-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_17228251-17382946

-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.8851_t
Valid prediction for GlimmerHMM_glimmerT_5481-T1
Valid prediction for GlimmerHMM_glimmerT_5488-T1
Valid prediction for snap_scaffold_2-snap.3380-T1
Valid prediction for GlimmerHMM_glimmerT_5503-T1
Valid prediction for snap_scaffold_2-snap.3416-T1
Valid prediction for snap_scaffold_2-snap.3404-T1
Valid prediction for HiQ_model.g3709.t1
Valid prediction for GlimmerHMM_glimmerT_5494-T1
Valid prediction for GeneMark_model.8864_t
Valid prediction for Augustus_model.g3720.t1
Valid prediction for snap_scaffold_2-snap.3383-T1
Valid prediction for GlimmerHMM_glimmerT_5490-T1
Valid prediction for Augustus_model.g3714.t1
Valid prediction for GlimmerHMM_glimmerT_5485-T1
Valid prediction for GeneMark_model.8844_t
Valid prediction for GeneMark_model.8874_t
Valid prediction for snap_scaffold_2-snap.3397-T1
Valid prediction for snap_scaffold_2-snap.3390-T1
Valid prediction for GeneMark_model.8843_t
Valid prediction for HiQ_model.g3711.t1
Valid prediction for GeneMark_model.8848_t
Valid prediction for GlimmerHMM_glimmerT_5499-T1
Valid prediction for GeneMark_model.8855_t
Valid prediction for GeneMark_model.8863_t
Valid prediction for Augustus_model.g3713.t1
Valid prediction for snap_scaffold_2-snap.3394-T1
Valid prediction for GeneMark_model.8861_t
Valid prediction for snap_scaffold_2-snap.3391-T1
Valid prediction for snap_scaffold_2-snap.3409-T1
Valid prediction for snap_scaffold_2-snap.3399-T1
Valid prediction for GeneMark_model.8846_t
Valid prediction for snap_scaffold_2-snap.3401-T1
Valid prediction for GlimmerHMM_glimmerT_5495-T1
Valid prediction for snap_scaffold_2-snap.3413-T1
Valid prediction for pasa_asmbl_25196.p1
Valid prediction for GeneMark_model.8876_t
Valid prediction for pasa_asmbl_25451.p1
Valid prediction for CodingQuarry_transcript_28761-T1
Valid prediction for GeneMark_model.8859_t
Valid prediction for GeneMark_model.8853_t
Valid prediction for Augustus_model.g3721.t1
Valid prediction for GeneMark_model.8872_t
Valid prediction for snap_scaffold_2-snap.3392-T1
Valid prediction for GeneMark_model.8858_t
Valid prediction for Augustus_model.g3712.t1
Valid prediction for GeneMark_model.8866_t
Valid prediction for GlimmerHMM_glimmerT_5483-T1
Valid prediction for snap_scaffold_2-snap.3412-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3402-T1
Valid prediction for snap_scaffold_2-snap.3384-T1
Valid prediction for GeneMark_model.8837_t
Valid prediction for GeneMark_model.8868_t
Valid prediction for GeneMark_model.8832_t
Valid prediction for GeneMark_model.8839_t
Valid prediction for snap_scaffold_2-snap.3378-T1
Valid prediction for GeneMark_model.8879_t
Valid prediction for GeneMark_model.8870_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 GeneMark_model.8860_t
Valid prediction for GeneMark_model.8852_t
Valid prediction for snap_scaffold_2-snap.3407-T1
Valid prediction for GeneMark_model.8831_t
Valid prediction for GeneMark_model.8877_t
Valid prediction for snap_scaffold_2-snap.3388-T1
Valid prediction for Augustus_model.g3727.t1
Valid prediction for GlimmerHMM_glimmerT_5491-T1
Valid prediction for GeneMark_model.8880_t
Valid prediction for GeneMark_model.8845_t
Valid prediction for GlimmerHMM_glimmerT_5496-T1
Valid prediction for GeneMark_model.8881_t
Valid prediction for snap_scaffold_2-snap.3389-T1
Valid prediction for GlimmerHMM_glimmerT_5486-T1
Valid prediction for GlimmerHMM_glimmerT_5487-T1
Valid prediction for GeneMark_model.8871_t
Valid prediction for GeneMark_model.8841_t
Valid prediction for GlimmerHMM_glimmerT_5502-T1
Valid prediction for Augustus_model.g3722.t1
Valid prediction for snap_scaffold_2-snap.3382-T1
Valid prediction for snap_scaffold_2-snap.3377-T1
Valid prediction for HiQ_model.g3710.t1
Valid prediction for GeneMark_model.8878_t
Valid prediction for Augustus_model.g3724.t1
Valid prediction for snap_scaffold_2-snap.3395-T1
Valid prediction for Augustus_model.g3723.t1
Valid prediction for GlimmerHMM_glimmerT_5492-T1
Valid prediction for snap_scaffold_2-snap.3405-T1
Valid prediction for snap_scaffold_2-snap.3400-T1
Valid prediction for snap_scaffold_2-snap.3386-T1
Valid prediction for Augustus_model.g3715.t1
Valid prediction for snap_scaffold_2-snap.3414-T1
Valid prediction for Augustus_model.g3716.t1
Valid prediction for GlimmerHMM_glimmerT_5480-T1
Valid prediction for GlimmerHMM_glimmerT_5501-T1
Valid prediction for snap_scaffold_2-snap.3411-T1
Valid prediction for Augustus_model.g3726.t1
Valid prediction for Augustus_model.g3718.t1
Valid prediction for snap_scaffold_2-snap.3398-T1
Valid prediction for GeneMark_model.8842_t
Valid prediction for pasa_asmbl_23730.p1
Valid prediction for GeneMark_model.8840_t
Valid prediction for GeneMark_model.8828_t
Valid prediction for GeneMark_model.8854_t
Valid prediction for GeneMark_model.8833_t
Valid prediction for snap_scaffold_2-snap.3396-T1
Valid prediction for GeneMark_model.8869_t
Valid prediction for GeneMark_model.8865_t
Valid prediction for GeneMark_model.8834_t
Valid prediction for GeneMark_model.8862_t
Valid prediction for snap_scaffold_2-snap.3406-T1
Valid prediction for GeneMark_model.8847_t
Valid prediction for Augustus_model.g3708.t1
Valid prediction for CodingQuarry_transcript_28760-T1
Valid prediction for Augustus_model.g3719.t1
Valid prediction for GlimmerHMM_glimmerT_5489-T1
Valid prediction for GlimmerHMM_glimmerT_5482-T1
Valid prediction for GlimmerHMM_glimmerT_5500-T1
Valid prediction for GlimmerHMM_glimmerT_5484-T1
Valid prediction for pasa_asmbl_23732.p1
Valid prediction for Augustus_model.g3717.t1
Valid prediction for GeneMark_model.8838_t
Valid prediction for GeneMark_model.8849_t
Valid prediction for GeneMark_model.8867_t
Valid prediction for GeneMark_model.8836_t
Valid prediction for GeneMark_model.8850_t
Valid prediction for snap_scaffold_2-snap.3393-T1
Sorry, intron length (8) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5493-T1
Valid prediction for GeneMark_model.8873_t
Valid prediction for snap_scaffold_2-snap.3379-T1
Valid prediction for snap_scaffold_2-snap.3385-T1
Valid prediction for GeneMark_model.8856_t
Valid prediction for Augustus_model.g3725.t1
Valid prediction for GeneMark_model.8857_t
Valid prediction for snap_scaffold_2-snap.3387-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.8830_t
Valid prediction for snap_scaffold_2-snap.3381-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5498-T1
Valid prediction for snap_scaffold_2-snap.3410-T1
Valid prediction for GlimmerHMM_glimmerT_5497-T1
Valid prediction for snap_scaffold_2-snap.3403-T1
Valid prediction for snap_scaffold_2-snap.3408-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26288, rend_intergenic: 26287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46627, rend_intergenic: 29920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56473, rend_intergenic: 46812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62806, rend_intergenic: 56658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65336, rend_intergenic: 63390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68436, rend_intergenic: 65734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77128, rend_intergenic: 71103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85435, rend_intergenic: 78655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102969, rend_intergenic: 98399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114300, rend_intergenic: 103728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130769, rend_intergenic: 122429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145816, rend_intergenic: 139207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154696
-exon list size: 712


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 26288, rend_intergenic: 26287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46627, rend_intergenic: 29920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56473, rend_intergenic: 46812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62806, rend_intergenic: 56658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65336, rend_intergenic: 63390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68436, rend_intergenic: 65734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77128, rend_intergenic: 71103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85435, rend_intergenic: 78655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102969, rend_intergenic: 98399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114300, rend_intergenic: 103728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130769, rend_intergenic: 122429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145816, rend_intergenic: 139207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support