmerHMM_glimmerT_24043-T1
Valid prediction for GlimmerHMM_glimmerT_24036-T1
Valid prediction for snap_scaffold_9-snap.3204-T1
Valid prediction for GeneMark_model.41242_t
Valid prediction for GlimmerHMM_glimmerT_24030-T1
Valid prediction for snap_scaffold_9-snap.3228-T1
Valid prediction for snap_scaffold_9-snap.3206-T1
Valid prediction for GlimmerHMM_glimmerT_24040-T1
Valid prediction for GeneMark_model.41248_t
Valid prediction for GeneMark_model.41229_t
Valid prediction for HiQ_model.g16102.t1
Valid prediction for snap_scaffold_9-snap.3218-T1
Valid prediction for GeneMark_model.41237_t
Valid prediction for GlimmerHMM_glimmerT_24039-T1
Valid prediction for Augustus_model.g16107.t1
Valid prediction for Augustus_model.g16100.t1
Valid prediction for GeneMark_model.41214_t
Valid prediction for snap_scaffold_9-snap.3213-T1
Valid prediction for snap_scaffold_9-snap.3202-T1
Valid prediction for GeneMark_model.41215_t
Valid prediction for Augustus_model.g16104.t1
Valid prediction for GeneMark_model.41245_t
Valid prediction for Augustus_model.g16101.t1
Valid prediction for snap_scaffold_9-snap.3211-T1
Valid prediction for GeneMark_model.41217_t
Valid prediction for snap_scaffold_9-snap.3217-T1
Valid prediction for snap_scaffold_9-snap.3222-T1
Valid prediction for GeneMark_model.41224_t
Valid prediction for GeneMark_model.41208_t
Valid prediction for snap_scaffold_9-snap.3199-T1
Valid prediction for Augustus_model.g16108.t1
Valid prediction for GlimmerHMM_glimmerT_24035-T1
Valid prediction for Augustus_model.g16106.t1
Valid prediction for GlimmerHMM_glimmerT_24047-T1
Valid prediction for snap_scaffold_9-snap.3224-T1
Valid prediction for GlimmerHMM_glimmerT_24033-T1
Valid prediction for GeneMark_model.41220_t
Valid prediction for GeneMark_model.41212_t
Valid prediction for GlimmerHMM_glimmerT_24045-T1
Valid prediction for GlimmerHMM_glimmerT_24046-T1
Valid prediction for snap_scaffold_9-snap.3223-T1
Valid prediction for GeneMark_model.41225_t
Valid prediction for snap_scaffold_9-snap.3197-T1
Valid prediction for GeneMark_model.41235_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 snap_scaffold_9-snap.3198-T1
Valid prediction for snap_scaffold_9-snap.3225-T1
Valid prediction for GeneMark_model.41236_t
Couldn't classify 124856, 124886
Couldn't classify 125780, 125878
Sorry, prediction pasa_asmbl_55519.p1 fails validation.
(AAA)	 AG	124856-124886	GT	AGG
(GGA)	 AG	124992-125098	GT	ATG
(ATC)	 AG	125227-125370	GT	AGG
(GTG)	 AG	125780-125878	GG	GGG
-recovered pasa_asmbl_55519.p1, internal, 124856, 124886
-recovered pasa_asmbl_55519.p1, internal, 124992, 125098
-recovered pasa_asmbl_55519.p1, internal, 125227, 125370
Valid prediction for snap_scaffold_9-snap.3212-T1
Valid prediction for GeneMark_model.41243_t
Couldn't classify 129635, 129880
Sorry, prediction pasa_asmbl_55517.p1 fails validation.
(GCC)	 TA	129635-129880	GT	AGG
(GGT)	 AG	130100-130192	TG	GAT
-recovered pasa_asmbl_55517.p1, terminal, 130100, 130192
Valid prediction for GeneMark_model.41222_t
Valid prediction for GlimmerHMM_glimmerT_24037-T1
Valid prediction for GeneMark_model.41211_t
Valid prediction for GeneMark_model.41244_t
Valid prediction for GeneMark_model.41241_t
Valid prediction for GeneMark_model.41228_t
Valid prediction for GeneMark_model.41239_t
Valid prediction for GeneMark_model.41213_t
Valid prediction for GlimmerHMM_glimmerT_24034-T1
Valid prediction for snap_scaffold_9-snap.3205-T1
Valid prediction for GeneMark_model.41219_t
Valid prediction for pasa_asmbl_55518.p1
Valid prediction for GeneMark_model.41221_t
Valid prediction for Augustus_model.g16105.t1
Valid prediction for snap_scaffold_9-snap.3220-T1
Valid prediction for GlimmerHMM_glimmerT_24044-T1
Valid prediction for snap_scaffold_9-snap.3210-T1
Valid prediction for snap_scaffold_9-snap.3200-T1
Valid prediction for Augustus_model.g16103.t1
Valid prediction for GeneMark_model.41223_t
Valid prediction for snap_scaffold_9-snap.3201-T1
Valid prediction for GeneMark_model.41240_t
Valid prediction for GeneMark_model.41246_t
Valid prediction for GeneMark_model.41234_t
Valid prediction for GeneMark_model.41216_t
Valid prediction for GeneMark_model.41209_t
Valid prediction for GlimmerHMM_glimmerT_24038-T1
Valid prediction for GeneMark_model.41233_t
Valid prediction for snap_scaffold_9-snap.3207-T1
Valid prediction for snap_scaffold_9-snap.3208-T1
Valid prediction for GeneMark_model.41232_t
Valid prediction for snap_scaffold_9-snap.3209-T1
Valid prediction for snap_scaffold_9-snap.3226-T1
Valid prediction for GeneMark_model.41218_t
Valid prediction for snap_scaffold_9-snap.3227-T1
Valid prediction for snap_scaffold_9-snap.3214-T1
Valid prediction for snap_scaffold_9-snap.3219-T1
Valid prediction for GeneMark_model.41231_t
Valid prediction for snap_scaffold_9-snap.3216-T1
Valid prediction for GeneMark_model.41227_t
Valid prediction for snap_scaffold_9-snap.3221-T1
Valid prediction for GeneMark_model.41238_t
Valid prediction for GeneMark_model.41230_t
Valid prediction for GlimmerHMM_glimmerT_24041-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11846, rend_intergenic: 10923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28337, rend_intergenic: 14988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47075, rend_intergenic: 33785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110373, rend_intergenic: 101697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113854, rend_intergenic: 111117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125133, rend_intergenic: 122155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160454, rend_intergenic: 141734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195875
-exon list size: 546


building trellis

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99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11846, rend_intergenic: 10923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28337, rend_intergenic: 14988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47075, rend_intergenic: 33785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110373, rend_intergenic: 101697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113854, rend_intergenic: 111117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125133, rend_intergenic: 122155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160454, rend_intergenic: 141734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support