-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_237628-492627

-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_30962-T1
Valid prediction for snap_scaffold_13-snap.72-T1
Valid prediction for snap_scaffold_13-snap.70-T1
Valid prediction for snap_scaffold_13-snap.61-T1
Valid prediction for snap_scaffold_13-snap.50-T1
Valid prediction for GlimmerHMM_glimmerT_30965-T1
Valid prediction for Augustus_model.g20556.t1
Valid prediction for Augustus_model.g20547.t1
Valid prediction for GlimmerHMM_glimmerT_30939-T1
Valid prediction for snap_scaffold_13-snap.95-T1
Valid prediction for snap_scaffold_13-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_30947-T1
Valid prediction for snap_scaffold_13-snap.62-T1
Valid prediction for Augustus_model.g20542.t1
Valid prediction for Augustus_model.g20534.t1
Valid prediction for Augustus_model.g20555.t1
Valid prediction for Augustus_model.g20527.t1
Valid prediction for Augustus_model.g20557.t1
Valid prediction for snap_scaffold_13-snap.90-T1
Valid prediction for snap_scaffold_13-snap.54-T1
Valid prediction for snap_scaffold_13-snap.86-T1
Couldn't classify 231318, 231701
Sorry, prediction pasa_asmbl_9355.p2 fails validation.
(GGG)	 GN	231318-231701	TA	TGT
Valid prediction for snap_scaffold_13-snap.96-T1
Valid prediction for GlimmerHMM_glimmerT_30941-T1
Valid prediction for Augustus_model.g20546.t1
Valid prediction for snap_scaffold_13-snap.84-T1
Valid prediction for snap_scaffold_13-snap.51-T1
Valid prediction for snap_scaffold_13-snap.92-T1
Valid prediction for snap_scaffold_13-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_30938-T1
Valid prediction for Augustus_model.g20553.t1
Valid prediction for HiQ_model.g20530.t1
Valid prediction for snap_scaffold_13-snap.91-T1
Valid prediction for snap_scaffold_13-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_30942-T1
Valid prediction for Augustus_model.g20539.t1
Valid prediction for snap_scaffold_13-snap.100-T1
Valid prediction for CodingQuarry_transcript_12826-T1
Valid prediction for snap_scaffold_13-snap.57-T1
Valid prediction for snap_scaffold_13-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_30955-T1
Valid prediction for GlimmerHMM_glimmerT_30964-T1
Valid prediction for snap_scaffold_13-snap.81-T1
Valid prediction for Augustus_model.g20552.t1
Valid prediction for Augustus_model.g20550.t1
Valid prediction for GlimmerHMM_glimmerT_30967-T1
Valid prediction for snap_scaffold_13-snap.94-T1
Valid prediction for snap_scaffold_13-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_30957-T1
Valid prediction for pasa_asmbl_10465.p1
Valid prediction for GlimmerHMM_glimmerT_30966-T1
Valid prediction for Augustus_model.g20528.t1
Valid prediction for snap_scaffold_13-snap.88-T1
Valid prediction for Augustus_model.g20549.t1
Valid prediction for GlimmerHMM_glimmerT_30968-T1
Valid prediction for GlimmerHMM_glimmerT_30946-T1
Valid prediction for GlimmerHMM_glimmerT_30952-T1
Valid prediction for GlimmerHMM_glimmerT_30961-T1
Valid prediction for snap_scaffold_13-snap.87-T1
Valid prediction for snap_scaffold_13-snap.52-T1
Valid prediction for Augustus_model.g20554.t1
Valid prediction for pasa_asmbl_10474.p1
Valid prediction for snap_scaffold_13-snap.89-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_13-snap.68-T1
Valid prediction for Augustus_model.g20529.t1
Valid prediction for snap_scaffold_13-snap.77-T1
Valid prediction for CodingQuarry_transcript_12838-T1
Valid prediction for GlimmerHMM_glimmerT_30951-T1
Valid prediction for snap_scaffold_13-snap.60-T1
Valid prediction for GlimmerHMM_glimmerT_30943-T1
Valid prediction for Augustus_model.g20543.t1
Valid prediction for pasa_asmbl_9332.p1
Valid prediction for pasa_asmbl_9352.p1
Valid prediction for snap_scaffold_13-snap.67-T1
Valid prediction for CodingQuarry_transcript_12829-T1
Valid prediction for HiQ_model.g20538.t1
Valid prediction for CodingQuarry_transcript_12833-T1
Valid prediction for GlimmerHMM_glimmerT_30948-T1
Valid prediction for Augustus_model.g20540.t1
Valid prediction for snap_scaffold_13-snap.66-T1
Valid prediction for Augustus_model.g20548.t1
Couldn't classify 196510, 196848
Sorry, prediction pasa_asmbl_9297.p1 fails validation.
(ATG)	 AC	196510-196848	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_30953-T1
Valid prediction for pasa_asmbl_9329.p1
Valid prediction for GlimmerHMM_glimmerT_30940-T1
Valid prediction for snap_scaffold_13-snap.55-T1
Valid prediction for snap_scaffold_13-snap.63-T1
Couldn't classify 129655, 130000
Sorry, prediction pasa_asmbl_9314.p1 fails validation.
(CAT)	 GA	129655-130000	GT	CGG
(GTA)	 AG	130219-130410	GT	TGG
(GCG)	 AG	131749-131842	GT	ACG
(TCA)	 AG	131936-132047	GT	AGG
(CTC)	 AG	132369-132422	GT	AGG
(TTC)	 AG	132611-132865	AA	GAA
-recovered pasa_asmbl_9314.p1, terminal, 132611, 132865
-recovered pasa_asmbl_9314.p1, internal, 130219, 130410
-recovered pasa_asmbl_9314.p1, internal, 131749, 131842
-recovered pasa_asmbl_9314.p1, internal, 131936, 132047
-recovered pasa_asmbl_9314.p1, internal, 132369, 132422
Valid prediction for CodingQuarry_transcript_12837-T1
Valid prediction for GlimmerHMM_glimmerT_30958-T1
Valid prediction for CodingQuarry_transcript_12832-T1
Valid prediction for Augustus_model.g20537.t1
Valid prediction for snap_scaffold_13-snap.59-T1
Valid prediction for Augustus_model.g20533.t1
Valid prediction for snap_scaffold_13-snap.80-T1
Valid prediction for snap_scaffold_13-snap.71-T1
Couldn't classify 115730, 116038
Sorry, prediction pasa_asmbl_9321.p3 fails validation.
(ATG)	 CG	115730-116038	GA	CGG
Valid prediction for GlimmerHMM_glimmerT_30944-T1
Valid prediction for GlimmerHMM_glimmerT_30954-T1
Valid prediction for Augustus_model.g20531.t1
Valid prediction for snap_scaffold_13-snap.93-T1
Valid prediction for HiQ_model.g20544.t1
Valid prediction for Augustus_model.g20541.t1
Valid prediction for pasa_asmbl_9305.p1
Valid prediction for snap_scaffold_13-snap.78-T1
Valid prediction for snap_scaffold_13-snap.79-T1
Valid prediction for Augustus_model.g20535.t1
Valid prediction for Augustus_model.g20532.t1
Valid prediction for GlimmerHMM_glimmerT_30960-T1
Couldn't classify 111776, 111906
Sorry, prediction pasa_asmbl_9323.p1 fails validation.
(ATG)	 GA	110557-110574	GT	AGG
(CGC)	 AG	110755-110910	GT	AGG
(AAT)	 AG	111086-111146	GT	TGG
(TGC)	 AG	111327-111533	GT	AGG
(ATG)	 AG	111776-111906	GT	CCG
-recovered pasa_asmbl_9323.p1, initial, 110557, 110574
add_exon() Sorry, pasa_asmbl_9323.p1 111776-111906-initial-1 is invalid.
-recovered pasa_asmbl_9323.p1, initial, 111776, 111906
-recovered pasa_asmbl_9323.p1, internal, 110755, 110910
-recovered pasa_asmbl_9323.p1, internal, 111086, 111146
-recovered pasa_asmbl_9323.p1, internal, 111327, 111533
-recovered pasa_asmbl_9323.p1, internal, 111776, 111906
Valid prediction for snap_scaffold_13-snap.58-T1
Valid prediction for Augustus_model.g20551.t1
Valid prediction for snap_scaffold_13-snap.75-T1
Valid prediction for Augustus_model.g20536.t1
Valid prediction for snap_scaffold_13-snap.64-T1
Valid prediction for snap_scaffold_13-snap.69-T1
Valid prediction for CodingQuarry_transcript_12834-T1
Valid prediction for CodingQuarry_transcript_12835-T1
Valid prediction for snap_scaffold_13-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_30950-T1
Valid prediction for snap_scaffold_13-snap.73-T1
Valid prediction for snap_scaffold_13-snap.99-T1
Couldn't classify 116960, 117186
Couldn't classify 122253, 122486
Sorry, prediction pasa_asmbl_9320.p1 fails validation.
(AAC)	 CA	116960-117186	GT	AGG
(CGG)	 AG	117536-117636	GT	AGG
(TGG)	 AG	119048-119312	GT	TGG
(GCA)	 AG	121940-122150	GT	AGG
(GTG)	 AG	122253-122486	TA	GGT
-recovered pasa_asmbl_9320.p1, internal, 117536, 117636
-recovered pasa_asmbl_9320.p1, internal, 119048, 119312
-recovered pasa_asmbl_9320.p1, internal, 121940, 122150
Valid prediction for pasa_asmbl_9300.p1
Valid prediction for GlimmerHMM_glimmerT_30963-T1
Valid prediction for CodingQuarry_transcript_12836-T1
Valid prediction for GlimmerHMM_glimmerT_30945-T1
Valid prediction for snap_scaffold_13-snap.76-T1
Valid prediction for snap_scaffold_13-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_30956-T1
Valid prediction for snap_scaffold_13-snap.85-T1
Valid prediction for CodingQuarry_transcript_12831-T1
Valid prediction for HiQ_model.g20545.t1
Valid prediction for snap_scaffold_13-snap.82-T1
Valid prediction for snap_scaffold_13-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_30959-T1
Valid prediction for GlimmerHMM_glimmerT_30949-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 127942, rend_intergenic: 124583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159823, rend_intergenic: 155811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222565, rend_intergenic: 218731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251581, rend_intergenic: 244140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 255000
-exon list size: 477


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 127942, rend_intergenic: 124583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159823, rend_intergenic: 155811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222565, rend_intergenic: 218731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251581, rend_intergenic: 244140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14466
-exon list size: 4


building trellis

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-found 1 predictions from path traversal

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