-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_2198656-2357486

-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_27194-T1
Valid prediction for GlimmerHMM_glimmerT_27186-T1
Valid prediction for snap_scaffold_11-snap.577-T1
Valid prediction for pasa_asmbl_5325.p1
Valid prediction for GlimmerHMM_glimmerT_27192-T1
Valid prediction for GeneMark_model.46898_t
Valid prediction for GeneMark_model.46905_t
Valid prediction for GlimmerHMM_glimmerT_27168-T1
Valid prediction for GeneMark_model.46895_t
Valid prediction for GeneMark_model.46938_t
Valid prediction for GeneMark_model.46915_t
Valid prediction for GlimmerHMM_glimmerT_27183-T1
Valid prediction for snap_scaffold_11-snap.556-T1
Valid prediction for snap_scaffold_11-snap.579-T1
Valid prediction for GeneMark_model.46926_t
Valid prediction for GlimmerHMM_glimmerT_27174-T1
Valid prediction for snap_scaffold_11-snap.576-T1
Valid prediction for Augustus_model.g18153.t1
Valid prediction for GlimmerHMM_glimmerT_27181-T1
Valid prediction for Augustus_model.g18148.t1
Valid prediction for GeneMark_model.46930_t
Valid prediction for GlimmerHMM_glimmerT_27191-T1
Valid prediction for snap_scaffold_11-snap.554-T1
Valid prediction for snap_scaffold_11-snap.558-T1
Valid prediction for GeneMark_model.46909_t
Valid prediction for snap_scaffold_11-snap.575-T1
Valid prediction for Augustus_model.g18147.t1
Valid prediction for GlimmerHMM_glimmerT_27179-T1
Valid prediction for GlimmerHMM_glimmerT_27171-T1
Valid prediction for GeneMark_model.46934_t
Valid prediction for HiQ_model.g18151.t1
Valid prediction for snap_scaffold_11-snap.569-T1
Valid prediction for GeneMark_model.46932_t
Valid prediction for Augustus_model.g18149.t1
Valid prediction for GlimmerHMM_glimmerT_27187-T1
Valid prediction for GeneMark_model.46922_t
Valid prediction for GeneMark_model.46924_t
Valid prediction for GlimmerHMM_glimmerT_27180-T1
Valid prediction for snap_scaffold_11-snap.580-T1
Valid prediction for snap_scaffold_11-snap.582-T1
Valid prediction for GeneMark_model.46919_t
Valid prediction for GeneMark_model.46897_t
Valid prediction for GlimmerHMM_glimmerT_27193-T1
Valid prediction for snap_scaffold_11-snap.581-T1
Valid prediction for snap_scaffold_11-snap.588-T1
Valid prediction for snap_scaffold_11-snap.557-T1
Valid prediction for snap_scaffold_11-snap.559-T1
Valid prediction for GeneMark_model.46920_t
Valid prediction for snap_scaffold_11-snap.562-T1
Valid prediction for snap_scaffold_11-snap.561-T1
Valid prediction for GlimmerHMM_glimmerT_27170-T1
Valid prediction for GeneMark_model.46911_t
Valid prediction for snap_scaffold_11-snap.590-T1
Valid prediction for GeneMark_model.46901_t
Valid prediction for GlimmerHMM_glimmerT_27196-T1
Valid prediction for Augustus_model.g18157.t1
Valid prediction for GeneMark_model.46894_t
Valid prediction for GlimmerHMM_glimmerT_27178-T1
Valid prediction for snap_scaffold_11-snap.566-T1
Valid prediction for GeneMark_model.46914_t
Valid prediction for snap_scaffold_11-snap.586-T1
Valid prediction for GeneMark_model.46910_t
Valid prediction for snap_scaffold_11-snap.572-T1
Valid prediction for GlimmerHMM_glimmerT_27169-T1
Valid prediction for snap_scaffold_11-snap.552-T1
Valid prediction for snap_scaffold_11-snap.570-T1
Valid prediction for GeneMark_model.46931_t
Valid prediction for GeneMark_model.46904_t
Valid prediction for snap_scaffold_11-snap.589-T1
Valid prediction for GeneMark_model.46928_t
Valid prediction for GeneMark_model.46917_t
Valid prediction for CodingQuarry_transcript_7962-T1
Valid prediction for GeneMark_model.46937_t
Valid prediction for GlimmerHMM_glimmerT_27188-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_11-snap.573-T1
Valid prediction for GlimmerHMM_glimmerT_27164-T1
Valid prediction for Augustus_model.g18145.t1
Valid prediction for snap_scaffold_11-snap.560-T1
Valid prediction for GeneMark_model.46927_t
Valid prediction for snap_scaffold_11-snap.555-T1
Valid prediction for snap_scaffold_11-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_27185-T1
Valid prediction for snap_scaffold_11-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_27167-T1
Valid prediction for GeneMark_model.46933_t
Valid prediction for snap_scaffold_11-snap.568-T1
Valid prediction for Augustus_model.g18154.t1
Valid prediction for snap_scaffold_11-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_27173-T1
Valid prediction for snap_scaffold_11-snap.591-T1
Valid prediction for pasa_asmbl_6461.p1
Valid prediction for GlimmerHMM_glimmerT_27175-T1
Valid prediction for snap_scaffold_11-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_27190-T1
Valid prediction for GlimmerHMM_glimmerT_27166-T1
Valid prediction for GeneMark_model.46912_t
Valid prediction for snap_scaffold_11-snap.567-T1
Valid prediction for snap_scaffold_11-snap.587-T1
Valid prediction for GeneMark_model.46936_t
Valid prediction for snap_scaffold_11-snap.584-T1
Valid prediction for GeneMark_model.46902_t
Valid prediction for GlimmerHMM_glimmerT_27195-T1
Valid prediction for GeneMark_model.46900_t
Valid prediction for Augustus_model.g18156.t1
Couldn't classify 72119, 72652
Sorry, prediction pasa_asmbl_6467.p1 fails validation.
(CCT)	 AG	72119-72652	GT	AGG
(TGT)	 AG	73282-73509	GT	AGG
(GTT)	 AG	73801-73940	GT	AGG
(GGA)	 AG	74147-74232	GT	CGG
(GAC)	 AG	74349-74461	GT	AAG
(CTG)	 AG	74581-74677	GT	ATG
(CTC)	 AG	75731-75813	GA	AGG
-recovered pasa_asmbl_6467.p1, terminal, 75731, 75813
-recovered pasa_asmbl_6467.p1, internal, 72119, 72652
-recovered pasa_asmbl_6467.p1, internal, 73282, 73509
-recovered pasa_asmbl_6467.p1, internal, 73801, 73940
-recovered pasa_asmbl_6467.p1, internal, 74147, 74232
-recovered pasa_asmbl_6467.p1, internal, 74349, 74461
-recovered pasa_asmbl_6467.p1, internal, 74581, 74677
Valid prediction for GeneMark_model.46925_t
Valid prediction for GeneMark_model.46893_t
Valid prediction for CodingQuarry_transcript_7961-T1
Valid prediction for snap_scaffold_11-snap.571-T1
Valid prediction for snap_scaffold_11-snap.551-T1
Valid prediction for CodingQuarry_transcript_7960-T1
Valid prediction for Augustus_model.g18146.t1
Valid prediction for GlimmerHMM_glimmerT_27177-T1
Valid prediction for snap_scaffold_11-snap.578-T1
Valid prediction for snap_scaffold_11-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_27176-T1
Valid prediction for GlimmerHMM_glimmerT_27165-T1
Valid prediction for GeneMark_model.46896_t
Valid prediction for GeneMark_model.46906_t
Valid prediction for GeneMark_model.46929_t
Valid prediction for snap_scaffold_11-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_27172-T1
Valid prediction for GeneMark_model.46918_t
Valid prediction for GlimmerHMM_glimmerT_27184-T1
Valid prediction for GlimmerHMM_glimmerT_27189-T1
Valid prediction for GeneMark_model.46913_t
Valid prediction for GeneMark_model.46908_t
Valid prediction for GlimmerHMM_glimmerT_27182-T1
Valid prediction for Augustus_model.g18152.t1
Valid prediction for Augustus_model.g18150.t1
Valid prediction for Augustus_model.g18155.t1
Valid prediction for GeneMark_model.46916_t
Valid prediction for GeneMark_model.46903_t
Valid prediction for GeneMark_model.46923_t
Valid prediction for GeneMark_model.46935_t
Valid prediction for HiQ_model.g18143.t1
Valid prediction for CodingQuarry_transcript_7963-T1
Valid prediction for HiQ_model.g18144.t1
Valid prediction for GeneMark_model.46921_t
Valid prediction for snap_scaffold_11-snap.553-T1
Valid prediction for GeneMark_model.46899_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13737, rend_intergenic: 12755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15767, rend_intergenic: 14754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23933, rend_intergenic: 16258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50165, rend_intergenic: 48349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65026, rend_intergenic: 61431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72735, rend_intergenic: 70898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77210, rend_intergenic: 76882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81173, rend_intergenic: 77691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87083, rend_intergenic: 83119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94963, rend_intergenic: 90914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122561, rend_intergenic: 107134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143429, rend_intergenic: 130405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150158, rend_intergenic: 147520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158831
-exon list size: 697


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13737, rend_intergenic: 12755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15767, rend_intergenic: 14754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23933, rend_intergenic: 16258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50165, rend_intergenic: 48349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65026, rend_intergenic: 61431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72735, rend_intergenic: 70898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77210, rend_intergenic: 76882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81173, rend_intergenic: 77691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87083, rend_intergenic: 83119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94963, rend_intergenic: 90914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122561, rend_intergenic: 107134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143429, rend_intergenic: 130405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150158, rend_intergenic: 147520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support