-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_3975011-4148862

-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.63244_t
Valid prediction for GlimmerHMM_glimmerT_36742-T1
Valid prediction for HiQ_model.g24665.t1
Valid prediction for GlimmerHMM_glimmerT_36720-T1
Valid prediction for GlimmerHMM_glimmerT_36741-T1
Valid prediction for snap_scaffold_15-snap.887-T1
Valid prediction for snap_scaffold_15-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_36744-T1
Valid prediction for Augustus_model.g24663.t1
Valid prediction for CodingQuarry_transcript_17922-T1
Valid prediction for GeneMark_model.63236_t
Valid prediction for snap_scaffold_15-snap.859-T1
Valid prediction for snap_scaffold_15-snap.879-T1
Valid prediction for pasa_asmbl_14066.p1
Valid prediction for GeneMark_model.63266_t
Valid prediction for GlimmerHMM_glimmerT_36717-T1
Valid prediction for snap_scaffold_15-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_36725-T1
Couldn't classify 119127, 119745
Sorry, prediction pasa_asmbl_14062.p1 fails validation.
(GGG)	 GA	119127-119745	GT	GGG
(ACA)	 AG	120509-120659	GT	AGG
(GAT)	 AG	121130-121190	GT	AAG
(GGC)	 AG	121721-121879	GT	AGG
(TGT)	 AG	121998-122180	GC	GAG
-recovered pasa_asmbl_14062.p1, terminal, 121998, 122180
-recovered pasa_asmbl_14062.p1, internal, 120509, 120659
-recovered pasa_asmbl_14062.p1, internal, 121130, 121190
-recovered pasa_asmbl_14062.p1, internal, 121721, 121879
-recovered pasa_asmbl_14062.p1, internal, 121998, 122180
Valid prediction for GeneMark_model.63229_t
Valid prediction for GeneMark_model.63251_t
Valid prediction for Augustus_model.g24660.t1
Valid prediction for Augustus_model.g24661.t1
Valid prediction for GeneMark_model.63234_t
Valid prediction for GlimmerHMM_glimmerT_36732-T1
Valid prediction for HiQ_model.g24668.t1
Valid prediction for Augustus_model.g24662.t1
Valid prediction for snap_scaffold_15-snap.876-T1
Valid prediction for GeneMark_model.63256_t
Valid prediction for GeneMark_model.63238_t
Valid prediction for GlimmerHMM_glimmerT_36716-T1
Valid prediction for GeneMark_model.63255_t
Valid prediction for snap_scaffold_15-snap.870-T1
Valid prediction for GeneMark_model.63228_t
Valid prediction for pasa_asmbl_14067.p1
Valid prediction for snap_scaffold_15-snap.868-T1
Valid prediction for snap_scaffold_15-snap.886-T1
Valid prediction for GeneMark_model.63242_t
Valid prediction for CodingQuarry_transcript_17923-T1
Couldn't classify 18359, 18592
Sorry, prediction pasa_asmbl_14059.p1 fails validation.
(TGT)	 CC	18359-18592	GT	AGG
(ATG)	 AG	19231-19389	GC	AGG
add_exon() Sorry, pasa_asmbl_14059.p1 19231-19389-initial-1 is invalid.
-recovered pasa_asmbl_14059.p1, initial, 19231, 19389
-recovered pasa_asmbl_14059.p1, terminal, 19231, 19389
-recovered pasa_asmbl_14059.p1, internal, 19231, 19389
Valid prediction for GlimmerHMM_glimmerT_36727-T1
Valid prediction for snap_scaffold_15-snap.884-T1
Valid prediction for GeneMark_model.63263_t
Valid prediction for GlimmerHMM_glimmerT_36738-T1
Valid prediction for GeneMark_model.63226_t
Valid prediction for HiQ_model.g24667.t1
Valid prediction for GlimmerHMM_glimmerT_36729-T1
Valid prediction for snap_scaffold_15-snap.866-T1
Valid prediction for GlimmerHMM_glimmerT_36733-T1
Valid prediction for GlimmerHMM_glimmerT_36730-T1
Valid prediction for GlimmerHMM_glimmerT_36734-T1
Valid prediction for GlimmerHMM_glimmerT_36724-T1
Valid prediction for Augustus_model.g24657.t1
Valid prediction for GlimmerHMM_glimmerT_36740-T1
Valid prediction for GeneMark_model.63253_t
Valid prediction for snap_scaffold_15-snap.862-T1
Valid prediction for snap_scaffold_15-snap.875-T1
Valid prediction for snap_scaffold_15-snap.878-T1
Valid prediction for GeneMark_model.63224_t
Valid prediction for snap_scaffold_15-snap.861-T1
Valid prediction for GeneMark_model.63248_t
Valid prediction for snap_scaffold_15-snap.863-T1
Valid prediction for GlimmerHMM_glimmerT_36723-T1
Valid prediction for GeneMark_model.63260_t
Valid prediction for GlimmerHMM_glimmerT_36722-T1
Valid prediction for snap_scaffold_15-snap.881-T1
Valid prediction for snap_scaffold_15-snap.858-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 GeneMark_model.63227_t
Valid prediction for GeneMark_model.63233_t
Valid prediction for GeneMark_model.63223_t
Valid prediction for snap_scaffold_15-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_36726-T1
Valid prediction for GeneMark_model.63264_t
Valid prediction for GeneMark_model.63230_t
Valid prediction for GlimmerHMM_glimmerT_36743-T1
Valid prediction for GlimmerHMM_glimmerT_36728-T1
Valid prediction for GlimmerHMM_glimmerT_36739-T1
Valid prediction for GlimmerHMM_glimmerT_36736-T1
Valid prediction for GeneMark_model.63252_t
Valid prediction for snap_scaffold_15-snap.869-T1
Valid prediction for snap_scaffold_15-snap.873-T1
Valid prediction for snap_scaffold_15-snap.882-T1
Valid prediction for GeneMark_model.63258_t
Valid prediction for snap_scaffold_15-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_36721-T1
Valid prediction for GeneMark_model.63249_t
Valid prediction for GeneMark_model.63235_t
Valid prediction for snap_scaffold_15-snap.877-T1
Valid prediction for snap_scaffold_15-snap.867-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_17924-T1
Valid prediction for GlimmerHMM_glimmerT_36737-T1
Valid prediction for GlimmerHMM_glimmerT_36719-T1
Valid prediction for HiQ_model.g24670.t1
Valid prediction for GeneMark_model.63237_t
Valid prediction for GlimmerHMM_glimmerT_36735-T1
Valid prediction for GeneMark_model.63240_t
Valid prediction for GeneMark_model.63232_t
Valid prediction for snap_scaffold_15-snap.888-T1
Valid prediction for snap_scaffold_15-snap.864-T1
Valid prediction for GlimmerHMM_glimmerT_36718-T1
Valid prediction for GeneMark_model.63239_t
Valid prediction for pasa_asmbl_15132.p1
Valid prediction for snap_scaffold_15-snap.885-T1
Valid prediction for snap_scaffold_15-snap.860-T1
Valid prediction for snap_scaffold_15-snap.883-T1
Valid prediction for GeneMark_model.63243_t
Valid prediction for snap_scaffold_15-snap.874-T1
Valid prediction for Augustus_model.g24658.t1
Valid prediction for CodingQuarry_transcript_17921-T1
Valid prediction for snap_scaffold_15-snap.856-T1
Valid prediction for GeneMark_model.63246_t
Valid prediction for GeneMark_model.63262_t
Valid prediction for Augustus_model.g24666.t1
Valid prediction for CodingQuarry_transcript_17925-T1
Valid prediction for GeneMark_model.63250_t
Valid prediction for pasa_asmbl_15140.p1
Valid prediction for HiQ_model.g24669.t1
Valid prediction for GlimmerHMM_glimmerT_36731-T1
Valid prediction for Augustus_model.g24656.t1
Valid prediction for snap_scaffold_15-snap.890-T1
Valid prediction for GeneMark_model.63241_t
Valid prediction for CodingQuarry_transcript_17926-T1
Valid prediction for GeneMark_model.63225_t
Valid prediction for Augustus_model.g24659.t1
Valid prediction for Augustus_model.g24664.t1
Valid prediction for GeneMark_model.63245_t
Couldn't classify 14962, 14980
Sorry, prediction pasa_asmbl_15136.p1 fails validation.
(CAC)	 AA	14962-14980	GT	AGG
(GGG)	 AG	15316-15435	GT	AGG
(GAG)	 AG	15744-15863	GT	AGG
(GCT)	 AG	16043-16143	AC	AGA
-recovered pasa_asmbl_15136.p1, terminal, 16043, 16143
-recovered pasa_asmbl_15136.p1, internal, 15316, 15435
-recovered pasa_asmbl_15136.p1, internal, 15744, 15863
Valid prediction for GeneMark_model.63254_t
Valid prediction for GeneMark_model.63247_t
Valid prediction for snap_scaffold_15-snap.857-T1
Valid prediction for snap_scaffold_15-snap.855-T1
Valid prediction for GeneMark_model.63265_t
Valid prediction for snap_scaffold_15-snap.865-T1
Valid prediction for Augustus_model.g24671.t1
Valid prediction for GeneMark_model.63257_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16190, rend_intergenic: 12461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35169, rend_intergenic: 22187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68805, rend_intergenic: 62614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80191, rend_intergenic: 73467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92418, rend_intergenic: 84855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102883, rend_intergenic: 94464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114503, rend_intergenic: 103463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116681, rend_intergenic: 114637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173852
-exon list size: 602


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 16190, rend_intergenic: 12461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35169, rend_intergenic: 22187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68805, rend_intergenic: 62614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80191, rend_intergenic: 73467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92418, rend_intergenic: 84855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102883, rend_intergenic: 94464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114503, rend_intergenic: 103463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116681, rend_intergenic: 114637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support