-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_12134879-12305389

-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.17247_t
Valid prediction for GlimmerHMM_glimmerT_10587-T1
Valid prediction for GlimmerHMM_glimmerT_10571-T1
Valid prediction for snap_scaffold_4-snap.2625-T1
Valid prediction for GeneMark_model.17235_t
Valid prediction for GlimmerHMM_glimmerT_10588-T1
Valid prediction for GeneMark_model.17271_t
Valid prediction for GlimmerHMM_glimmerT_10583-T1
Valid prediction for GeneMark_model.17259_t
Valid prediction for GlimmerHMM_glimmerT_10574-T1
Valid prediction for GeneMark_model.17265_t
Valid prediction for snap_scaffold_4-snap.2621-T1
Valid prediction for snap_scaffold_4-snap.2595-T1
Valid prediction for GlimmerHMM_glimmerT_10568-T1
Valid prediction for snap_scaffold_4-snap.2604-T1
Valid prediction for snap_scaffold_4-snap.2618-T1
Valid prediction for GeneMark_model.17261_t
Valid prediction for GeneMark_model.17250_t
Valid prediction for snap_scaffold_4-snap.2626-T1
Valid prediction for GlimmerHMM_glimmerT_10580-T1
Valid prediction for GeneMark_model.17245_t
Valid prediction for GeneMark_model.17263_t
Valid prediction for GeneMark_model.17254_t
Valid prediction for GeneMark_model.17234_t
Valid prediction for Augustus_model.g6922.t1
Valid prediction for GlimmerHMM_glimmerT_10586-T1
Valid prediction for Augustus_model.g6919.t1
Valid prediction for GeneMark_model.17266_t
Valid prediction for snap_scaffold_4-snap.2607-T1
Valid prediction for snap_scaffold_4-snap.2613-T1
Valid prediction for GeneMark_model.17269_t
Valid prediction for GlimmerHMM_glimmerT_10569-T1
Valid prediction for snap_scaffold_4-snap.2616-T1
Valid prediction for snap_scaffold_4-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_10577-T1
Valid prediction for Augustus_model.g6918.t1
Valid prediction for Augustus_model.g6932.t1
Valid prediction for GlimmerHMM_glimmerT_10564-T1
Valid prediction for GlimmerHMM_glimmerT_10566-T1
Valid prediction for snap_scaffold_4-snap.2608-T1
Valid prediction for GeneMark_model.17252_t
Valid prediction for GlimmerHMM_glimmerT_10561-T1
Valid prediction for snap_scaffold_4-snap.2597-T1
Valid prediction for snap_scaffold_4-snap.2599-T1
Valid prediction for GeneMark_model.17237_t
Valid prediction for GeneMark_model.17257_t
Valid prediction for snap_scaffold_4-snap.2593-T1
Valid prediction for GeneMark_model.17243_t
Valid prediction for GeneMark_model.17241_t
Valid prediction for Augustus_model.g6929.t1
Valid prediction for Augustus_model.g6927.t1
Valid prediction for GeneMark_model.17240_t
Valid prediction for Augustus_model.g6921.t1
Valid prediction for GeneMark_model.17238_t
Valid prediction for GeneMark_model.17227_t
Valid prediction for Augustus_model.g6924.t1
Valid prediction for GeneMark_model.17231_t
Valid prediction for snap_scaffold_4-snap.2610-T1
Valid prediction for GeneMark_model.17225_t
Valid prediction for Augustus_model.g6933.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 Augustus_model.g6915.t1
Valid prediction for Augustus_model.g6926.t1
Valid prediction for GeneMark_model.17256_t
Valid prediction for Augustus_model.g6916.t1
Valid prediction for snap_scaffold_4-snap.2606-T1
Valid prediction for Augustus_model.g6917.t1
Valid prediction for GeneMark_model.17270_t
Valid prediction for GeneMark_model.17229_t
Valid prediction for GeneMark_model.17242_t
Valid prediction for snap_scaffold_4-snap.2605-T1
Valid prediction for snap_scaffold_4-snap.2598-T1
Valid prediction for Augustus_model.g6936.t1
Valid prediction for GeneMark_model.17258_t
Valid prediction for GlimmerHMM_glimmerT_10589-T1
Valid prediction for GeneMark_model.17253_t
Valid prediction for GeneMark_model.17268_t
Valid prediction for snap_scaffold_4-snap.2624-T1
Valid prediction for GeneMark_model.17232_t
Valid prediction for snap_scaffold_4-snap.2611-T1
Valid prediction for GeneMark_model.17272_t
Valid prediction for GlimmerHMM_glimmerT_10590-T1
Valid prediction for Augustus_model.g6928.t1
Valid prediction for Augustus_model.g6930.t1
Valid prediction for GlimmerHMM_glimmerT_10575-T1
Valid prediction for GlimmerHMM_glimmerT_10576-T1
Valid prediction for GlimmerHMM_glimmerT_10581-T1
Valid prediction for GeneMark_model.17239_t
Valid prediction for snap_scaffold_4-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_10584-T1
Valid prediction for GeneMark_model.17267_t
Valid prediction for GlimmerHMM_glimmerT_10578-T1
Valid prediction for snap_scaffold_4-snap.2600-T1
Valid prediction for GlimmerHMM_glimmerT_10579-T1
Valid prediction for GeneMark_model.17264_t
Valid prediction for GlimmerHMM_glimmerT_10570-T1
Valid prediction for Augustus_model.g6920.t1
Valid prediction for snap_scaffold_4-snap.2596-T1
Valid prediction for GeneMark_model.17228_t
Valid prediction for GlimmerHMM_glimmerT_10573-T1
Valid prediction for CodingQuarry_transcript_49034-T1
Valid prediction for GeneMark_model.17244_t
Valid prediction for snap_scaffold_4-snap.2617-T1
Valid prediction for HiQ_model.g6925.t1
Valid prediction for Augustus_model.g6923.t1
Valid prediction for GeneMark_model.17246_t
Valid prediction for snap_scaffold_4-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_10562-T1
Valid prediction for Augustus_model.g6931.t1
Valid prediction for snap_scaffold_4-snap.2619-T1
Valid prediction for GeneMark_model.17230_t
Valid prediction for GeneMark_model.17260_t
Valid prediction for GeneMark_model.17255_t
Valid prediction for GlimmerHMM_glimmerT_10591-T1
Valid prediction for snap_scaffold_4-snap.2603-T1
Valid prediction for GeneMark_model.17236_t
Valid prediction for GlimmerHMM_glimmerT_10565-T1
Valid prediction for snap_scaffold_4-snap.2622-T1
Valid prediction for GeneMark_model.17226_t
Valid prediction for snap_scaffold_4-snap.2601-T1
Valid prediction for GeneMark_model.17262_t
Couldn't classify 60524, 60613
Sorry, prediction pasa_asmbl_41637.p1 fails validation.
(TCA)	 AC	60524-60613	GT	AGG
(GTG)	 AG	60717-60876	GT	GGG
(TGT)	 AG	60997-61607	GA	GAG
-recovered pasa_asmbl_41637.p1, terminal, 60997, 61607
-recovered pasa_asmbl_41637.p1, internal, 60717, 60876
Valid prediction for CodingQuarry_transcript_49035-T1
Valid prediction for GlimmerHMM_glimmerT_10593-T1
Valid prediction for GeneMark_model.17251_t
Valid prediction for GlimmerHMM_glimmerT_10592-T1
Valid prediction for Augustus_model.g6934.t1
Valid prediction for GlimmerHMM_glimmerT_10563-T1
Valid prediction for GlimmerHMM_glimmerT_10585-T1
Valid prediction for snap_scaffold_4-snap.2594-T1
Valid prediction for snap_scaffold_4-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_10567-T1
Valid prediction for snap_scaffold_4-snap.2614-T1
Valid prediction for GeneMark_model.17248_t
Valid prediction for GeneMark_model.17249_t
Valid prediction for Augustus_model.g6935.t1
Valid prediction for GeneMark_model.17233_t
Valid prediction for snap_scaffold_4-snap.2609-T1
Valid prediction for GlimmerHMM_glimmerT_10582-T1
Valid prediction for GlimmerHMM_glimmerT_10572-T1
Valid prediction for snap_scaffold_4-snap.2620-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9204, rend_intergenic: 8521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18290, rend_intergenic: 9951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18920, rend_intergenic: 18798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28574, rend_intergenic: 20035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37871, rend_intergenic: 34329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47071, rend_intergenic: 42290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47446, rend_intergenic: 47337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60388, rend_intergenic: 49932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76684, rend_intergenic: 65702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110407, rend_intergenic: 108905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120899, rend_intergenic: 117144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125470, rend_intergenic: 121043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140632, rend_intergenic: 136549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170102, rend_intergenic: 155231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170511
-exon list size: 698


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 9204, rend_intergenic: 8521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18290, rend_intergenic: 9951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18920, rend_intergenic: 18798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28574, rend_intergenic: 20035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37871, rend_intergenic: 34329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47071, rend_intergenic: 42290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47446, rend_intergenic: 47337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60388, rend_intergenic: 49932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76684, rend_intergenic: 65702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110407, rend_intergenic: 108905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120899, rend_intergenic: 117144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125470, rend_intergenic: 121043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140632, rend_intergenic: 136549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170102, rend_intergenic: 155231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support