-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3710103-3844912

-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 Augustus_model.g38963.t1
Valid prediction for GlimmerHMM_glimmerT_58477-T1
Valid prediction for GlimmerHMM_glimmerT_58464-T1
Valid prediction for snap_scaffold_27-snap.913-T1
Valid prediction for GlimmerHMM_glimmerT_58479-T1
Valid prediction for GeneMark_model.101639_t
Valid prediction for GlimmerHMM_glimmerT_58471-T1
Valid prediction for snap_scaffold_27-snap.904-T1
Valid prediction for GeneMark_model.101666_t
Valid prediction for Augustus_model.g38959.t1
Valid prediction for Augustus_model.g38952.t1
Valid prediction for snap_scaffold_27-snap.932-T1
Valid prediction for GeneMark_model.101628_t
Valid prediction for GeneMark_model.101632_t
Valid prediction for GeneMark_model.101659_t
Valid prediction for Augustus_model.g38962.t1
Valid prediction for GeneMark_model.101637_t
Valid prediction for snap_scaffold_27-snap.929-T1
Valid prediction for snap_scaffold_27-snap.909-T1
Valid prediction for GeneMark_model.101670_t
Valid prediction for Augustus_model.g38964.t1
Valid prediction for GlimmerHMM_glimmerT_58463-T1
Valid prediction for snap_scaffold_27-snap.901-T1
Valid prediction for snap_scaffold_27-snap.934-T1
Valid prediction for snap_scaffold_27-snap.916-T1
Valid prediction for GeneMark_model.101644_t
Valid prediction for snap_scaffold_27-snap.903-T1
Valid prediction for GeneMark_model.101656_t
Valid prediction for snap_scaffold_27-snap.926-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g38955.t1
Valid prediction for GeneMark_model.101664_t
Valid prediction for GeneMark_model.101668_t
Couldn't classify 63415, 63481
Sorry, prediction pasa_asmbl_36185.p2 fails validation.
(GAC)	 AC	63415-63481	GT	AGG
(GCC)	 AG	63571-63713	GT	AGG
(GGT)	 AG	63815-63970	GT	AGG
(CAA)	 AG	64110-64124	CG	GAC
-recovered pasa_asmbl_36185.p2, terminal, 64110, 64124
-recovered pasa_asmbl_36185.p2, internal, 63571, 63713
-recovered pasa_asmbl_36185.p2, internal, 63815, 63970
Valid prediction for GeneMark_model.101634_t
Valid prediction for Augustus_model.g38960.t1
Valid prediction for GlimmerHMM_glimmerT_58475-T1
Valid prediction for GeneMark_model.101629_t
Valid prediction for Augustus_model.g38961.t1
Valid prediction for GlimmerHMM_glimmerT_58461-T1
Valid prediction for GeneMark_model.101672_t
Valid prediction for GlimmerHMM_glimmerT_58473-T1
Valid prediction for GlimmerHMM_glimmerT_58459-T1
Valid prediction for Augustus_model.g38958.t1
Valid prediction for GlimmerHMM_glimmerT_58476-T1
Valid prediction for snap_scaffold_27-snap.922-T1
Valid prediction for GlimmerHMM_glimmerT_58469-T1
Valid prediction for Augustus_model.g38947.t1
Valid prediction for GeneMark_model.101654_t
Valid prediction for GeneMark_model.101662_t
Valid prediction for GlimmerHMM_glimmerT_58478-T1
Valid prediction for GlimmerHMM_glimmerT_58455-T1
Valid prediction for Augustus_model.g38944.t1
Valid prediction for GlimmerHMM_glimmerT_58472-T1
Valid prediction for GeneMark_model.101641_t
Valid prediction for Augustus_model.g38965.t1
Valid prediction for snap_scaffold_27-snap.914-T1
Valid prediction for snap_scaffold_27-snap.908-T1
Valid prediction for snap_scaffold_27-snap.928-T1
Valid prediction for GeneMark_model.101630_t
Valid prediction for snap_scaffold_27-snap.919-T1
Valid prediction for GeneMark_model.101648_t
Valid prediction for Augustus_model.g38948.t1
Valid prediction for GlimmerHMM_glimmerT_58468-T1
Valid prediction for HiQ_model.g38950.t1
Valid prediction for GeneMark_model.101645_t
Valid prediction for Augustus_model.g38957.t1
Valid prediction for snap_scaffold_27-snap.923-T1
Valid prediction for snap_scaffold_27-snap.918-T1
Valid prediction for GeneMark_model.101651_t
Valid prediction for snap_scaffold_27-snap.906-T1
Valid prediction for snap_scaffold_27-snap.899-T1
Valid prediction for snap_scaffold_27-snap.896-T1
Valid prediction for snap_scaffold_27-snap.924-T1
Valid prediction for snap_scaffold_27-snap.900-T1
Couldn't classify 36645, 36770
Sorry, prediction pasa_asmbl_36183.p1 fails validation.
(GTG)	 AG	36645-36770	GT	CTG
(GTG)	 AG	36893-37103	GT	AGG
(CGA)	 AG	37249-37417	GT	CGG
(TCA)	 AG	38346-38433	CC	GAC
-recovered pasa_asmbl_36183.p1, terminal, 38346, 38433
-recovered pasa_asmbl_36183.p1, internal, 36645, 36770
-recovered pasa_asmbl_36183.p1, internal, 36893, 37103
-recovered pasa_asmbl_36183.p1, internal, 37249, 37417
Valid prediction for Augustus_model.g38946.t1
Valid prediction for GlimmerHMM_glimmerT_58480-T1
Valid prediction for snap_scaffold_27-snap.902-T1
Valid prediction for snap_scaffold_27-snap.898-T1
Valid prediction for GeneMark_model.101652_t
Valid prediction for GlimmerHMM_glimmerT_58457-T1
Valid prediction for GeneMark_model.101658_t

-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.g38951.t1
Valid prediction for GlimmerHMM_glimmerT_58465-T1
Valid prediction for GeneMark_model.101650_t
Valid prediction for GlimmerHMM_glimmerT_58466-T1
Valid prediction for GeneMark_model.101667_t
Valid prediction for GeneMark_model.101646_t
Valid prediction for snap_scaffold_27-snap.907-T1
Valid prediction for snap_scaffold_27-snap.910-T1
Valid prediction for GeneMark_model.101671_t
Valid prediction for snap_scaffold_27-snap.897-T1
Valid prediction for snap_scaffold_27-snap.933-T1
Valid prediction for snap_scaffold_27-snap.925-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.101653_t
Valid prediction for Augustus_model.g38956.t1
Valid prediction for Augustus_model.g38949.t1
Valid prediction for GeneMark_model.101642_t
Valid prediction for GeneMark_model.101661_t
Valid prediction for GeneMark_model.101669_t
Valid prediction for GeneMark_model.101640_t
Valid prediction for GlimmerHMM_glimmerT_58481-T1
Valid prediction for snap_scaffold_27-snap.920-T1
Valid prediction for snap_scaffold_27-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_58458-T1
Valid prediction for snap_scaffold_27-snap.915-T1
Valid prediction for snap_scaffold_27-snap.911-T1
Valid prediction for GeneMark_model.101655_t
Valid prediction for GeneMark_model.101660_t
Valid prediction for GlimmerHMM_glimmerT_58474-T1
Valid prediction for GeneMark_model.101665_t
Valid prediction for snap_scaffold_27-snap.921-T1
Valid prediction for Augustus_model.g38953.t1
Valid prediction for GeneMark_model.101663_t
Valid prediction for GeneMark_model.101635_t
Valid prediction for Augustus_model.g38945.t1
Valid prediction for snap_scaffold_27-snap.930-T1
Valid prediction for GeneMark_model.101657_t
Valid prediction for GlimmerHMM_glimmerT_58462-T1
Valid prediction for GeneMark_model.101636_t
Valid prediction for Augustus_model.g38954.t1
Valid prediction for snap_scaffold_27-snap.917-T1
Valid prediction for GeneMark_model.101649_t
Valid prediction for GeneMark_model.101643_t
Valid prediction for GlimmerHMM_glimmerT_58470-T1
Valid prediction for GlimmerHMM_glimmerT_58467-T1
Valid prediction for GeneMark_model.101673_t
Valid prediction for snap_scaffold_27-snap.931-T1
Valid prediction for GeneMark_model.101633_t
Valid prediction for GlimmerHMM_glimmerT_58460-T1
Valid prediction for GeneMark_model.101647_t
Valid prediction for pasa_asmbl_36872.p1
Valid prediction for CodingQuarry_transcript_41768-T1
Valid prediction for GeneMark_model.101638_t
Valid prediction for GlimmerHMM_glimmerT_58454-T1
Valid prediction for snap_scaffold_27-snap.927-T1
Valid prediction for GlimmerHMM_glimmerT_58456-T1
Valid prediction for GeneMark_model.101631_t
Valid prediction for snap_scaffold_27-snap.912-T1
Valid prediction for snap_scaffold_27-snap.895-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13693, rend_intergenic: 11824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47231, rend_intergenic: 42045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49268, rend_intergenic: 47743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79856, rend_intergenic: 76591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86538, rend_intergenic: 81204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99563, rend_intergenic: 86669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108269, rend_intergenic: 99573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114255, rend_intergenic: 112507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119986, rend_intergenic: 114592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127749, rend_intergenic: 120497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130944, rend_intergenic: 129469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134344, rend_intergenic: 131280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134810
-exon list size: 649


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 13693, rend_intergenic: 11824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47231, rend_intergenic: 42045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49268, rend_intergenic: 47743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79856, rend_intergenic: 76591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86538, rend_intergenic: 81204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99563, rend_intergenic: 86669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108269, rend_intergenic: 99573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114255, rend_intergenic: 112507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119986, rend_intergenic: 114592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127749, rend_intergenic: 120497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130944, rend_intergenic: 129469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134344, rend_intergenic: 131280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support