-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_2208849-2337063

-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 Augustus_model.g38749.t1
Valid prediction for snap_scaffold_27-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_58179-T1
Valid prediction for GeneMark_model.101254_t
Valid prediction for snap_scaffold_27-snap.541-T1
Valid prediction for GeneMark_model.101262_t
Valid prediction for GlimmerHMM_glimmerT_58170-T1
Valid prediction for GlimmerHMM_glimmerT_58161-T1
Valid prediction for Augustus_model.g38750.t1
Valid prediction for GeneMark_model.101272_t
Valid prediction for snap_scaffold_27-snap.542-T1
Valid prediction for GeneMark_model.101235_t
Valid prediction for GeneMark_model.101271_t
Valid prediction for GeneMark_model.101234_t
Valid prediction for GlimmerHMM_glimmerT_58155-T1
Valid prediction for Augustus_model.g38743.t1
Valid prediction for GeneMark_model.101238_t
Valid prediction for snap_scaffold_27-snap.534-T1
Valid prediction for snap_scaffold_27-snap.536-T1
Valid prediction for HiQ_model.g38755.t1
Valid prediction for GlimmerHMM_glimmerT_58159-T1
Valid prediction for GeneMark_model.101259_t
Valid prediction for snap_scaffold_27-snap.551-T1
Valid prediction for GlimmerHMM_glimmerT_58164-T1
Valid prediction for snap_scaffold_27-snap.552-T1
Valid prediction for Augustus_model.g38748.t1
Valid prediction for GlimmerHMM_glimmerT_58168-T1
Valid prediction for Augustus_model.g38742.t1
Valid prediction for Augustus_model.g38740.t1
Valid prediction for snap_scaffold_27-snap.517-T1
Valid prediction for snap_scaffold_27-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_58181-T1
Valid prediction for GlimmerHMM_glimmerT_58167-T1
Valid prediction for GlimmerHMM_glimmerT_58151-T1
Valid prediction for GeneMark_model.101274_t
Valid prediction for GlimmerHMM_glimmerT_58177-T1
Valid prediction for GeneMark_model.101269_t
Valid prediction for GlimmerHMM_glimmerT_58180-T1
Valid prediction for GlimmerHMM_glimmerT_58178-T1
Valid prediction for GlimmerHMM_glimmerT_58157-T1
Valid prediction for snap_scaffold_27-snap.553-T1
Valid prediction for snap_scaffold_27-snap.518-T1
Valid prediction for snap_scaffold_27-snap.527-T1
Valid prediction for snap_scaffold_27-snap.550-T1
Valid prediction for GeneMark_model.101251_t
Valid prediction for GeneMark_model.101257_t
Valid prediction for snap_scaffold_27-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_58173-T1
Valid prediction for snap_scaffold_27-snap.540-T1
Valid prediction for snap_scaffold_27-snap.528-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58182-T1
Valid prediction for GeneMark_model.101264_t
Valid prediction for GlimmerHMM_glimmerT_58165-T1
Valid prediction for GeneMark_model.101276_t
Valid prediction for GeneMark_model.101243_t
Valid prediction for HiQ_model.g38758.t1
Valid prediction for GeneMark_model.101247_t
Valid prediction for Augustus_model.g38757.t1
Valid prediction for snap_scaffold_27-snap.524-T1
Valid prediction for GeneMark_model.101249_t
Valid prediction for snap_scaffold_27-snap.549-T1
Valid prediction for GeneMark_model.101241_t
Valid prediction for GlimmerHMM_glimmerT_58154-T1
Valid prediction for pasa_asmbl_36037.p1
Valid prediction for snap_scaffold_27-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_58176-T1
Valid prediction for GeneMark_model.101236_t
Valid prediction for GeneMark_model.101256_t
Valid prediction for CodingQuarry_transcript_41710-T1
Valid prediction for GeneMark_model.101245_t
Valid prediction for GeneMark_model.101267_t
Valid prediction for GeneMark_model.101275_t
Valid prediction for snap_scaffold_27-snap.520-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 GeneMark_model.101248_t
Valid prediction for Augustus_model.g38745.t1
Valid prediction for Augustus_model.g38739.t1
Valid prediction for GeneMark_model.101263_t
Valid prediction for GeneMark_model.101246_t
Valid prediction for Augustus_model.g38752.t1
Valid prediction for Augustus_model.g38751.t1
Valid prediction for GlimmerHMM_glimmerT_58163-T1
Valid prediction for Augustus_model.g38744.t1
Valid prediction for snap_scaffold_27-snap.537-T1
Valid prediction for snap_scaffold_27-snap.544-T1
Valid prediction for GeneMark_model.101273_t
Valid prediction for snap_scaffold_27-snap.547-T1
Valid prediction for GeneMark_model.101265_t
Valid prediction for snap_scaffold_27-snap.530-T1
Valid prediction for snap_scaffold_27-snap.539-T1
Valid prediction for GeneMark_model.101268_t
Valid prediction for snap_scaffold_27-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_58152-T1
Valid prediction for GeneMark_model.101237_t
Valid prediction for GlimmerHMM_glimmerT_58172-T1
Valid prediction for Augustus_model.g38746.t1
Valid prediction for GlimmerHMM_glimmerT_58174-T1
Valid prediction for GlimmerHMM_glimmerT_58166-T1
Couldn't classify 28644, 28649
Couldn't classify 29636, 29777
Sorry, prediction pasa_asmbl_36772.p1 fails validation.
(CCA)	 GG	28644-28649	GT	TGG
(TCC)	 AG	29082-29180	GT	AGG
(TCC)	 AG	29298-29413	GT	CAG
(GGA)	 AG	29636-29777	GT	TGG
-recovered pasa_asmbl_36772.p1, internal, 29082, 29180
-recovered pasa_asmbl_36772.p1, internal, 29298, 29413
-recovered pasa_asmbl_36772.p1, internal, 29636, 29777
Valid prediction for snap_scaffold_27-snap.545-T1
Valid prediction for GeneMark_model.101261_t
Valid prediction for snap_scaffold_27-snap.526-T1
Valid prediction for GeneMark_model.101233_t
Valid prediction for snap_scaffold_27-snap.525-T1
Valid prediction for Augustus_model.g38756.t1
Valid prediction for Augustus_model.g38753.t1
Valid prediction for GlimmerHMM_glimmerT_58169-T1
Valid prediction for GlimmerHMM_glimmerT_58175-T1
Valid prediction for GlimmerHMM_glimmerT_58171-T1
Valid prediction for GeneMark_model.101260_t
Valid prediction for Augustus_model.g38741.t1
Valid prediction for GeneMark_model.101250_t
Valid prediction for snap_scaffold_27-snap.516-T1
Valid prediction for snap_scaffold_27-snap.529-T1
Valid prediction for snap_scaffold_27-snap.523-T1
Valid prediction for snap_scaffold_27-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_58162-T1
Valid prediction for GeneMark_model.101244_t
Valid prediction for snap_scaffold_27-snap.515-T1
Valid prediction for Augustus_model.g38747.t1
Valid prediction for snap_scaffold_27-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_58156-T1
Valid prediction for GeneMark_model.101253_t
Valid prediction for GlimmerHMM_glimmerT_58153-T1
Valid prediction for GlimmerHMM_glimmerT_58160-T1
Valid prediction for GeneMark_model.101266_t
Valid prediction for snap_scaffold_27-snap.543-T1
Valid prediction for GeneMark_model.101255_t
Valid prediction for snap_scaffold_27-snap.546-T1
Valid prediction for Augustus_model.g38754.t1
Valid prediction for snap_scaffold_27-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_58158-T1
Valid prediction for snap_scaffold_27-snap.548-T1
Valid prediction for GeneMark_model.101239_t
Valid prediction for GeneMark_model.101258_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29088, rend_intergenic: 27517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37804, rend_intergenic: 34807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46158, rend_intergenic: 44278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103651, rend_intergenic: 100353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128215
-exon list size: 506


building trellis

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92.9    
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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 29088, rend_intergenic: 27517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37804, rend_intergenic: 34807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46158, rend_intergenic: 44278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103651, rend_intergenic: 100353  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