-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_4206334-4381948

-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_17-snap.895-T1
Valid prediction for HiQ_model.g26744.t1
Valid prediction for GlimmerHMM_glimmerT_40167-T1
Valid prediction for snap_scaffold_17-snap.908-T1
Valid prediction for snap_scaffold_17-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_40152-T1
Couldn't classify 35032, 35175
Sorry, prediction pasa_asmbl_18774.p1 fails validation.
(ATG)	 GC	27220-27271	GT	AGG
(CCT)	 AG	27718-27846	GT	CGG
(GGT)	 AG	28082-28215	GT	AGG
(GGG)	 AG	28296-28373	GT	AGG
(AGC)	 AG	28670-28748	GT	AGG
(GAG)	 AG	29028-29153	GT	AGG
(TTA)	 AG	29461-29545	GT	GGG
(GAT)	 AG	29692-29793	GT	CAG
(CCG)	 AG	29903-29987	GT	AGG
(CTC)	 AG	30602-30757	GT	AGG
(TTT)	 AG	30908-30977	GT	TGG
(GCG)	 AG	31221-31331	GT	TGG
(GAG)	 AG	31896-32109	GT	AGG
(CCA)	 AG	32332-32465	GT	AGG
(AAT)	 AG	32621-32811	GT	AAG
(AGT)	 AG	32900-32981	GT	TGG
(ACA)	 AG	33186-33268	GT	AGG
(GAG)	 AG	34072-34116	GT	AGG
(ATT)	 AG	34442-34546	GT	AGG
(ACA)	 AG	34783-34869	GC	AGG
(CTC)	 AG	35032-35175	CT	CCC
-recovered pasa_asmbl_18774.p1, initial, 27220, 27271
-recovered pasa_asmbl_18774.p1, internal, 27718, 27846
-recovered pasa_asmbl_18774.p1, internal, 28082, 28215
-recovered pasa_asmbl_18774.p1, internal, 28296, 28373
-recovered pasa_asmbl_18774.p1, internal, 28670, 28748
-recovered pasa_asmbl_18774.p1, internal, 29028, 29153
-recovered pasa_asmbl_18774.p1, internal, 29461, 29545
-recovered pasa_asmbl_18774.p1, internal, 29692, 29793
-recovered pasa_asmbl_18774.p1, internal, 29903, 29987
-recovered pasa_asmbl_18774.p1, internal, 30602, 30757
-recovered pasa_asmbl_18774.p1, internal, 30908, 30977
-recovered pasa_asmbl_18774.p1, internal, 31221, 31331
-recovered pasa_asmbl_18774.p1, internal, 31896, 32109
-recovered pasa_asmbl_18774.p1, internal, 32332, 32465
-recovered pasa_asmbl_18774.p1, internal, 32621, 32811
-recovered pasa_asmbl_18774.p1, internal, 32900, 32981
-recovered pasa_asmbl_18774.p1, internal, 33186, 33268
-recovered pasa_asmbl_18774.p1, internal, 34072, 34116
-recovered pasa_asmbl_18774.p1, internal, 34442, 34546
-recovered pasa_asmbl_18774.p1, internal, 34783, 34869
Valid prediction for Augustus_model.g26739.t1
Valid prediction for GlimmerHMM_glimmerT_40150-T1
Valid prediction for Augustus_model.g26746.t1
Valid prediction for GlimmerHMM_glimmerT_40166-T1
Valid prediction for snap_scaffold_17-snap.890-T1
Valid prediction for snap_scaffold_17-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_40146-T1
Valid prediction for snap_scaffold_17-snap.898-T1
Valid prediction for snap_scaffold_17-snap.886-T1
Valid prediction for snap_scaffold_17-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_40154-T1
Valid prediction for snap_scaffold_17-snap.901-T1
Valid prediction for GlimmerHMM_glimmerT_40149-T1
Valid prediction for snap_scaffold_17-snap.903-T1
Valid prediction for snap_scaffold_17-snap.884-T1
Valid prediction for GlimmerHMM_glimmerT_40145-T1
Valid prediction for GlimmerHMM_glimmerT_40161-T1
Valid prediction for Augustus_model.g26738.t1
Valid prediction for GlimmerHMM_glimmerT_40155-T1
Valid prediction for GlimmerHMM_glimmerT_40148-T1
Valid prediction for HiQ_model.g26741.t1
Valid prediction for snap_scaffold_17-snap.899-T1
Valid prediction for pasa_asmbl_18775.p1
Valid prediction for snap_scaffold_17-snap.913-T1
Valid prediction for snap_scaffold_17-snap.881-T1
Valid prediction for HiQ_model.g26750.t1
Valid prediction for snap_scaffold_17-snap.891-T1
Valid prediction for Augustus_model.g26747.t1
Valid prediction for HiQ_model.g26745.t1
Valid prediction for snap_scaffold_17-snap.914-T1
Valid prediction for pasa_asmbl_18776.p1
Valid prediction for snap_scaffold_17-snap.909-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_17-snap.897-T1
Valid prediction for GlimmerHMM_glimmerT_40162-T1
Valid prediction for GlimmerHMM_glimmerT_40165-T1
Valid prediction for snap_scaffold_17-snap.883-T1
Valid prediction for Augustus_model.g26743.t1
Valid prediction for GlimmerHMM_glimmerT_40147-T1
Couldn't classify 87635, 87696
Couldn't classify 89274, 89354
Sorry, prediction pasa_asmbl_17849.p1 fails validation.
(AGA)	 AG	87635-87696	GT	AGG
(CAT)	 AG	87990-88121	GC	AGG
(GGA)	 AG	88262-88361	GT	ATG
(CCC)	 AG	88472-88663	GT	AGG
(GGC)	 AG	89274-89354	CC	CGC
-recovered pasa_asmbl_17849.p1, internal, 87635, 87696
-recovered pasa_asmbl_17849.p1, internal, 87990, 88121
-recovered pasa_asmbl_17849.p1, internal, 88262, 88361
-recovered pasa_asmbl_17849.p1, internal, 88472, 88663
Valid prediction for GlimmerHMM_glimmerT_40168-T1
Valid prediction for snap_scaffold_17-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_40160-T1
Valid prediction for snap_scaffold_17-snap.902-T1
Valid prediction for HiQ_model.g26751.t1
Valid prediction for GlimmerHMM_glimmerT_40153-T1
Valid prediction for snap_scaffold_17-snap.900-T1
Valid prediction for snap_scaffold_17-snap.894-T1
Valid prediction for snap_scaffold_17-snap.885-T1
Valid prediction for Augustus_model.g26749.t1
Valid prediction for CodingQuarry_transcript_21947-T1
Valid prediction for CodingQuarry_transcript_21946-T1
Valid prediction for Augustus_model.g26752.t1
Valid prediction for GlimmerHMM_glimmerT_40157-T1
Valid prediction for HiQ_model.g26754.t1
Valid prediction for Augustus_model.g26748.t1
Valid prediction for Augustus_model.g26755.t1
Valid prediction for GlimmerHMM_glimmerT_40151-T1
Valid prediction for GlimmerHMM_glimmerT_40169-T1
Valid prediction for Augustus_model.g26740.t1
Valid prediction for snap_scaffold_17-snap.906-T1
Couldn't classify 69744, 69788
Couldn't classify 73433, 73609
Sorry, prediction pasa_asmbl_17853.p1 fails validation.
(AAA)	 AG	69744-69788	GT	AGG
(ATG)	 AG	71237-71341	GT	CGG
(GTG)	 AG	72979-73051	GT	AGG
(GTC)	 AG	73175-73284	GT	AGG
(TGG)	 AG	73433-73609	GA	TGG
-recovered pasa_asmbl_17853.p1, initial, 71237, 71341
-recovered pasa_asmbl_17853.p1, internal, 69744, 69788
-recovered pasa_asmbl_17853.p1, internal, 71237, 71341
-recovered pasa_asmbl_17853.p1, internal, 72979, 73051
-recovered pasa_asmbl_17853.p1, internal, 73175, 73284
Couldn't classify 85069, 85122
Sorry, prediction pasa_asmbl_17851.p1 fails validation.
(ATG)	 TA	82507-82567	GT	CGG
(ATG)	 AG	84090-84199	GT	AGG
(GAT)	 AG	84449-84706	GT	CGG
(GAG)	 AG	85069-85122	CA	ACC
-recovered pasa_asmbl_17851.p1, initial, 82507, 82567
add_exon() Sorry, pasa_asmbl_17851.p1 84090-84199-initial-1 is invalid.
-recovered pasa_asmbl_17851.p1, initial, 84090, 84199
-recovered pasa_asmbl_17851.p1, internal, 84090, 84199
-recovered pasa_asmbl_17851.p1, internal, 84449, 84706
Valid prediction for pasa_asmbl_17855.p1
Valid prediction for GlimmerHMM_glimmerT_40156-T1
Valid prediction for snap_scaffold_17-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_40158-T1
Couldn't classify 85791, 85874
Couldn't classify 87154, 87291
Sorry, prediction pasa_asmbl_17850.p1 fails validation.
(GAG)	 AG	85791-85874	GT	CGG
(AGC)	 AG	85973-86108	GT	GGG
(TGG)	 AG	86476-86648	GT	GTG
(GAG)	 AG	86758-86991	GT	CTG
(TGT)	 AG	87154-87291	AG	AGA
-recovered pasa_asmbl_17850.p1, internal, 85791, 85874
-recovered pasa_asmbl_17850.p1, internal, 85973, 86108
-recovered pasa_asmbl_17850.p1, internal, 86476, 86648
-recovered pasa_asmbl_17850.p1, internal, 86758, 86991
Valid prediction for snap_scaffold_17-snap.907-T1
Valid prediction for GlimmerHMM_glimmerT_40159-T1
Valid prediction for snap_scaffold_17-snap.904-T1
Valid prediction for snap_scaffold_17-snap.892-T1
Valid prediction for Augustus_model.g26753.t1
Valid prediction for snap_scaffold_17-snap.905-T1
Valid prediction for snap_scaffold_17-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_40163-T1
Valid prediction for pasa_asmbl_17846.p1
Valid prediction for snap_scaffold_17-snap.910-T1
Valid prediction for snap_scaffold_17-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_40164-T1
Valid prediction for snap_scaffold_17-snap.896-T1
Valid prediction for Augustus_model.g26742.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26371, rend_intergenic: 26101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52762, rend_intergenic: 45938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69699, rend_intergenic: 63767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77098, rend_intergenic: 74042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93109, rend_intergenic: 79963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100225, rend_intergenic: 94552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103748, rend_intergenic: 101451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119132, rend_intergenic: 108634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136454, rend_intergenic: 129425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155218, rend_intergenic: 149047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175615
-exon list size: 455


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 26371, rend_intergenic: 26101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52762, rend_intergenic: 45938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69699, rend_intergenic: 63767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77098, rend_intergenic: 74042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93109, rend_intergenic: 79963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100225, rend_intergenic: 94552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103748, rend_intergenic: 101451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119132, rend_intergenic: 108634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136454, rend_intergenic: 129425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155218, rend_intergenic: 149047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support