-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_1864412-2067663

-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_13-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_31844-T1
Valid prediction for GlimmerHMM_glimmerT_31839-T1
Valid prediction for GlimmerHMM_glimmerT_31842-T1
Valid prediction for snap_scaffold_13-snap.345-T1
Valid prediction for GeneMark_model.54687_t
Valid prediction for GeneMark_model.54731_t
Valid prediction for snap_scaffold_13-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_31833-T1
Valid prediction for snap_scaffold_13-snap.376-T1
Valid prediction for snap_scaffold_13-snap.346-T1
Valid prediction for snap_scaffold_13-snap.384-T1
Valid prediction for GeneMark_model.54686_t
Valid prediction for GeneMark_model.54708_t
Valid prediction for GeneMark_model.54710_t
Valid prediction for GeneMark_model.54717_t
Valid prediction for GeneMark_model.54722_t
Valid prediction for Augustus_model.g21294.t1
Valid prediction for GeneMark_model.54726_t
Valid prediction for Augustus_model.g21295.t1
Valid prediction for GeneMark_model.54697_t
Valid prediction for Augustus_model.g21288.t1
Valid prediction for GlimmerHMM_glimmerT_31835-T1
Valid prediction for GlimmerHMM_glimmerT_31829-T1
Valid prediction for GlimmerHMM_glimmerT_31827-T1
Valid prediction for Augustus_model.g21303.t1
Valid prediction for CodingQuarry_transcript_12838-T1
Valid prediction for snap_scaffold_13-snap.378-T1
Couldn't classify 117149, 117349
Sorry, prediction pasa_asmbl_10544.p1 fails validation.
(CCT)	 AG	117149-117349	GT	CGG
(TTG)	 AG	117475-117576	GT	GGG
(GAA)	 AG	117692-117799	GT	AAG
(CAA)	 AG	117921-118115	AA	AGA
-recovered pasa_asmbl_10544.p1, terminal, 117921, 118115
-recovered pasa_asmbl_10544.p1, internal, 117149, 117349
-recovered pasa_asmbl_10544.p1, internal, 117475, 117576
-recovered pasa_asmbl_10544.p1, internal, 117692, 117799
Valid prediction for GeneMark_model.54699_t
Valid prediction for snap_scaffold_13-snap.374-T1
Valid prediction for snap_scaffold_13-snap.370-T1
Valid prediction for Augustus_model.g21297.t1
Valid prediction for GeneMark_model.54730_t
Valid prediction for snap_scaffold_13-snap.386-T1
Valid prediction for snap_scaffold_13-snap.367-T1
Valid prediction for HiQ_model.g21296.t1
Valid prediction for GeneMark_model.54707_t
Valid prediction for snap_scaffold_13-snap.352-T1
Valid prediction for GeneMark_model.54693_t
Valid prediction for snap_scaffold_13-snap.361-T1
Valid prediction for snap_scaffold_13-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_31837-T1
Valid prediction for GeneMark_model.54728_t
Valid prediction for GeneMark_model.54689_t
Valid prediction for GeneMark_model.54720_t
Valid prediction for GlimmerHMM_glimmerT_31828-T1
Valid prediction for GlimmerHMM_glimmerT_31840-T1
Valid prediction for snap_scaffold_13-snap.377-T1
Valid prediction for snap_scaffold_13-snap.371-T1
Valid prediction for GeneMark_model.54712_t
Valid prediction for GeneMark_model.54724_t
Valid prediction for Augustus_model.g21300.t1
Valid prediction for snap_scaffold_13-snap.385-T1
Valid prediction for snap_scaffold_13-snap.366-T1
Valid prediction for Augustus_model.g21299.t1
Valid prediction for GeneMark_model.54700_t
Valid prediction for GeneMark_model.54704_t
Valid prediction for GeneMark_model.54695_t
Valid prediction for GlimmerHMM_glimmerT_31830-T1
Valid prediction for GlimmerHMM_glimmerT_31846-T1
Valid prediction for GlimmerHMM_glimmerT_31841-T1
Valid prediction for snap_scaffold_13-snap.355-T1
Valid prediction for GeneMark_model.54705_t
Valid prediction for GlimmerHMM_glimmerT_31850-T1
Valid prediction for snap_scaffold_13-snap.368-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31845-T1
Valid prediction for GeneMark_model.54698_t
Valid prediction for snap_scaffold_13-snap.349-T1
Valid prediction for GeneMark_model.54714_t
Valid prediction for GlimmerHMM_glimmerT_31838-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.54688_t
Valid prediction for snap_scaffold_13-snap.365-T1
Valid prediction for snap_scaffold_13-snap.351-T1
Valid prediction for snap_scaffold_13-snap.348-T1
Valid prediction for snap_scaffold_13-snap.389-T1
Valid prediction for snap_scaffold_13-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_31834-T1
Valid prediction for snap_scaffold_13-snap.360-T1
Valid prediction for snap_scaffold_13-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_31854-T1
Valid prediction for GeneMark_model.54732_t
Valid prediction for GeneMark_model.54716_t
Valid prediction for GeneMark_model.54727_t
Valid prediction for Augustus_model.g21290.t1
Valid prediction for Augustus_model.g21298.t1
Valid prediction for snap_scaffold_13-snap.383-T1
Valid prediction for snap_scaffold_13-snap.358-T1
Valid prediction for snap_scaffold_13-snap.357-T1
Valid prediction for CodingQuarry_transcript_12837-T1
Valid prediction for Augustus_model.g21289.t1
Valid prediction for GeneMark_model.54691_t
Valid prediction for Augustus_model.g21305.t1
Valid prediction for GeneMark_model.54711_t
Valid prediction for Augustus_model.g21307.t1
Valid prediction for GlimmerHMM_glimmerT_31848-T1
Valid prediction for GeneMark_model.54729_t
Valid prediction for GeneMark_model.54715_t
Valid prediction for GlimmerHMM_glimmerT_31836-T1
Valid prediction for snap_scaffold_13-snap.387-T1
Valid prediction for snap_scaffold_13-snap.362-T1
Valid prediction for GeneMark_model.54694_t
Valid prediction for snap_scaffold_13-snap.388-T1
Valid prediction for GeneMark_model.54692_t
Valid prediction for snap_scaffold_13-snap.350-T1
Valid prediction for Augustus_model.g21304.t1
Valid prediction for GeneMark_model.54718_t
Valid prediction for snap_scaffold_13-snap.369-T1
Valid prediction for GeneMark_model.54702_t
Valid prediction for snap_scaffold_13-snap.380-T1
Valid prediction for snap_scaffold_13-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_31831-T1
Valid prediction for GeneMark_model.54706_t
Valid prediction for GeneMark_model.54719_t
Valid prediction for snap_scaffold_13-snap.347-T1
Valid prediction for snap_scaffold_13-snap.372-T1
Valid prediction for snap_scaffold_13-snap.391-T1
Valid prediction for Augustus_model.g21301.t1
Valid prediction for GeneMark_model.54690_t
Valid prediction for GlimmerHMM_glimmerT_31832-T1
Valid prediction for GlimmerHMM_glimmerT_31843-T1
Valid prediction for snap_scaffold_13-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_31849-T1
Couldn't classify 131345, 131427
Sorry, prediction pasa_asmbl_10402.p1 fails validation.
(TGT)	 TG	131345-131427	GT	AGG
(GTG)	 AG	131627-131750	GT	TGG
(GTG)	 AG	131868-131983	GT	ACG
(GTT)	 AG	132123-132195	GG	GAG
-recovered pasa_asmbl_10402.p1, terminal, 132123, 132195
-recovered pasa_asmbl_10402.p1, internal, 131627, 131750
-recovered pasa_asmbl_10402.p1, internal, 131868, 131983
Valid prediction for GeneMark_model.54725_t
Valid prediction for GlimmerHMM_glimmerT_31847-T1
Valid prediction for GlimmerHMM_glimmerT_31851-T1
Valid prediction for Augustus_model.g21291.t1
Valid prediction for snap_scaffold_13-snap.382-T1
Valid prediction for snap_scaffold_13-snap.353-T1
Valid prediction for snap_scaffold_13-snap.359-T1
Valid prediction for GeneMark_model.54709_t
Valid prediction for GlimmerHMM_glimmerT_31852-T1
Valid prediction for GeneMark_model.54696_t
Valid prediction for Augustus_model.g21302.t1
Valid prediction for GeneMark_model.54733_t
Couldn't classify 130615, 130950
Sorry, prediction pasa_asmbl_9394.p1 fails validation.
(ATG)	 CA	129946-130045	GT	AGG
(ATA)	 AG	130142-130275	GT	AGG
(GAT)	 AG	130615-130950	TC	TGT
-recovered pasa_asmbl_9394.p1, initial, 129946, 130045
-recovered pasa_asmbl_9394.p1, internal, 130142, 130275
Valid prediction for Augustus_model.g21306.t1
Valid prediction for Augustus_model.g21293.t1
Valid prediction for GeneMark_model.54721_t
Valid prediction for CodingQuarry_transcript_12836-T1
Valid prediction for GeneMark_model.54723_t
Valid prediction for snap_scaffold_13-snap.363-T1
Valid prediction for snap_scaffold_13-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_31853-T1
Valid prediction for Augustus_model.g21292.t1
Valid prediction for GeneMark_model.54703_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38949, rend_intergenic: 34216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41823, rend_intergenic: 40055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43647, rend_intergenic: 42241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83474, rend_intergenic: 80322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127232, rend_intergenic: 125106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133871, rend_intergenic: 130889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139503, rend_intergenic: 134062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156977, rend_intergenic: 142436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203252
-exon list size: 672


building trellis

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99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 38949, rend_intergenic: 34216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41823, rend_intergenic: 40055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43647, rend_intergenic: 42241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83474, rend_intergenic: 80322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127232, rend_intergenic: 125106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133871, rend_intergenic: 130889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139503, rend_intergenic: 134062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156977, rend_intergenic: 142436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support