-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_11841543-12006075

-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 GlimmerHMM_glimmerT_46053-T1
Valid prediction for GeneMark_model.80223_t
Valid prediction for snap_scaffold_19-snap.2333-T1
Valid prediction for snap_scaffold_19-snap.2345-T1
Valid prediction for GlimmerHMM_glimmerT_46045-T1
Valid prediction for snap_scaffold_19-snap.2335-T1
Valid prediction for snap_scaffold_19-snap.2341-T1
Valid prediction for Augustus_model.g30729.t1
Valid prediction for CodingQuarry_transcript_25766-T1
Valid prediction for snap_scaffold_19-snap.2332-T1
Valid prediction for HiQ_model.g30726.t1
Valid prediction for Augustus_model.g30718.t1
Valid prediction for GlimmerHMM_glimmerT_46066-T1
Couldn't classify 151636, 151656
Sorry, prediction pasa_asmbl_22540.p2 fails validation.
(GCC)	 GA	151636-151656	GT	AGG
(GCG)	 AG	151861-152061	GT	CCG
(GTG)	 AG	153157-153294	GG	GAG
-recovered pasa_asmbl_22540.p2, terminal, 153157, 153294
-recovered pasa_asmbl_22540.p2, internal, 151861, 152061
Valid prediction for GeneMark_model.80213_t
Valid prediction for GeneMark_model.80211_t
Valid prediction for GlimmerHMM_glimmerT_46071-T1
Valid prediction for GlimmerHMM_glimmerT_46065-T1
Valid prediction for GlimmerHMM_glimmerT_46055-T1
Valid prediction for snap_scaffold_19-snap.2319-T1
Valid prediction for GeneMark_model.80254_t
Valid prediction for GeneMark_model.80257_t
Valid prediction for GeneMark_model.80240_t
Couldn't classify 147695, 147979
Couldn't classify 148169, 148216
Sorry, prediction pasa_asmbl_22735.p1 fails validation.
(CTA)	 CC	147695-147979	GT	AGG
(AAA)	 AG	148169-148216	GA	AGG
Valid prediction for snap_scaffold_19-snap.2339-T1
Valid prediction for GeneMark_model.80242_t
Valid prediction for GeneMark_model.80252_t
Valid prediction for GeneMark_model.80215_t
Valid prediction for GlimmerHMM_glimmerT_46067-T1
Valid prediction for Augustus_model.g30724.t1
Valid prediction for GlimmerHMM_glimmerT_46054-T1
Valid prediction for GeneMark_model.80229_t
Valid prediction for snap_scaffold_19-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_46061-T1
Valid prediction for GeneMark_model.80210_t
Valid prediction for GlimmerHMM_glimmerT_46048-T1
Valid prediction for GeneMark_model.80226_t
Valid prediction for CodingQuarry_transcript_25765-T1
Valid prediction for GeneMark_model.80231_t
Valid prediction for GeneMark_model.80233_t
Couldn't classify 144146, 144293
Sorry, prediction pasa_asmbl_22539.p1 fails validation.
(GAC)	 TA	144146-144293	GT	AGG
(GCC)	 AG	144431-144954	AA	GAA
-recovered pasa_asmbl_22539.p1, terminal, 144431, 144954
Valid prediction for GlimmerHMM_glimmerT_46069-T1
Valid prediction for CodingQuarry_transcript_25767-T1
Valid prediction for GeneMark_model.80251_t
Valid prediction for GeneMark_model.80247_t
Valid prediction for GlimmerHMM_glimmerT_46070-T1
Valid prediction for HiQ_model.g30719.t1
Valid prediction for snap_scaffold_19-snap.2342-T1
Valid prediction for GeneMark_model.80236_t
Valid prediction for GeneMark_model.80225_t
Valid prediction for snap_scaffold_19-snap.2348-T1
Valid prediction for snap_scaffold_19-snap.2329-T1
Valid prediction for snap_scaffold_19-snap.2326-T1
Valid prediction for GeneMark_model.80246_t
Valid prediction for pasa_asmbl_22536.p1
Valid prediction for snap_scaffold_19-snap.2328-T1
Valid prediction for Augustus_model.g30725.t1
Valid prediction for GeneMark_model.80221_t
Valid prediction for snap_scaffold_19-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_46049-T1
Valid prediction for GeneMark_model.80220_t
Valid prediction for Augustus_model.g30723.t1
Valid prediction for snap_scaffold_19-snap.2351-T1
Valid prediction for snap_scaffold_19-snap.2349-T1
Valid prediction for Augustus_model.g30715.t1
Valid prediction for Augustus_model.g30730.t1
Valid prediction for HiQ_model.g30717.t1
Valid prediction for GlimmerHMM_glimmerT_46050-T1
Valid prediction for GeneMark_model.80255_t
Valid prediction for GeneMark_model.80227_t
Couldn't classify 136725, 136880
Sorry, prediction pasa_asmbl_22538.p1 fails validation.
(ATG)	 AA	134064-134091	GT	CGG
(ACC)	 AG	135081-135337	GT	AGG
(GTG)	 AG	136725-136880	GG	GAG
-recovered pasa_asmbl_22538.p1, initial, 134064, 134091
-recovered pasa_asmbl_22538.p1, internal, 135081, 135337
Valid prediction for Augustus_model.g30727.t1
Valid prediction for snap_scaffold_19-snap.2330-T1
Valid prediction for GlimmerHMM_glimmerT_46039-T1
Valid prediction for Augustus_model.g30721.t1
Valid prediction for GlimmerHMM_glimmerT_46046-T1
Valid prediction for snap_scaffold_19-snap.2337-T1
Valid prediction for pasa_asmbl_22535.p1
Valid prediction for snap_scaffold_19-snap.2353-T1
Valid prediction for GeneMark_model.80217_t
Valid prediction for GeneMark_model.80234_t
Valid prediction for GeneMark_model.80249_t
Valid prediction for GeneMark_model.80238_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 snap_scaffold_19-snap.2317-T1
Valid prediction for GeneMark_model.80232_t
Valid prediction for GlimmerHMM_glimmerT_46057-T1
Valid prediction for GlimmerHMM_glimmerT_46042-T1
Valid prediction for Augustus_model.g30713.t1
Valid prediction for GeneMark_model.80253_t
Valid prediction for snap_scaffold_19-snap.2338-T1
Valid prediction for GeneMark_model.80235_t
Valid prediction for Augustus_model.g30722.t1
Valid prediction for GlimmerHMM_glimmerT_46068-T1
Valid prediction for GlimmerHMM_glimmerT_46041-T1
Valid prediction for GeneMark_model.80243_t
Valid prediction for snap_scaffold_19-snap.2320-T1
Valid prediction for Augustus_model.g30728.t1
Valid prediction for GeneMark_model.80230_t
Valid prediction for GeneMark_model.80222_t
Valid prediction for GlimmerHMM_glimmerT_46052-T1
Valid prediction for snap_scaffold_19-snap.2327-T1
Valid prediction for HiQ_model.g30716.t1
Valid prediction for GlimmerHMM_glimmerT_46064-T1
Valid prediction for GlimmerHMM_glimmerT_46059-T1
Valid prediction for GeneMark_model.80250_t
Valid prediction for GeneMark_model.80216_t
Valid prediction for snap_scaffold_19-snap.2318-T1
Valid prediction for Augustus_model.g30714.t1
Valid prediction for GeneMark_model.80218_t
Valid prediction for GeneMark_model.80237_t
Valid prediction for GlimmerHMM_glimmerT_46062-T1
Valid prediction for snap_scaffold_19-snap.2334-T1
Valid prediction for snap_scaffold_19-snap.2336-T1
Valid prediction for Augustus_model.g30720.t1
Couldn't classify 129797, 130546
Sorry, prediction pasa_asmbl_21648.p1 fails validation.
(GGG)	 TA	129797-130546	GT	CGG
Valid prediction for GeneMark_model.80244_t
Valid prediction for GlimmerHMM_glimmerT_46051-T1
Valid prediction for GeneMark_model.80228_t
Valid prediction for GeneMark_model.80212_t
Valid prediction for snap_scaffold_19-snap.2344-T1
Valid prediction for GeneMark_model.80241_t
Valid prediction for snap_scaffold_19-snap.2343-T1
Valid prediction for GeneMark_model.80214_t
Valid prediction for GeneMark_model.80219_t
Valid prediction for snap_scaffold_19-snap.2347-T1
Valid prediction for Augustus_model.g30711.t1
Valid prediction for Augustus_model.g30710.t1
Valid prediction for snap_scaffold_19-snap.2350-T1
Valid prediction for snap_scaffold_19-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_46044-T1
Valid prediction for CodingQuarry_transcript_25768-T1
Valid prediction for snap_scaffold_19-snap.2323-T1
Valid prediction for GeneMark_model.80256_t
Valid prediction for Augustus_model.g30712.t1
Valid prediction for GeneMark_model.80245_t
Valid prediction for snap_scaffold_19-snap.2321-T1
Valid prediction for snap_scaffold_19-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_46043-T1
Valid prediction for GeneMark_model.80239_t
Valid prediction for GeneMark_model.80258_t
Valid prediction for GeneMark_model.80248_t
Valid prediction for GlimmerHMM_glimmerT_46060-T1
Valid prediction for GlimmerHMM_glimmerT_46058-T1
Valid prediction for snap_scaffold_19-snap.2324-T1
Valid prediction for snap_scaffold_19-snap.2340-T1
Valid prediction for GlimmerHMM_glimmerT_46063-T1
Valid prediction for GlimmerHMM_glimmerT_46040-T1
Valid prediction for Augustus_model.g30731.t1
Valid prediction for GlimmerHMM_glimmerT_46056-T1
Valid prediction for GlimmerHMM_glimmerT_46047-T1
Valid prediction for GeneMark_model.80224_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52841, rend_intergenic: 45983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76959, rend_intergenic: 75429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78939, rend_intergenic: 77847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86881, rend_intergenic: 85790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90161, rend_intergenic: 86943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92484, rend_intergenic: 90206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100747, rend_intergenic: 93134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118584, rend_intergenic: 101186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125258, rend_intergenic: 118584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127044, rend_intergenic: 125332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130409, rend_intergenic: 127331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144530, rend_intergenic: 134981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153294, rend_intergenic: 148711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164533
-exon list size: 640


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 52841, rend_intergenic: 45983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76959, rend_intergenic: 75429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78939, rend_intergenic: 77847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86881, rend_intergenic: 85790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90161, rend_intergenic: 86943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92484, rend_intergenic: 90206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100747, rend_intergenic: 93134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118584, rend_intergenic: 101186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125258, rend_intergenic: 118584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127044, rend_intergenic: 125332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130409, rend_intergenic: 127331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144530, rend_intergenic: 134981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153294, rend_intergenic: 148711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support