-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_17536748-17724401

-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: +)Couldn't classify 174163, 175275
Sorry, prediction pasa_asmbl_47719.p1 fails validation.
(CAC)	 CC	174163-175275	GC	CAG
Valid prediction for GlimmerHMM_glimmerT_16863-T1
Valid prediction for snap_scaffold_6-snap.3712-T1
Valid prediction for GeneMark_model.28227_t
Valid prediction for Augustus_model.g11324.t1
Valid prediction for snap_scaffold_6-snap.3716-T1
Valid prediction for GeneMark_model.28219_t
Valid prediction for HiQ_model.g11334.t1
Valid prediction for snap_scaffold_6-snap.3727-T1
Valid prediction for GeneMark_model.28205_t
Valid prediction for GlimmerHMM_glimmerT_16856-T1
Valid prediction for snap_scaffold_6-snap.3722-T1
Valid prediction for Augustus_model.g11341.t1
Valid prediction for GlimmerHMM_glimmerT_16858-T1
Valid prediction for snap_scaffold_6-snap.3748-T1
Valid prediction for snap_scaffold_6-snap.3743-T1
Valid prediction for GlimmerHMM_glimmerT_16840-T1
Valid prediction for GeneMark_model.28215_t
Valid prediction for Augustus_model.g11342.t1
Valid prediction for GeneMark_model.28207_t
Valid prediction for snap_scaffold_6-snap.3718-T1
Valid prediction for GlimmerHMM_glimmerT_16866-T1
Valid prediction for Augustus_model.g11323.t1
Valid prediction for snap_scaffold_6-snap.3715-T1
Valid prediction for snap_scaffold_6-snap.3730-T1
Valid prediction for snap_scaffold_6-snap.3725-T1
Valid prediction for snap_scaffold_6-snap.3728-T1
Valid prediction for GlimmerHMM_glimmerT_16843-T1
Valid prediction for GeneMark_model.28226_t
Valid prediction for GeneMark_model.28200_t
Valid prediction for GeneMark_model.28236_t
Valid prediction for GlimmerHMM_glimmerT_16839-T1
Valid prediction for snap_scaffold_6-snap.3710-T1
Valid prediction for snap_scaffold_6-snap.3720-T1
Valid prediction for snap_scaffold_6-snap.3745-T1
Valid prediction for GlimmerHMM_glimmerT_16867-T1
Valid prediction for GlimmerHMM_glimmerT_16852-T1
Valid prediction for snap_scaffold_6-snap.3726-T1
Valid prediction for snap_scaffold_6-snap.3724-T1
Valid prediction for GeneMark_model.28202_t
Valid prediction for snap_scaffold_6-snap.3749-T1
Valid prediction for GeneMark_model.28198_t
Valid prediction for GlimmerHMM_glimmerT_16861-T1
Valid prediction for GeneMark_model.28234_t
Valid prediction for GlimmerHMM_glimmerT_16845-T1
Couldn't classify 173553, 173807
Sorry, prediction pasa_asmbl_47717.p2 fails validation.
(ATG)	 AT	173332-173433	GT	AGG
(GGG)	 AG	173553-173807	AA	CCA
-recovered pasa_asmbl_47717.p2, initial, 173332, 173433
Valid prediction for Augustus_model.g11325.t1
Valid prediction for GlimmerHMM_glimmerT_16836-T1
Valid prediction for snap_scaffold_6-snap.3713-T1
Valid prediction for GlimmerHMM_glimmerT_16859-T1
Valid prediction for snap_scaffold_6-snap.3738-T1
Valid prediction for snap_scaffold_6-snap.3737-T1
Valid prediction for GeneMark_model.28239_t
Valid prediction for Augustus_model.g11326.t1
Valid prediction for GlimmerHMM_glimmerT_16850-T1
Valid prediction for snap_scaffold_6-snap.3741-T1
Valid prediction for CodingQuarry_transcript_55262-T1
Valid prediction for GeneMark_model.28221_t
Valid prediction for GlimmerHMM_glimmerT_16846-T1
Valid prediction for snap_scaffold_6-snap.3751-T1
Valid prediction for Augustus_model.g11335.t1
Valid prediction for Augustus_model.g11322.t1
Couldn't classify 87666, 89045
Sorry, prediction pasa_asmbl_47708.p1 fails validation.
(TGC)	 AA	87666-89045	AA	AAA
Valid prediction for GeneMark_model.28209_t
Valid prediction for snap_scaffold_6-snap.3740-T1
Valid prediction for GeneMark_model.28216_t
Valid prediction for Augustus_model.g11319.t1
Valid prediction for snap_scaffold_6-snap.3719-T1
Valid prediction for GlimmerHMM_glimmerT_16868-T1
Valid prediction for GlimmerHMM_glimmerT_16841-T1
Valid prediction for GlimmerHMM_glimmerT_16844-T1
Valid prediction for GeneMark_model.28211_t
Valid prediction for pasa_asmbl_47710.p1

-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.g11332.t1
Valid prediction for GlimmerHMM_glimmerT_16855-T1
Valid prediction for GlimmerHMM_glimmerT_16864-T1
Valid prediction for GlimmerHMM_glimmerT_16848-T1
Valid prediction for Augustus_model.g11320.t1
Valid prediction for snap_scaffold_6-snap.3736-T1
Valid prediction for snap_scaffold_6-snap.3734-T1
Valid prediction for GeneMark_model.28220_t
Valid prediction for Augustus_model.g11321.t1
Valid prediction for GeneMark_model.28217_t
Valid prediction for GeneMark_model.28235_t
Valid prediction for GlimmerHMM_glimmerT_16842-T1
Valid prediction for snap_scaffold_6-snap.3747-T1
Valid prediction for snap_scaffold_6-snap.3731-T1
Valid prediction for snap_scaffold_6-snap.3739-T1
Valid prediction for Augustus_model.g11336.t1
Valid prediction for GlimmerHMM_glimmerT_16854-T1
Couldn't classify 75365, 75814
Sorry, prediction pasa_asmbl_49131.p1 fails validation.
(ATG)	 GC	75365-75814	GA	GTG
Couldn't classify 76878, 76979
Sorry, prediction pasa_asmbl_49130.p1 fails validation.
(GCC)	 TC	76878-76979	GT	TGG
(AAA)	 AG	77114-77334	GT	GAG
(CAT)	 AG	79233-79338	GG	AAG
-recovered pasa_asmbl_49130.p1, terminal, 79233, 79338
-recovered pasa_asmbl_49130.p1, internal, 77114, 77334
Valid prediction for GlimmerHMM_glimmerT_16862-T1
Valid prediction for GeneMark_model.28223_t
Valid prediction for snap_scaffold_6-snap.3729-T1
Valid prediction for Augustus_model.g11338.t1
Valid prediction for GlimmerHMM_glimmerT_16838-T1
Valid prediction for GeneMark_model.28201_t
Valid prediction for GlimmerHMM_glimmerT_16835-T1
Valid prediction for GeneMark_model.28199_t
Valid prediction for GeneMark_model.28229_t
Valid prediction for GeneMark_model.28218_t
Valid prediction for GeneMark_model.28237_t
Valid prediction for GeneMark_model.28231_t
Valid prediction for GlimmerHMM_glimmerT_16853-T1
Valid prediction for Augustus_model.g11339.t1
Valid prediction for GlimmerHMM_glimmerT_16847-T1
Valid prediction for snap_scaffold_6-snap.3735-T1
Valid prediction for snap_scaffold_6-snap.3733-T1
Valid prediction for Augustus_model.g11340.t1
Valid prediction for snap_scaffold_6-snap.3714-T1
Valid prediction for snap_scaffold_6-snap.3723-T1
Valid prediction for Augustus_model.g11331.t1
Valid prediction for snap_scaffold_6-snap.3711-T1
Valid prediction for snap_scaffold_6-snap.3721-T1
Valid prediction for GeneMark_model.28197_t
Valid prediction for GeneMark_model.28212_t
Valid prediction for GeneMark_model.28214_t
Valid prediction for Augustus_model.g11318.t1
Valid prediction for GlimmerHMM_glimmerT_16849-T1
Valid prediction for Augustus_model.g11327.t1
Valid prediction for GeneMark_model.28206_t
Valid prediction for GeneMark_model.28204_t
Valid prediction for GeneMark_model.28208_t
Valid prediction for GlimmerHMM_glimmerT_16865-T1
Valid prediction for snap_scaffold_6-snap.3742-T1
Valid prediction for GeneMark_model.28196_t
Valid prediction for GlimmerHMM_glimmerT_16851-T1
Valid prediction for GeneMark_model.28203_t
Valid prediction for snap_scaffold_6-snap.3732-T1
Valid prediction for Augustus_model.g11333.t1
Valid prediction for GlimmerHMM_glimmerT_16860-T1
Valid prediction for snap_scaffold_6-snap.3717-T1
Valid prediction for Augustus_model.g11330.t1
Valid prediction for Augustus_model.g11328.t1
Valid prediction for GeneMark_model.28228_t
Valid prediction for GeneMark_model.28233_t
Valid prediction for Augustus_model.g11337.t1
Valid prediction for snap_scaffold_6-snap.3746-T1
Valid prediction for GeneMark_model.28225_t
Valid prediction for GlimmerHMM_glimmerT_16837-T1
Valid prediction for GeneMark_model.28210_t
Valid prediction for GeneMark_model.28238_t
Valid prediction for GeneMark_model.28222_t
Valid prediction for snap_scaffold_6-snap.3744-T1
Valid prediction for GeneMark_model.28213_t
Valid prediction for GlimmerHMM_glimmerT_16857-T1
Valid prediction for snap_scaffold_6-snap.3750-T1
Valid prediction for Augustus_model.g11329.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5789, rend_intergenic: 3689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15571, rend_intergenic: 6965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19685, rend_intergenic: 15578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29260, rend_intergenic: 23373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33598, rend_intergenic: 29288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44156, rend_intergenic: 37710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80579, rend_intergenic: 78068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125092, rend_intergenic: 118784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144120, rend_intergenic: 139292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149067, rend_intergenic: 146377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156986, rend_intergenic: 149841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185015, rend_intergenic: 177948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187654
-exon list size: 653


building trellis

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-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 5789, rend_intergenic: 3689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15571, rend_intergenic: 6965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19685, rend_intergenic: 15578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29260, rend_intergenic: 23373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33598, rend_intergenic: 29288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44156, rend_intergenic: 37710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80579, rend_intergenic: 78068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125092, rend_intergenic: 118784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144120, rend_intergenic: 139292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149067, rend_intergenic: 146377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156986, rend_intergenic: 149841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185015, rend_intergenic: 177948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support