-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_1274506-1536078

-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_15-snap.268-T1
Valid prediction for Augustus_model.g23749.t1
Valid prediction for snap_scaffold_15-snap.296-T1
Couldn't classify 125622, 125738
Couldn't classify 126494, 126537
Sorry, prediction pasa_asmbl_15945.p1 fails validation.
(GAG)	 TG	125622-125738	GT	AGG
(AGC)	 AG	126123-126273	GT	TGG
(GGG)	 AG	126494-126537	GA	TGG
-recovered pasa_asmbl_15945.p1, internal, 126123, 126273
Valid prediction for GlimmerHMM_glimmerT_35606-T1
Valid prediction for GlimmerHMM_glimmerT_35595-T1
Valid prediction for GlimmerHMM_glimmerT_35608-T1
Valid prediction for GlimmerHMM_glimmerT_35583-T1
Valid prediction for snap_scaffold_15-snap.294-T1
Valid prediction for Augustus_model.g23757.t1
Valid prediction for CodingQuarry_transcript_17904-T1
Valid prediction for Augustus_model.g23759.t1
Valid prediction for snap_scaffold_15-snap.284-T1
Valid prediction for snap_scaffold_15-snap.288-T1
Valid prediction for snap_scaffold_15-snap.259-T1
Valid prediction for snap_scaffold_15-snap.265-T1
Valid prediction for snap_scaffold_15-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_35591-T1
Valid prediction for Augustus_model.g23760.t1
Valid prediction for snap_scaffold_15-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_35596-T1
Valid prediction for snap_scaffold_15-snap.258-T1
Valid prediction for Augustus_model.g23753.t1
Couldn't classify 74734, 74889
Sorry, prediction pasa_asmbl_15007.p1 fails validation.
(TTC)	 AC	74734-74889	GT	TTG
(GTC)	 AG	75874-76347	TA	AGT
-recovered pasa_asmbl_15007.p1, terminal, 75874, 76347
Couldn't classify 132946, 133098
Sorry, prediction pasa_asmbl_15009.p2 fails validation.
(CTG)	 AC	132946-133098	GT	AGG
(GAG)	 AG	133570-133731	GT	AGG
(GGC)	 AG	134324-134461	GT	AGG
(GTG)	 AG	134563-134701	GT	AGG
(GTG)	 AG	134934-135109	GT	AGG
(GGC)	 AG	135230-135361	GT	AGG
(CGC)	 AG	135708-135846	GT	CGG
(AAG)	 AG	135942-136042	GG	GAG
-recovered pasa_asmbl_15009.p2, terminal, 135942, 136042
-recovered pasa_asmbl_15009.p2, internal, 133570, 133731
-recovered pasa_asmbl_15009.p2, internal, 134324, 134461
-recovered pasa_asmbl_15009.p2, internal, 134563, 134701
-recovered pasa_asmbl_15009.p2, internal, 134934, 135109
-recovered pasa_asmbl_15009.p2, internal, 135230, 135361
-recovered pasa_asmbl_15009.p2, internal, 135708, 135846
Valid prediction for snap_scaffold_15-snap.285-T1
Valid prediction for snap_scaffold_15-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_35594-T1
Valid prediction for snap_scaffold_15-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_35609-T1
Valid prediction for Augustus_model.g23765.t1
Valid prediction for GlimmerHMM_glimmerT_35602-T1
Valid prediction for snap_scaffold_15-snap.307-T1
Valid prediction for Augustus_model.g23747.t1
Couldn't classify 191666, 191794
Sorry, prediction pasa_asmbl_15011.p1 fails validation.
(TCC)	 GA	191666-191794	GT	AGG
(GCA)	 AG	192116-192268	GT	AGG
(TCG)	 AG	193981-194283	CC	GAC
-recovered pasa_asmbl_15011.p1, terminal, 193981, 194283
-recovered pasa_asmbl_15011.p1, internal, 192116, 192268
Valid prediction for Augustus_model.g23764.t1
Couldn't classify 237798, 237963
Sorry, prediction pasa_asmbl_15014.p1 fails validation.
(ATG)	 TA	232712-232775	GT	AAG
(CTA)	 AG	233523-233632	GT	AGG
(GTC)	 AG	233920-234023	GT	GGG
(TCA)	 AG	234155-234243	GT	AGG
(GTG)	 AG	236158-236233	GT	AGG
(CGT)	 AG	237798-237963	CC	GAC
-recovered pasa_asmbl_15014.p1, initial, 232712, 232775
add_exon() Sorry, pasa_asmbl_15014.p1 234155-234243-terminal-2 is invalid.
-recovered pasa_asmbl_15014.p1, terminal, 234155, 234243
-recovered pasa_asmbl_15014.p1, internal, 233523, 233632
-recovered pasa_asmbl_15014.p1, internal, 233920, 234023
-recovered pasa_asmbl_15014.p1, internal, 234155, 234243
-recovered pasa_asmbl_15014.p1, internal, 236158, 236233
Valid prediction for GlimmerHMM_glimmerT_35598-T1
Valid prediction for Augustus_model.g23750.t1
Valid prediction for snap_scaffold_15-snap.303-T1
Valid prediction for Augustus_model.g23761.t1
Valid prediction for GlimmerHMM_glimmerT_35604-T1
Valid prediction for snap_scaffold_15-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_35588-T1
Valid prediction for GlimmerHMM_glimmerT_35599-T1
Valid prediction for snap_scaffold_15-snap.276-T1
Valid prediction for Augustus_model.g23754.t1
Valid prediction for snap_scaffold_15-snap.283-T1
Valid prediction for snap_scaffold_15-snap.305-T1
Couldn't classify 65169, 65561
Sorry, prediction pasa_asmbl_15006.p1 fails validation.
(CAC)	 AG	65169-65561	GA	GAG
Valid prediction for snap_scaffold_15-snap.298-T1
Valid prediction for snap_scaffold_15-snap.281-T1
Valid prediction for CodingQuarry_transcript_17903-T1
Valid prediction for snap_scaffold_15-snap.264-T1
Valid prediction for snap_scaffold_15-snap.297-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 snap_scaffold_15-snap.261-T1
Couldn't classify 172848, 172914
Couldn't classify 173020, 174347
Sorry, prediction pasa_asmbl_13948.p1 fails validation.
(GTG)	 GC	172848-172914	GT	AGG
(ATT)	 AG	173020-174347	AC	TTA
Couldn't classify 36591, 36667
Sorry, prediction pasa_asmbl_13954.p1 fails validation.
(ATG)	 CT	33596-34009	GT	AGG
(GTG)	 AG	34187-34335	GT	GAG
(TGT)	 AG	34654-34796	GT	TGG
(GAG)	 AG	35135-35289	GT	AAG
(GTT)	 AG	35445-35580	GT	TGG
(GGT)	 AG	36591-36667	AA	TGA
-recovered pasa_asmbl_13954.p1, initial, 33596, 34009
-recovered pasa_asmbl_13954.p1, internal, 34187, 34335
-recovered pasa_asmbl_13954.p1, internal, 34654, 34796
-recovered pasa_asmbl_13954.p1, internal, 35135, 35289
-recovered pasa_asmbl_13954.p1, internal, 35445, 35580
Valid prediction for Augustus_model.g23751.t1
Valid prediction for GlimmerHMM_glimmerT_35601-T1
Valid prediction for snap_scaffold_15-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_35589-T1
Valid prediction for GlimmerHMM_glimmerT_35607-T1
Valid prediction for snap_scaffold_15-snap.304-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.274-T1
Valid prediction for pasa_asmbl_13958.p1
Valid prediction for Augustus_model.g23748.t1
Valid prediction for snap_scaffold_15-snap.263-T1
Valid prediction for GlimmerHMM_glimmerT_35586-T1
Valid prediction for GlimmerHMM_glimmerT_35593-T1
Valid prediction for GlimmerHMM_glimmerT_35585-T1
Valid prediction for snap_scaffold_15-snap.273-T1
Valid prediction for snap_scaffold_15-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_35587-T1
Valid prediction for GlimmerHMM_glimmerT_35584-T1
Valid prediction for Augustus_model.g23755.t1
Valid prediction for snap_scaffold_15-snap.300-T1
Valid prediction for snap_scaffold_15-snap.270-T1
Valid prediction for snap_scaffold_15-snap.278-T1
Valid prediction for snap_scaffold_15-snap.299-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g23746.t1
Valid prediction for CodingQuarry_transcript_17905-T1
Couldn't classify 174672, 175552
Sorry, prediction pasa_asmbl_13947.p1 fails validation.
(TCC)	 TT	174672-175552	GT	AAG
(GGA)	 AG	175754-175853	GT	AAG
(ATT)	 AG	175983-176045	TC	GAT
-recovered pasa_asmbl_13947.p1, terminal, 175983, 176045
-recovered pasa_asmbl_13947.p1, internal, 175754, 175853
Valid prediction for snap_scaffold_15-snap.308-T1
Valid prediction for CodingQuarry_transcript_17906-T1
Valid prediction for snap_scaffold_15-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_35590-T1
Valid prediction for snap_scaffold_15-snap.302-T1
Valid prediction for Augustus_model.g23758.t1
Valid prediction for snap_scaffold_15-snap.279-T1
Valid prediction for snap_scaffold_15-snap.269-T1
Valid prediction for HiQ_model.g23762.t1
Couldn't classify 112724, 112825
Couldn't classify 113503, 113643
Sorry, prediction pasa_asmbl_13950.p1 fails validation.
(CAG)	 AC	112724-112825	GT	AGG
(ATT)	 AG	113196-113309	GT	AGG
(CAG)	 AG	113503-113643	GC	CTG
-recovered pasa_asmbl_13950.p1, internal, 113196, 113309
-recovered pasa_asmbl_13950.p1, internal, 113503, 113643
Valid prediction for GlimmerHMM_glimmerT_35592-T1
Valid prediction for Augustus_model.g23756.t1
Valid prediction for GlimmerHMM_glimmerT_35597-T1
Valid prediction for snap_scaffold_15-snap.275-T1
Valid prediction for snap_scaffold_15-snap.266-T1
Valid prediction for Augustus_model.g23745.t1
Valid prediction for snap_scaffold_15-snap.260-T1
Valid prediction for snap_scaffold_15-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_35603-T1
Valid prediction for snap_scaffold_15-snap.306-T1
Valid prediction for snap_scaffold_15-snap.277-T1
Valid prediction for CodingQuarry_transcript_17907-T1
Valid prediction for snap_scaffold_15-snap.287-T1
Valid prediction for snap_scaffold_15-snap.286-T1
Valid prediction for HiQ_model.g23763.t1
Valid prediction for snap_scaffold_15-snap.293-T1
Valid prediction for snap_scaffold_15-snap.280-T1
Valid prediction for GlimmerHMM_glimmerT_35600-T1
Valid prediction for Augustus_model.g23752.t1
Valid prediction for GlimmerHMM_glimmerT_35605-T1
Valid prediction for GlimmerHMM_glimmerT_35582-T1
Valid prediction for snap_scaffold_15-snap.291-T1
Valid prediction for snap_scaffold_15-snap.282-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 59165, rend_intergenic: 57516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66317, rend_intergenic: 61544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74534, rend_intergenic: 68060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143604, rend_intergenic: 111428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158123, rend_intergenic: 149244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160856, rend_intergenic: 159693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168413, rend_intergenic: 162999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192482, rend_intergenic: 177293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 192743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239873, rend_intergenic: 235679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247667, rend_intergenic: 247090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250365, rend_intergenic: 248072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261573
-exon list size: 563


building trellis

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-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 59165, rend_intergenic: 57516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66317, rend_intergenic: 61544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74534, rend_intergenic: 68060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143604, rend_intergenic: 111428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158123, rend_intergenic: 149244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160856, rend_intergenic: 159693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168413, rend_intergenic: 162999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192482, rend_intergenic: 177293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 192743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239873, rend_intergenic: 235679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247667, rend_intergenic: 247090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250365, rend_intergenic: 248072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12604
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11711
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support