-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_203232-364914

-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_3-snap.59-T1
Valid prediction for snap_scaffold_3-snap.75-T1
Valid prediction for Augustus_model.g3936.t1
Valid prediction for GlimmerHMM_glimmerT_5965-T1
Valid prediction for snap_scaffold_3-snap.64-T1
Valid prediction for Augustus_model.g3937.t1
Valid prediction for snap_scaffold_3-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_5969-T1
Valid prediction for Augustus_model.g3932.t1
Valid prediction for snap_scaffold_3-snap.57-T1
Valid prediction for Augustus_model.g3928.t1
Valid prediction for snap_scaffold_3-snap.62-T1
Valid prediction for GeneMark_model.9756_t
Valid prediction for snap_scaffold_3-snap.86-T1
Valid prediction for Augustus_model.g3933.t1
Valid prediction for Augustus_model.g3930.t1
Valid prediction for GeneMark_model.9750_t
Valid prediction for snap_scaffold_3-snap.89-T1
Valid prediction for GeneMark_model.9770_t
Valid prediction for snap_scaffold_3-snap.67-T1
Valid prediction for GeneMark_model.9752_t
Valid prediction for snap_scaffold_3-snap.52-T1
Valid prediction for snap_scaffold_3-snap.58-T1
Valid prediction for GeneMark_model.9765_t
Valid prediction for snap_scaffold_3-snap.74-T1
Valid prediction for snap_scaffold_3-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_5966-T1
Valid prediction for snap_scaffold_3-snap.55-T1
Valid prediction for snap_scaffold_3-snap.47-T1
Valid prediction for snap_scaffold_3-snap.50-T1
Valid prediction for GeneMark_model.9785_t
Valid prediction for Augustus_model.g3925.t1
Valid prediction for snap_scaffold_3-snap.80-T1
Valid prediction for snap_scaffold_3-snap.90-T1
Valid prediction for snap_scaffold_3-snap.72-T1
Valid prediction for GeneMark_model.9775_t
Valid prediction for snap_scaffold_3-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_5979-T1
Valid prediction for GeneMark_model.9787_t
Valid prediction for GeneMark_model.9762_t
Valid prediction for snap_scaffold_3-snap.69-T1
Valid prediction for GeneMark_model.9790_t
Valid prediction for GeneMark_model.9760_t
Valid prediction for GeneMark_model.9767_t
Valid prediction for GeneMark_model.9783_t
Valid prediction for snap_scaffold_3-snap.53-T1
Valid prediction for GeneMark_model.9776_t
Valid prediction for GeneMark_model.9758_t
Valid prediction for GlimmerHMM_glimmerT_5963-T1
Valid prediction for GeneMark_model.9753_t
Valid prediction for GeneMark_model.9754_t
Valid prediction for GlimmerHMM_glimmerT_5982-T1
Valid prediction for GlimmerHMM_glimmerT_5964-T1
Valid prediction for snap_scaffold_3-snap.61-T1
Valid prediction for snap_scaffold_3-snap.66-T1
Valid prediction for snap_scaffold_3-snap.83-T1
Valid prediction for GeneMark_model.9780_t
Valid prediction for GeneMark_model.9778_t
Valid prediction for GeneMark_model.9773_t
Valid prediction for snap_scaffold_3-snap.81-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.9786_t
Valid prediction for GeneMark_model.9788_t
Valid prediction for GeneMark_model.9782_t
Valid prediction for snap_scaffold_3-snap.88-T1
Valid prediction for Augustus_model.g3931.t1
Valid prediction for GlimmerHMM_glimmerT_5962-T1
Valid prediction for GeneMark_model.9779_t
Valid prediction for snap_scaffold_3-snap.54-T1
Valid prediction for GlimmerHMM_glimmerT_5967-T1
Valid prediction for snap_scaffold_3-snap.48-T1
Valid prediction for snap_scaffold_3-snap.70-T1
Valid prediction for snap_scaffold_3-snap.63-T1
Valid prediction for Augustus_model.g3935.t1
Valid prediction for snap_scaffold_3-snap.44-T1
Valid prediction for GeneMark_model.9789_t
Valid prediction for GlimmerHMM_glimmerT_5983-T1
Valid prediction for GeneMark_model.9777_t
Valid prediction for GeneMark_model.9761_t
Valid prediction for GeneMark_model.9781_t
Valid prediction for snap_scaffold_3-snap.60-T1
Valid prediction for GeneMark_model.9757_t
Valid prediction for GlimmerHMM_glimmerT_5970-T1
Valid prediction for GeneMark_model.9772_t
Valid prediction for snap_scaffold_3-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_5980-T1
Valid prediction for snap_scaffold_3-snap.51-T1
Valid prediction for GeneMark_model.9755_t
Valid prediction for snap_scaffold_3-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_5974-T1
Valid prediction for snap_scaffold_3-snap.68-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.9766_t
Valid prediction for snap_scaffold_3-snap.79-T1
Valid prediction for GeneMark_model.9774_t
Valid prediction for GeneMark_model.9791_t
Valid prediction for Augustus_model.g3927.t1
Valid prediction for GlimmerHMM_glimmerT_5973-T1
Valid prediction for snap_scaffold_3-snap.78-T1
Valid prediction for snap_scaffold_3-snap.82-T1
Valid prediction for GeneMark_model.9784_t
Valid prediction for GeneMark_model.9768_t
Valid prediction for snap_scaffold_3-snap.77-T1
Valid prediction for GeneMark_model.9759_t
Valid prediction for GlimmerHMM_glimmerT_5978-T1
Valid prediction for Augustus_model.g3934.t1
Valid prediction for GlimmerHMM_glimmerT_5971-T1
Valid prediction for snap_scaffold_3-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_5972-T1
Valid prediction for snap_scaffold_3-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_5975-T1
Valid prediction for GlimmerHMM_glimmerT_5977-T1
Valid prediction for GeneMark_model.9764_t
Valid prediction for snap_scaffold_3-snap.65-T1
Valid prediction for GeneMark_model.9763_t
Valid prediction for Augustus_model.g3929.t1
Valid prediction for Augustus_model.g3926.t1
Valid prediction for snap_scaffold_3-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_5976-T1
Valid prediction for GeneMark_model.9771_t
Valid prediction for snap_scaffold_3-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_5981-T1
Valid prediction for snap_scaffold_3-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_5968-T1
Valid prediction for GeneMark_model.9769_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6552, rend_intergenic: 2112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14219, rend_intergenic: 11019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29139, rend_intergenic: 23451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33500, rend_intergenic: 30462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38441, rend_intergenic: 36701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44774, rend_intergenic: 39734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67798, rend_intergenic: 62515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79908, rend_intergenic: 73825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88016, rend_intergenic: 86733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91634, rend_intergenic: 89171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94942, rend_intergenic: 92810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128212, rend_intergenic: 120254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133652, rend_intergenic: 131907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135683, rend_intergenic: 133906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143171, rend_intergenic: 137663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143840, rend_intergenic: 143839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149440, rend_intergenic: 145768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161683
-exon list size: 648


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 6552, rend_intergenic: 2112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14219, rend_intergenic: 11019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29139, rend_intergenic: 23451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33500, rend_intergenic: 30462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38441, rend_intergenic: 36701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44774, rend_intergenic: 39734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67798, rend_intergenic: 62515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79908, rend_intergenic: 73825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88016, rend_intergenic: 86733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91634, rend_intergenic: 89171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94942, rend_intergenic: 92810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128212, rend_intergenic: 120254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133652, rend_intergenic: 131907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135683, rend_intergenic: 133906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143171, rend_intergenic: 137663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143840, rend_intergenic: 143839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149440, rend_intergenic: 145768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 6 predictions persist after filtering for low support