-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_14606826-14778622

-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.53899_t
Valid prediction for GeneMark_model.53888_t
Valid prediction for snap_scaffold_12-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_31205-T1
Valid prediction for GlimmerHMM_glimmerT_31206-T1
Valid prediction for snap_scaffold_12-snap.2808-T1
Valid prediction for GeneMark_model.53886_t
Valid prediction for GeneMark_model.53862_t
Valid prediction for snap_scaffold_12-snap.2817-T1
Valid prediction for GeneMark_model.53870_t
Valid prediction for snap_scaffold_12-snap.2805-T1
Valid prediction for Augustus_model.g20811.t1
Valid prediction for Augustus_model.g20807.t1
Valid prediction for GeneMark_model.53891_t
Valid prediction for snap_scaffold_12-snap.2795-T1
Valid prediction for GlimmerHMM_glimmerT_31194-T1
Valid prediction for GeneMark_model.53901_t
Valid prediction for Augustus_model.g20795.t1
Valid prediction for snap_scaffold_12-snap.2783-T1
Valid prediction for snap_scaffold_12-snap.2789-T1
Valid prediction for GeneMark_model.53878_t
Valid prediction for GlimmerHMM_glimmerT_31189-T1
Valid prediction for GeneMark_model.53859_t
Valid prediction for GeneMark_model.53909_t
Valid prediction for GeneMark_model.53883_t
Valid prediction for GeneMark_model.53866_t
Valid prediction for snap_scaffold_12-snap.2786-T1
Valid prediction for GeneMark_model.53856_t
Valid prediction for snap_scaffold_12-snap.2813-T1
Valid prediction for GlimmerHMM_glimmerT_31216-T1
Valid prediction for GeneMark_model.53867_t
Valid prediction for Augustus_model.g20797.t1
Valid prediction for GeneMark_model.53896_t
Valid prediction for GeneMark_model.53880_t
Valid prediction for GeneMark_model.53894_t
Valid prediction for snap_scaffold_12-snap.2815-T1
Valid prediction for snap_scaffold_12-snap.2791-T1
Valid prediction for GeneMark_model.53874_t
Valid prediction for GeneMark_model.53864_t
Valid prediction for GlimmerHMM_glimmerT_31201-T1
Valid prediction for Augustus_model.g20806.t1
Valid prediction for snap_scaffold_12-snap.2790-T1
Valid prediction for snap_scaffold_12-snap.2807-T1
Valid prediction for snap_scaffold_12-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_31186-T1
Valid prediction for Augustus_model.g20800.t1
Valid prediction for GlimmerHMM_glimmerT_31197-T1
Valid prediction for GeneMark_model.53907_t
Valid prediction for GeneMark_model.53905_t
Valid prediction for GlimmerHMM_glimmerT_31210-T1
Valid prediction for GeneMark_model.53884_t
Valid prediction for snap_scaffold_12-snap.2800-T1
Valid prediction for GeneMark_model.53876_t
Valid prediction for GeneMark_model.53860_t
Valid prediction for Augustus_model.g20809.t1
Valid prediction for GeneMark_model.53863_t
Valid prediction for GlimmerHMM_glimmerT_31183-T1
Valid prediction for GeneMark_model.53872_t
Valid prediction for GeneMark_model.53903_t
Valid prediction for GlimmerHMM_glimmerT_31184-T1
Valid prediction for snap_scaffold_12-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_31190-T1
Valid prediction for GeneMark_model.53889_t
Valid prediction for GlimmerHMM_glimmerT_31212-T1
Valid prediction for Augustus_model.g20808.t1
Valid prediction for snap_scaffold_12-snap.2799-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 GlimmerHMM_glimmerT_31213-T1
Valid prediction for GeneMark_model.53893_t
Valid prediction for snap_scaffold_12-snap.2814-T1
Valid prediction for GeneMark_model.53868_t
Valid prediction for snap_scaffold_12-snap.2792-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31191-T1
Valid prediction for snap_scaffold_12-snap.2794-T1
Valid prediction for Augustus_model.g20802.t1
Valid prediction for GeneMark_model.53857_t
Valid prediction for Augustus_model.g20805.t1
Valid prediction for Augustus_model.g20799.t1
Valid prediction for GeneMark_model.53861_t
Valid prediction for snap_scaffold_12-snap.2784-T1
Valid prediction for snap_scaffold_12-snap.2810-T1
Valid prediction for snap_scaffold_12-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_31204-T1
Valid prediction for GlimmerHMM_glimmerT_31198-T1
Valid prediction for snap_scaffold_12-snap.2787-T1
Valid prediction for snap_scaffold_12-snap.2818-T1
Valid prediction for snap_scaffold_12-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_31192-T1
Valid prediction for GeneMark_model.53902_t
Valid prediction for snap_scaffold_12-snap.2819-T1
Valid prediction for GeneMark_model.53890_t
Valid prediction for Augustus_model.g20810.t1
Valid prediction for snap_scaffold_12-snap.2802-T1
Valid prediction for GlimmerHMM_glimmerT_31185-T1
Valid prediction for Augustus_model.g20796.t1
Valid prediction for GeneMark_model.53881_t
Valid prediction for Augustus_model.g20798.t1
Valid prediction for GlimmerHMM_glimmerT_31203-T1
Valid prediction for GlimmerHMM_glimmerT_31193-T1
Valid prediction for GeneMark_model.53885_t
Valid prediction for GeneMark_model.53871_t
Valid prediction for GeneMark_model.53908_t
Valid prediction for GeneMark_model.53887_t
Valid prediction for GeneMark_model.53882_t
Valid prediction for GlimmerHMM_glimmerT_31202-T1
Valid prediction for GeneMark_model.53898_t
Valid prediction for snap_scaffold_12-snap.2809-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.53897_t
Valid prediction for GlimmerHMM_glimmerT_31188-T1
Valid prediction for GeneMark_model.53858_t
Valid prediction for snap_scaffold_12-snap.2806-T1
Valid prediction for GeneMark_model.53904_t
Valid prediction for GeneMark_model.53879_t
Valid prediction for GlimmerHMM_glimmerT_31217-T1
Valid prediction for GlimmerHMM_glimmerT_31195-T1
Valid prediction for GeneMark_model.53875_t
Valid prediction for Augustus_model.g20803.t1
Valid prediction for GlimmerHMM_glimmerT_31208-T1
Valid prediction for Augustus_model.g20801.t1
Valid prediction for Augustus_model.g20804.t1
Valid prediction for GlimmerHMM_glimmerT_31200-T1
Valid prediction for GlimmerHMM_glimmerT_31187-T1
Valid prediction for GeneMark_model.53895_t
Valid prediction for GeneMark_model.53869_t
Valid prediction for snap_scaffold_12-snap.2803-T1
Valid prediction for GlimmerHMM_glimmerT_31199-T1
Valid prediction for snap_scaffold_12-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_31196-T1
Valid prediction for snap_scaffold_12-snap.2788-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.53892_t
Valid prediction for snap_scaffold_12-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_31215-T1
Valid prediction for snap_scaffold_12-snap.2796-T1
Valid prediction for GlimmerHMM_glimmerT_31214-T1
Valid prediction for snap_scaffold_12-snap.2798-T1
Valid prediction for GeneMark_model.53873_t
Valid prediction for snap_scaffold_12-snap.2816-T1
Valid prediction for GeneMark_model.53900_t
Valid prediction for GlimmerHMM_glimmerT_31211-T1
Valid prediction for Augustus_model.g20794.t1
Valid prediction for GeneMark_model.53865_t
Valid prediction for GlimmerHMM_glimmerT_31209-T1
Valid prediction for GlimmerHMM_glimmerT_31207-T1
Valid prediction for snap_scaffold_12-snap.2785-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 24473, rend_intergenic: 24470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 149721, rend_intergenic: 149718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27882, rend_intergenic: 18704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31063, rend_intergenic: 28553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45018, rend_intergenic: 31998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58780, rend_intergenic: 53334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74435, rend_intergenic: 63782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99440, rend_intergenic: 82369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105969, rend_intergenic: 103534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118941, rend_intergenic: 117663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121990, rend_intergenic: 120143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128845, rend_intergenic: 128080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138248, rend_intergenic: 135457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158095, rend_intergenic: 155440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161600, rend_intergenic: 158523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169083, rend_intergenic: 166480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171797
-exon list size: 710


building trellis

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-found 41 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 24473, rend_intergenic: 24470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 149721, rend_intergenic: 149718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27882, rend_intergenic: 18704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31063, rend_intergenic: 28553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45018, rend_intergenic: 31998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58780, rend_intergenic: 53334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74435, rend_intergenic: 63782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99440, rend_intergenic: 82369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105969, rend_intergenic: 103534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118941, rend_intergenic: 117663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121990, rend_intergenic: 120143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128845, rend_intergenic: 128080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138248, rend_intergenic: 135457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158095, rend_intergenic: 155440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161600, rend_intergenic: 158523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169083, rend_intergenic: 166480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support