-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_3348898-3542539

-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_29693-T1
Valid prediction for GeneMark_model.51291_t
Valid prediction for Augustus_model.g19756.t1
Valid prediction for snap_scaffold_12-snap.682-T1
Valid prediction for GeneMark_model.51277_t
Valid prediction for GeneMark_model.51284_t
Valid prediction for snap_scaffold_12-snap.687-T1
Valid prediction for snap_scaffold_12-snap.696-T1
Valid prediction for GeneMark_model.51306_t
Valid prediction for GlimmerHMM_glimmerT_29676-T1
Valid prediction for snap_scaffold_12-snap.689-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29685-T1
Valid prediction for HiQ_model.g19750.t1
Valid prediction for GeneMark_model.51304_t
Valid prediction for GeneMark_model.51288_t
Valid prediction for GlimmerHMM_glimmerT_29679-T1
Couldn't classify 2922, 3038
Sorry, prediction pasa_asmbl_8511.p1 fails validation.
(ATG)	 TC	1984-2106	GT	AGG
(ACA)	 AG	2244-2536	GT	AAG
(TGG)	 AG	2637-2745	GT	AGG
(GTG)	 AG	2922-3038	TT	ACT
-recovered pasa_asmbl_8511.p1, initial, 1984, 2106
-recovered pasa_asmbl_8511.p1, internal, 2244, 2536
-recovered pasa_asmbl_8511.p1, internal, 2637, 2745
Valid prediction for snap_scaffold_12-snap.709-T1
Couldn't classify 4203, 4275
Sorry, prediction pasa_asmbl_9184.p2 fails validation.
(GGC)	 AT	4203-4275	GT	AGG
(AGT)	 AG	4522-4748	CG	GAC
-recovered pasa_asmbl_9184.p2, terminal, 4522, 4748
Valid prediction for GlimmerHMM_glimmerT_29677-T1
Valid prediction for Augustus_model.g19762.t1
Valid prediction for CodingQuarry_transcript_10128-T1
Valid prediction for snap_scaffold_12-snap.702-T1
Valid prediction for GeneMark_model.51296_t
Valid prediction for snap_scaffold_12-snap.706-T1
Valid prediction for GlimmerHMM_glimmerT_29681-T1
Valid prediction for GeneMark_model.51308_t
Valid prediction for Augustus_model.g19749.t1
Valid prediction for snap_scaffold_12-snap.683-T1
Couldn't classify 51392, 51392
Sorry, prediction pasa_asmbl_8520.p1 fails validation.
(ATG)	 AA	49390-49405	GT	AGG
(CTC)	 AG	50386-50461	GT	GAG
(TAA)	 AG	50684-50870	GT	TTG
(ATT)	 AG	51100-51212	GT	TGG
(AAT)	 AG	51392-51392	AT	GAA
-recovered pasa_asmbl_8520.p1, initial, 49390, 49405
-recovered pasa_asmbl_8520.p1, internal, 50386, 50461
-recovered pasa_asmbl_8520.p1, internal, 50684, 50870
-recovered pasa_asmbl_8520.p1, internal, 51100, 51212
Valid prediction for GeneMark_model.51273_t
Valid prediction for GlimmerHMM_glimmerT_29695-T1
Couldn't classify 51392, 51392
Sorry, prediction CodingQuarry_transcript_10131-T1 fails validation.
(ATG)	 AA	49390-49405	GT	AGG
(CTC)	 AG	50386-50461	GT	GAG
(TAA)	 AG	50684-50870	GT	TTG
(ATT)	 AG	51100-51212	GT	TGG
(AAT)	 AG	51392-51392	AT	GAA
-recovered CodingQuarry_transcript_10131-T1, initial, 49390, 49405
-recovered CodingQuarry_transcript_10131-T1, internal, 50386, 50461
-recovered CodingQuarry_transcript_10131-T1, internal, 50684, 50870
-recovered CodingQuarry_transcript_10131-T1, internal, 51100, 51212
Valid prediction for GeneMark_model.51300_t
Valid prediction for snap_scaffold_12-snap.694-T1
Couldn't classify 18159, 18221
Couldn't classify 20006, 20110
Sorry, prediction pasa_asmbl_8515.p1 fails validation.
(GGC)	 CT	18159-18221	GT	AGG
(AAA)	 AG	18450-18587	GT	AGG
(GGG)	 AG	19137-19241	GT	ACG
(GTG)	 AG	19391-19483	GT	TGG
(ACG)	 AG	20006-20110	TA	AGT
-recovered pasa_asmbl_8515.p1, internal, 18450, 18587
-recovered pasa_asmbl_8515.p1, internal, 19137, 19241
-recovered pasa_asmbl_8515.p1, internal, 19391, 19483
Valid prediction for GlimmerHMM_glimmerT_29699-T1
Couldn't classify 16377, 16536
Couldn't classify 16902, 17074
Sorry, prediction pasa_asmbl_8514.p1 fails validation.
(GCC)	 CA	16377-16536	GT	AGG
(GGC)	 AG	16902-17074	GG	AAG
Valid prediction for Augustus_model.g19757.t1
Valid prediction for GeneMark_model.51302_t
Valid prediction for GlimmerHMM_glimmerT_29686-T1
Valid prediction for GeneMark_model.51286_t
Valid prediction for GlimmerHMM_glimmerT_29678-T1
Valid prediction for GeneMark_model.51275_t
Valid prediction for snap_scaffold_12-snap.712-T1
Valid prediction for GeneMark_model.51294_t
Valid prediction for snap_scaffold_12-snap.704-T1
Valid prediction for GeneMark_model.51279_t
Valid prediction for snap_scaffold_12-snap.703-T1
Valid prediction for GeneMark_model.51271_t
Valid prediction for snap_scaffold_12-snap.692-T1
Valid prediction for HiQ_model.g19754.t1
Valid prediction for GlimmerHMM_glimmerT_29688-T1
Valid prediction for GeneMark_model.51282_t
Valid prediction for Augustus_model.g19755.t1
Valid prediction for Augustus_model.g19748.t1
Valid prediction for snap_scaffold_12-snap.695-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.g19764.t1
Valid prediction for GlimmerHMM_glimmerT_29680-T1
Valid prediction for GeneMark_model.51301_t
Couldn't classify 157613, 157725
Sorry, prediction pasa_asmbl_7493.p1 fails validation.
(GAG)	 AG	157613-157725	GT	AGG
(GCC)	 AG	158285-158426	GT	AGG
(AAA)	 AG	158960-159094	GT	TGG
(GTT)	 AG	159329-159451	CT	AGC
-recovered pasa_asmbl_7493.p1, terminal, 159329, 159451
-recovered pasa_asmbl_7493.p1, internal, 157613, 157725
-recovered pasa_asmbl_7493.p1, internal, 158285, 158426
-recovered pasa_asmbl_7493.p1, internal, 158960, 159094
Valid prediction for snap_scaffold_12-snap.693-T1
Valid prediction for Augustus_model.g19767.t1
Valid prediction for GeneMark_model.51295_t
Valid prediction for snap_scaffold_12-snap.690-T1
Valid prediction for GeneMark_model.51278_t
Valid prediction for snap_scaffold_12-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_29689-T1
Valid prediction for GlimmerHMM_glimmerT_29684-T1
Valid prediction for GeneMark_model.51303_t
Valid prediction for snap_scaffold_12-snap.685-T1
Valid prediction for snap_scaffold_12-snap.705-T1
Valid prediction for snap_scaffold_12-snap.698-T1
Valid prediction for GeneMark_model.51307_t
Valid prediction for GeneMark_model.51293_t
Valid prediction for GlimmerHMM_glimmerT_29698-T1
Valid prediction for Augustus_model.g19759.t1
Valid prediction for snap_scaffold_12-snap.714-T1
Valid prediction for snap_scaffold_12-snap.686-T1
Valid prediction for CodingQuarry_transcript_10129-T1
Valid prediction for GlimmerHMM_glimmerT_29700-T1
Valid prediction for GlimmerHMM_glimmerT_29690-T1
Valid prediction for GeneMark_model.51287_t
Valid prediction for GlimmerHMM_glimmerT_29694-T1
Valid prediction for Augustus_model.g19765.t1
Valid prediction for GeneMark_model.51272_t
Valid prediction for HiQ_model.g19752.t1
Valid prediction for snap_scaffold_12-snap.713-T1
Couldn't classify 144797, 144899
Sorry, prediction pasa_asmbl_8370.p1 fails validation.
(AAG)	 TA	144797-144899	GT	AAG
(TTC)	 AG	145559-145679	GT	AGG
(TGA)	 AG	145864-145987	GT	TGG
(CTG)	 AG	146397-146540	GT	CGG
(GAT)	 AG	146723-146834	GT	GGG
(ATC)	 AG	146940-146971	GT	CTG
(GAC)	 AG	147208-147332	GT	AAG
(GCC)	 AG	147641-147698	GT	AGG
(GAC)	 AG	147832-147963	GT	AGG
(GCT)	 AG	148238-148366	GT	AGG
(CAC)	 AG	148858-148930	GT	AGG
(GTC)	 AG	149238-149302	GT	TGG
(ATC)	 AG	149439-149534	GT	AGG
(CCT)	 AG	149652-149755	GT	AAG
(GCA)	 AG	149960-150037	GT	TCG
(CCT)	 AG	150239-150376	GT	GGG
(CCA)	 AG	150613-150650	GT	AGG
(GCA)	 AG	150771-150930	GT	CTG
(GGA)	 AG	151223-151397	TC	AGT
-recovered pasa_asmbl_8370.p1, terminal, 151223, 151397
-recovered pasa_asmbl_8370.p1, internal, 145559, 145679
-recovered pasa_asmbl_8370.p1, internal, 145864, 145987
-recovered pasa_asmbl_8370.p1, internal, 146397, 146540
-recovered pasa_asmbl_8370.p1, internal, 146723, 146834
-recovered pasa_asmbl_8370.p1, internal, 146940, 146971
-recovered pasa_asmbl_8370.p1, internal, 147208, 147332
-recovered pasa_asmbl_8370.p1, internal, 147641, 147698
-recovered pasa_asmbl_8370.p1, internal, 147832, 147963
-recovered pasa_asmbl_8370.p1, internal, 148238, 148366
-recovered pasa_asmbl_8370.p1, internal, 148858, 148930
-recovered pasa_asmbl_8370.p1, internal, 149238, 149302
-recovered pasa_asmbl_8370.p1, internal, 149439, 149534
-recovered pasa_asmbl_8370.p1, internal, 149652, 149755
-recovered pasa_asmbl_8370.p1, internal, 149960, 150037
-recovered pasa_asmbl_8370.p1, internal, 150239, 150376
-recovered pasa_asmbl_8370.p1, internal, 150613, 150650
-recovered pasa_asmbl_8370.p1, internal, 150771, 150930
Valid prediction for GeneMark_model.51299_t
Valid prediction for GeneMark_model.51298_t
Valid prediction for GeneMark_model.51289_t
Valid prediction for GlimmerHMM_glimmerT_29691-T1
Valid prediction for snap_scaffold_12-snap.697-T1
Valid prediction for GeneMark_model.51285_t
Valid prediction for snap_scaffold_12-snap.688-T1
Valid prediction for pasa_asmbl_7494.p1
Valid prediction for GlimmerHMM_glimmerT_29696-T1
Valid prediction for snap_scaffold_12-snap.715-T1
Valid prediction for snap_scaffold_12-snap.684-T1
Valid prediction for snap_scaffold_12-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_29692-T1
Valid prediction for Augustus_model.g19760.t1
Valid prediction for snap_scaffold_12-snap.710-T1
Valid prediction for GeneMark_model.51276_t
Valid prediction for GeneMark_model.51283_t
Valid prediction for GeneMark_model.51292_t
Valid prediction for GlimmerHMM_glimmerT_29697-T1
Valid prediction for Augustus_model.g19758.t1
Valid prediction for snap_scaffold_12-snap.707-T1
Valid prediction for GeneMark_model.51281_t
Valid prediction for snap_scaffold_12-snap.691-T1
Valid prediction for Augustus_model.g19766.t1
Valid prediction for Augustus_model.g19763.t1
Valid prediction for CodingQuarry_transcript_10130-T1
Valid prediction for snap_scaffold_12-snap.701-T1
Valid prediction for snap_scaffold_12-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_29682-T1
Valid prediction for GeneMark_model.51274_t
Valid prediction for GeneMark_model.51290_t
Valid prediction for snap_scaffold_12-snap.700-T1
Valid prediction for snap_scaffold_12-snap.716-T1
Valid prediction for GeneMark_model.51297_t
Valid prediction for Augustus_model.g19751.t1
Valid prediction for GeneMark_model.51280_t
Valid prediction for Augustus_model.g19761.t1
Valid prediction for GlimmerHMM_glimmerT_29683-T1
Valid prediction for GlimmerHMM_glimmerT_29687-T1
Valid prediction for HiQ_model.g19753.t1
Valid prediction for GeneMark_model.51305_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14134, rend_intergenic: 8911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15785, rend_intergenic: 14331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22655, rend_intergenic: 19878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43323, rend_intergenic: 42246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65717, rend_intergenic: 63981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164758, rend_intergenic: 161184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193642
-exon list size: 531


building trellis

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99.1    
99.2    
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99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 14134, rend_intergenic: 8911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15785, rend_intergenic: 14331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22655, rend_intergenic: 19878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43323, rend_intergenic: 42246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65717, rend_intergenic: 63981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164758, rend_intergenic: 161184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support