-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_3112680-3266816

-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 GeneMark_model.38192_t
Couldn't classify 19635, 20392
Couldn't classify 20637, 20727
Sorry, prediction pasa_asmbl_53857.p1 fails validation.
(GAG)	 CG	19635-20392	GT	AGG
(CAG)	 AG	20637-20727	GT	AGG
-recovered pasa_asmbl_53857.p1, internal, 20637, 20727
Valid prediction for GlimmerHMM_glimmerT_22294-T1
Valid prediction for snap_scaffold_9-snap.651-T1
Valid prediction for GeneMark_model.38198_t
Valid prediction for GeneMark_model.38217_t
Valid prediction for snap_scaffold_9-snap.680-T1
Valid prediction for GeneMark_model.38222_t
Valid prediction for snap_scaffold_9-snap.652-T1
Valid prediction for GeneMark_model.38226_t
Valid prediction for snap_scaffold_9-snap.667-T1
Valid prediction for CodingQuarry_transcript_61967-T1
Valid prediction for Augustus_model.g14927.t1
Valid prediction for snap_scaffold_9-snap.657-T1
Valid prediction for GeneMark_model.38201_t
Valid prediction for Augustus_model.g14930.t1
Valid prediction for snap_scaffold_9-snap.649-T1
Valid prediction for snap_scaffold_9-snap.663-T1
Valid prediction for GeneMark_model.38203_t
Valid prediction for snap_scaffold_9-snap.666-T1
Valid prediction for snap_scaffold_9-snap.669-T1
Couldn't classify 15585, 15614
Sorry, prediction pasa_asmbl_53856.p1 fails validation.
(ATG)	 CC	12966-12984	GT	CGG
(AGG)	 AG	13310-13523	GT	AGG
(CCT)	 AG	13662-13809	GT	AGG
(GTG)	 AG	15585-15614	CA	GGC
-recovered pasa_asmbl_53856.p1, initial, 12966, 12984
-recovered pasa_asmbl_53856.p1, internal, 13310, 13523
-recovered pasa_asmbl_53856.p1, internal, 13662, 13809
Valid prediction for GlimmerHMM_glimmerT_22301-T1
Valid prediction for snap_scaffold_9-snap.686-T1
Valid prediction for GlimmerHMM_glimmerT_22307-T1
Valid prediction for snap_scaffold_9-snap.675-T1
Valid prediction for snap_scaffold_9-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_22306-T1
Couldn't classify 36551, 36810
Sorry, prediction pasa_asmbl_53859.p1 fails validation.
(GGT)	 GT	36551-36810	GT	AGG
(CAG)	 AG	36963-37143	GT	AGG
(GCC)	 AG	37496-37630	TA	GAT
-recovered pasa_asmbl_53859.p1, terminal, 37496, 37630
-recovered pasa_asmbl_53859.p1, internal, 36963, 37143
Valid prediction for Augustus_model.g14919.t1
Valid prediction for GeneMark_model.38221_t
Valid prediction for snap_scaffold_9-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_22315-T1
Valid prediction for GlimmerHMM_glimmerT_22318-T1
Valid prediction for Augustus_model.g14931.t1
Valid prediction for GeneMark_model.38205_t
Valid prediction for GlimmerHMM_glimmerT_22311-T1
Valid prediction for GeneMark_model.38200_t
Valid prediction for GeneMark_model.38219_t
Valid prediction for snap_scaffold_9-snap.682-T1
Valid prediction for GlimmerHMM_glimmerT_22305-T1
Valid prediction for GeneMark_model.38212_t
Valid prediction for GeneMark_model.38187_t
Valid prediction for Augustus_model.g14918.t1
Valid prediction for GeneMark_model.38224_t
Valid prediction for GlimmerHMM_glimmerT_22297-T1
Valid prediction for GlimmerHMM_glimmerT_22292-T1
Valid prediction for GeneMark_model.38214_t
Valid prediction for GlimmerHMM_glimmerT_22319-T1
Valid prediction for pasa_asmbl_53862.p1
Valid prediction for GeneMark_model.38185_t
Valid prediction for GeneMark_model.38228_t
Valid prediction for snap_scaffold_9-snap.655-T1
Valid prediction for GeneMark_model.38194_t
Valid prediction for Augustus_model.g14932.t1
Valid prediction for Augustus_model.g14933.t1
Valid prediction for GeneMark_model.38207_t
Valid prediction for snap_scaffold_9-snap.661-T1
Valid prediction for Augustus_model.g14921.t1
Couldn't classify 144807, 146705
Sorry, prediction pasa_asmbl_53863.p1 fails validation.
(ATG)	 CT	144807-146705	GG	GCG
Valid prediction for GlimmerHMM_glimmerT_22303-T1
Valid prediction for GlimmerHMM_glimmerT_22316-T1
Valid prediction for GlimmerHMM_glimmerT_22320-T1
Valid prediction for snap_scaffold_9-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_22312-T1
Valid prediction for snap_scaffold_9-snap.685-T1
Valid prediction for HiQ_model.g14920.t1
Valid prediction for GeneMark_model.38188_t
Valid prediction for GeneMark_model.38190_t
Valid prediction for snap_scaffold_9-snap.659-T1
Valid prediction for snap_scaffold_9-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_22296-T1
Valid prediction for CodingQuarry_transcript_61968-T1
Valid prediction for GlimmerHMM_glimmerT_22293-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_9-snap.650-T1
Valid prediction for GeneMark_model.38191_t
Valid prediction for Augustus_model.g14929.t1
Valid prediction for snap_scaffold_9-snap.654-T1
Valid prediction for snap_scaffold_9-snap.660-T1
Valid prediction for snap_scaffold_9-snap.677-T1
Valid prediction for GeneMark_model.38189_t
Valid prediction for GlimmerHMM_glimmerT_22295-T1
Valid prediction for GeneMark_model.38206_t
Valid prediction for snap_scaffold_9-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_22298-T1
Valid prediction for snap_scaffold_9-snap.653-T1
Valid prediction for GeneMark_model.38199_t
Valid prediction for snap_scaffold_9-snap.673-T1
Valid prediction for GeneMark_model.38227_t
Valid prediction for snap_scaffold_9-snap.676-T1
Valid prediction for GeneMark_model.38186_t
Valid prediction for snap_scaffold_9-snap.671-T1
Valid prediction for snap_scaffold_9-snap.658-T1
Valid prediction for GeneMark_model.38204_t
Valid prediction for GeneMark_model.38208_t
Valid prediction for GeneMark_model.38211_t
Valid prediction for GlimmerHMM_glimmerT_22302-T1
Valid prediction for GlimmerHMM_glimmerT_22314-T1
Valid prediction for GeneMark_model.38215_t
Valid prediction for GeneMark_model.38218_t
Couldn't classify 103305, 103413
Couldn't classify 104272, 104372
Sorry, prediction pasa_asmbl_55716.p1 fails validation.
(GGC)	 AT	103305-103413	GT	AGG
(CTT)	 AG	103889-104017	GT	CCG
(AGT)	 AG	104272-104372	GG	CTG
-recovered pasa_asmbl_55716.p1, internal, 103889, 104017
Valid prediction for GlimmerHMM_glimmerT_22299-T1
Valid prediction for GeneMark_model.38225_t
Valid prediction for GeneMark_model.38184_t
Valid prediction for GeneMark_model.38209_t
Valid prediction for Augustus_model.g14928.t1
Valid prediction for GeneMark_model.38195_t
Valid prediction for GlimmerHMM_glimmerT_22317-T1
Valid prediction for GlimmerHMM_glimmerT_22308-T1
Valid prediction for snap_scaffold_9-snap.662-T1
Valid prediction for GlimmerHMM_glimmerT_22300-T1
Valid prediction for GeneMark_model.38210_t
Valid prediction for Augustus_model.g14922.t1
Valid prediction for GeneMark_model.38202_t
Valid prediction for snap_scaffold_9-snap.656-T1
Valid prediction for GlimmerHMM_glimmerT_22304-T1
Valid prediction for GlimmerHMM_glimmerT_22313-T1
Valid prediction for snap_scaffold_9-snap.668-T1
Valid prediction for snap_scaffold_9-snap.678-T1
Valid prediction for GeneMark_model.38220_t
Valid prediction for snap_scaffold_9-snap.674-T1
Valid prediction for Augustus_model.g14923.t1
Valid prediction for GeneMark_model.38193_t
Valid prediction for snap_scaffold_9-snap.683-T1
Valid prediction for GeneMark_model.38196_t
Valid prediction for Augustus_model.g14925.t1
Valid prediction for GeneMark_model.38213_t
Valid prediction for GeneMark_model.38223_t
Valid prediction for GlimmerHMM_glimmerT_22309-T1
Valid prediction for snap_scaffold_9-snap.681-T1
Valid prediction for Augustus_model.g14926.t1
Valid prediction for snap_scaffold_9-snap.670-T1
Valid prediction for GlimmerHMM_glimmerT_22310-T1
Valid prediction for GeneMark_model.38216_t
Valid prediction for Augustus_model.g14924.t1
Valid prediction for Augustus_model.g14917.t1
Valid prediction for GeneMark_model.38230_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8814, rend_intergenic: 8606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13619, rend_intergenic: 10230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20477, rend_intergenic: 13637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29153, rend_intergenic: 22295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29505, rend_intergenic: 29153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35028, rend_intergenic: 29938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44158, rend_intergenic: 39343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50872, rend_intergenic: 45218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54556, rend_intergenic: 51293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58652, rend_intergenic: 56054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65948, rend_intergenic: 60851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70673, rend_intergenic: 65976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95561, rend_intergenic: 93474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105838, rend_intergenic: 96318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120909, rend_intergenic: 113327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122860, rend_intergenic: 121577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127221, rend_intergenic: 126768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137701, rend_intergenic: 127755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154137
-exon list size: 678


building trellis

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-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 8814, rend_intergenic: 8606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13619, rend_intergenic: 10230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20477, rend_intergenic: 13637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29153, rend_intergenic: 22295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29505, rend_intergenic: 29153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35028, rend_intergenic: 29938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44158, rend_intergenic: 39343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50872, rend_intergenic: 45218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54556, rend_intergenic: 51293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58652, rend_intergenic: 56054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65948, rend_intergenic: 60851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70673, rend_intergenic: 65976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95561, rend_intergenic: 93474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105838, rend_intergenic: 96318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120909, rend_intergenic: 113327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122860, rend_intergenic: 121577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127221, rend_intergenic: 126768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137701, rend_intergenic: 127755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support