-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_12909815-13156729

-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_14-snap.2652-T1
Valid prediction for snap_scaffold_14-snap.2664-T1
Valid prediction for Augustus_model.g23354.t1
Valid prediction for Augustus_model.g23350.t1
Valid prediction for GlimmerHMM_glimmerT_34942-T1
Valid prediction for Augustus_model.g23358.t1
Valid prediction for Augustus_model.g23361.t1
Valid prediction for GlimmerHMM_glimmerT_34913-T1
Valid prediction for GlimmerHMM_glimmerT_34937-T1
Valid prediction for Augustus_model.g23357.t1
Valid prediction for snap_scaffold_14-snap.2687-T1
Sorry, intron length (8) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2685-T1
Valid prediction for snap_scaffold_14-snap.2655-T1
Valid prediction for Augustus_model.g23366.t1
Valid prediction for snap_scaffold_14-snap.2693-T1
Valid prediction for snap_scaffold_14-snap.2651-T1
Valid prediction for Augustus_model.g23353.t1
Valid prediction for GlimmerHMM_glimmerT_34921-T1
Valid prediction for GlimmerHMM_glimmerT_34934-T1
Valid prediction for snap_scaffold_14-snap.2653-T1
Valid prediction for GlimmerHMM_glimmerT_34948-T1
Valid prediction for snap_scaffold_14-snap.2682-T1
Valid prediction for GlimmerHMM_glimmerT_34938-T1
Valid prediction for snap_scaffold_14-snap.2665-T1
Valid prediction for snap_scaffold_14-snap.2686-T1
Valid prediction for snap_scaffold_14-snap.2660-T1
Valid prediction for snap_scaffold_14-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_34936-T1
Valid prediction for snap_scaffold_14-snap.2640-T1
Valid prediction for GlimmerHMM_glimmerT_34915-T1
Valid prediction for Augustus_model.g23365.t1
Valid prediction for Augustus_model.g23356.t1
Valid prediction for snap_scaffold_14-snap.2639-T1
Valid prediction for snap_scaffold_14-snap.2675-T1
Valid prediction for snap_scaffold_14-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_34926-T1
Valid prediction for GlimmerHMM_glimmerT_34943-T1
Valid prediction for Augustus_model.g23349.t1
Valid prediction for GlimmerHMM_glimmerT_34925-T1
Valid prediction for GlimmerHMM_glimmerT_34918-T1
Valid prediction for Augustus_model.g23363.t1
Valid prediction for Augustus_model.g23368.t1
Valid prediction for GlimmerHMM_glimmerT_34924-T1
Valid prediction for snap_scaffold_14-snap.2661-T1
Valid prediction for GlimmerHMM_glimmerT_34908-T1
Valid prediction for Augustus_model.g23352.t1
Valid prediction for Augustus_model.g23364.t1
Valid prediction for GlimmerHMM_glimmerT_34914-T1
Valid prediction for Augustus_model.g23351.t1
Valid prediction for snap_scaffold_14-snap.2670-T1
Valid prediction for snap_scaffold_14-snap.2646-T1
Valid prediction for snap_scaffold_14-snap.2673-T1
Valid prediction for GlimmerHMM_glimmerT_34927-T1
Valid prediction for GlimmerHMM_glimmerT_34910-T1
Valid prediction for snap_scaffold_14-snap.2669-T1
Valid prediction for Augustus_model.g23362.t1
Valid prediction for Augustus_model.g23373.t1
Valid prediction for snap_scaffold_14-snap.2648-T1
Valid prediction for snap_scaffold_14-snap.2649-T1
Valid prediction for GlimmerHMM_glimmerT_34917-T1
Valid prediction for snap_scaffold_14-snap.2690-T1
Valid prediction for snap_scaffold_14-snap.2684-T1
Valid prediction for GlimmerHMM_glimmerT_34919-T1
Valid prediction for snap_scaffold_14-snap.2677-T1
Valid prediction for GlimmerHMM_glimmerT_34935-T1
Valid prediction for snap_scaffold_14-snap.2667-T1
Valid prediction for GlimmerHMM_glimmerT_34940-T1
Valid prediction for snap_scaffold_14-snap.2689-T1
Valid prediction for GlimmerHMM_glimmerT_34930-T1
Valid prediction for snap_scaffold_14-snap.2656-T1
Valid prediction for snap_scaffold_14-snap.2645-T1
Valid prediction for snap_scaffold_14-snap.2691-T1
Valid prediction for Augustus_model.g23371.t1
Valid prediction for GlimmerHMM_glimmerT_34945-T1
Valid prediction for GlimmerHMM_glimmerT_34947-T1
Valid prediction for Augustus_model.g23369.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_34922-T1
Valid prediction for Augustus_model.g23359.t1
Valid prediction for GlimmerHMM_glimmerT_34944-T1
Valid prediction for GlimmerHMM_glimmerT_34916-T1
Valid prediction for Augustus_model.g23370.t1
Valid prediction for GlimmerHMM_glimmerT_34946-T1
Couldn't classify 113260, 113408
Sorry, prediction pasa_asmbl_13630.p1 fails validation.
(GTG)	 CG	113260-113408	GT	AGG
(GAG)	 AG	114043-114272	GT	AGG
(TGT)	 AG	115714-115877	GT	AGG
(GGC)	 AG	117347-117525	GT	AGG
(GCA)	 AG	118931-119108	CC	GAC
-recovered pasa_asmbl_13630.p1, terminal, 118931, 119108
-recovered pasa_asmbl_13630.p1, internal, 114043, 114272
-recovered pasa_asmbl_13630.p1, internal, 115714, 115877
-recovered pasa_asmbl_13630.p1, internal, 117347, 117525
Valid prediction for GlimmerHMM_glimmerT_34932-T1
Valid prediction for snap_scaffold_14-snap.2650-T1
Valid prediction for Augustus_model.g23367.t1
Valid prediction for GlimmerHMM_glimmerT_34933-T1
Valid prediction for snap_scaffold_14-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_34928-T1
Valid prediction for GlimmerHMM_glimmerT_34912-T1
Valid prediction for GlimmerHMM_glimmerT_34939-T1
Valid prediction for snap_scaffold_14-snap.2680-T1
Valid prediction for GlimmerHMM_glimmerT_34911-T1
Valid prediction for Augustus_model.g23348.t1
Valid prediction for snap_scaffold_14-snap.2671-T1
Valid prediction for snap_scaffold_14-snap.2659-T1
Valid prediction for snap_scaffold_14-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_34949-T1
Valid prediction for Augustus_model.g23374.t1
Valid prediction for Augustus_model.g23360.t1
Valid prediction for GlimmerHMM_glimmerT_34931-T1
Valid prediction for Augustus_model.g23355.t1
Valid prediction for GlimmerHMM_glimmerT_34929-T1
Valid prediction for snap_scaffold_14-snap.2683-T1
Valid prediction for snap_scaffold_14-snap.2637-T1
Valid prediction for snap_scaffold_14-snap.2654-T1
Valid prediction for GlimmerHMM_glimmerT_34907-T1
Valid prediction for snap_scaffold_14-snap.2681-T1
Valid prediction for GlimmerHMM_glimmerT_34923-T1
Valid prediction for snap_scaffold_14-snap.2644-T1
Valid prediction for snap_scaffold_14-snap.2663-T1
Valid prediction for snap_scaffold_14-snap.2672-T1
Valid prediction for snap_scaffold_14-snap.2657-T1
Valid prediction for snap_scaffold_14-snap.2674-T1
Valid prediction for snap_scaffold_14-snap.2688-T1
Valid prediction for snap_scaffold_14-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_34941-T1
Valid prediction for snap_scaffold_14-snap.2658-T1
Valid prediction for Augustus_model.g23372.t1
Valid prediction for snap_scaffold_14-snap.2678-T1
Valid prediction for snap_scaffold_14-snap.2643-T1
Valid prediction for snap_scaffold_14-snap.2662-T1
Valid prediction for snap_scaffold_14-snap.2679-T1
Valid prediction for snap_scaffold_14-snap.2676-T1
Valid prediction for snap_scaffold_14-snap.2647-T1
Valid prediction for snap_scaffold_14-snap.2692-T1
Valid prediction for GlimmerHMM_glimmerT_34920-T1
Valid prediction for GlimmerHMM_glimmerT_34909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25035, rend_intergenic: 6679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25445, rend_intergenic: 25160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31598, rend_intergenic: 25583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39930, rend_intergenic: 35646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54435, rend_intergenic: 42403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59988, rend_intergenic: 55962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62693, rend_intergenic: 61081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74377, rend_intergenic: 71102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91378, rend_intergenic: 84867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95368, rend_intergenic: 91385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98850, rend_intergenic: 96692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108896, rend_intergenic: 101202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117698, rend_intergenic: 113702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124660, rend_intergenic: 118641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 127808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143230, rend_intergenic: 131004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148608, rend_intergenic: 143246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151757, rend_intergenic: 151585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155368, rend_intergenic: 152172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168967, rend_intergenic: 156284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180974, rend_intergenic: 170523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213609, rend_intergenic: 181279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221764, rend_intergenic: 214253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228157, rend_intergenic: 224341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240382, rend_intergenic: 233849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246557, rend_intergenic: 240424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 246915
-exon list size: 513


building trellis

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-found 50 predictions from path traversal
Error with prediction: snap lend_intergenic: 25035, rend_intergenic: 6679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25445, rend_intergenic: 25160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31598, rend_intergenic: 25583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39930, rend_intergenic: 35646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54435, rend_intergenic: 42403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59988, rend_intergenic: 55962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62693, rend_intergenic: 61081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74377, rend_intergenic: 71102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91378, rend_intergenic: 84867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95368, rend_intergenic: 91385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98850, rend_intergenic: 96692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108896, rend_intergenic: 101202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117698, rend_intergenic: 113702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124660, rend_intergenic: 118641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 127808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143230, rend_intergenic: 131004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148608, rend_intergenic: 143246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151757, rend_intergenic: 151585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155368, rend_intergenic: 152172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168967, rend_intergenic: 156284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180974, rend_intergenic: 170523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213609, rend_intergenic: 181279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221764, rend_intergenic: 214253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228157, rend_intergenic: 224341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240382, rend_intergenic: 233849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246557, rend_intergenic: 240424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support