-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_3709358-3895903

-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 GlimmerHMM_glimmerT_29722-T1
Valid prediction for snap_scaffold_12-snap.758-T1
Valid prediction for GeneMark_model.51373_t
Valid prediction for HiQ_model.g19796.t1
Valid prediction for GlimmerHMM_glimmerT_29748-T1
Valid prediction for Augustus_model.g19793.t1
Valid prediction for GeneMark_model.51405_t
Valid prediction for GlimmerHMM_glimmerT_29732-T1
Valid prediction for CodingQuarry_transcript_10139-T1
Valid prediction for snap_scaffold_12-snap.785-T1
Valid prediction for HiQ_model.g19792.t1
Valid prediction for GlimmerHMM_glimmerT_29729-T1
Valid prediction for GeneMark_model.51368_t
Valid prediction for snap_scaffold_12-snap.776-T1
Valid prediction for GeneMark_model.51362_t
Valid prediction for pasa_asmbl_8534.p1
Valid prediction for snap_scaffold_12-snap.771-T1
Valid prediction for snap_scaffold_12-snap.798-T1
Valid prediction for snap_scaffold_12-snap.793-T1
Valid prediction for GeneMark_model.51399_t
Valid prediction for snap_scaffold_12-snap.773-T1
Valid prediction for pasa_asmbl_8531.p1
Valid prediction for GeneMark_model.51401_t
Valid prediction for CodingQuarry_transcript_10137-T1
Valid prediction for GeneMark_model.51369_t
Valid prediction for GeneMark_model.51354_t
Valid prediction for GeneMark_model.51383_t
Valid prediction for Augustus_model.g19803.t1
Valid prediction for snap_scaffold_12-snap.789-T1
Valid prediction for GeneMark_model.51375_t
Valid prediction for snap_scaffold_12-snap.799-T1
Valid prediction for snap_scaffold_12-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_29737-T1
Valid prediction for Augustus_model.g19797.t1
Valid prediction for GeneMark_model.51356_t
Valid prediction for snap_scaffold_12-snap.756-T1
Valid prediction for snap_scaffold_12-snap.797-T1
Valid prediction for snap_scaffold_12-snap.780-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29728-T1
Valid prediction for GeneMark_model.51398_t
Valid prediction for GeneMark_model.51403_t
Valid prediction for GeneMark_model.51385_t
Valid prediction for GlimmerHMM_glimmerT_29745-T1
Valid prediction for Augustus_model.g19800.t1
Valid prediction for snap_scaffold_12-snap.779-T1
Valid prediction for snap_scaffold_12-snap.762-T1
Valid prediction for Augustus_model.g19788.t1
Valid prediction for GeneMark_model.51379_t
Valid prediction for snap_scaffold_12-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_29740-T1
Valid prediction for GlimmerHMM_glimmerT_29733-T1
Valid prediction for snap_scaffold_12-snap.794-T1
Valid prediction for GeneMark_model.51376_t
Valid prediction for GeneMark_model.51364_t
Valid prediction for GeneMark_model.51360_t
Valid prediction for GeneMark_model.51366_t
Valid prediction for snap_scaffold_12-snap.796-T1
Valid prediction for GeneMark_model.51400_t
Valid prediction for GeneMark_model.51390_t
Valid prediction for Augustus_model.g19802.t1
Valid prediction for GeneMark_model.51372_t
Valid prediction for GeneMark_model.51395_t
Valid prediction for snap_scaffold_12-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_29726-T1
Valid prediction for GeneMark_model.51358_t
Valid prediction for GlimmerHMM_glimmerT_29746-T1
Valid prediction for GeneMark_model.51370_t
Valid prediction for snap_scaffold_12-snap.769-T1
Valid prediction for snap_scaffold_12-snap.774-T1
Valid prediction for CodingQuarry_transcript_10136-T1
Valid prediction for snap_scaffold_12-snap.787-T1
Valid prediction for snap_scaffold_12-snap.791-T1
Valid prediction for GeneMark_model.51387_t
Valid prediction for GlimmerHMM_glimmerT_29727-T1
Valid prediction for GeneMark_model.51350_t
Valid prediction for snap_scaffold_12-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_29743-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 GlimmerHMM_glimmerT_29747-T1
Valid prediction for GlimmerHMM_glimmerT_29734-T1
Valid prediction for GeneMark_model.51404_t
Valid prediction for GlimmerHMM_glimmerT_29744-T1
Valid prediction for pasa_asmbl_7508.p1
Valid prediction for GeneMark_model.51353_t
Valid prediction for snap_scaffold_12-snap.767-T1
Valid prediction for snap_scaffold_12-snap.757-T1
Valid prediction for Augustus_model.g19801.t1
Valid prediction for snap_scaffold_12-snap.766-T1
Valid prediction for snap_scaffold_12-snap.768-T1
Valid prediction for GeneMark_model.51389_t
Valid prediction for GlimmerHMM_glimmerT_29731-T1
Valid prediction for Augustus_model.g19795.t1
Valid prediction for GeneMark_model.51402_t
Valid prediction for GeneMark_model.51388_t
Valid prediction for GeneMark_model.51382_t
Valid prediction for Augustus_model.g19789.t1
Couldn't classify 95955, 96831
Sorry, prediction pasa_asmbl_7504.p1 fails validation.
(GGT)	 AT	95955-96831	GT	CGG
(GGA)	 AG	96986-97115	GT	AAG
(ATT)	 AG	97269-97325	GT	AGG
(GCA)	 AG	97407-97530	GT	CAG
(GAG)	 AG	98510-98611	GT	AGG
(GTG)	 AG	98992-99174	AG	AGA
-recovered pasa_asmbl_7504.p1, terminal, 98992, 99174
-recovered pasa_asmbl_7504.p1, internal, 96986, 97115
-recovered pasa_asmbl_7504.p1, internal, 97269, 97325
-recovered pasa_asmbl_7504.p1, internal, 97407, 97530
-recovered pasa_asmbl_7504.p1, internal, 98510, 98611
Valid prediction for GeneMark_model.51396_t
Valid prediction for GlimmerHMM_glimmerT_29738-T1
Valid prediction for snap_scaffold_12-snap.783-T1
Valid prediction for GeneMark_model.51349_t
Valid prediction for GeneMark_model.51377_t
Valid prediction for snap_scaffold_12-snap.760-T1
Valid prediction for GeneMark_model.51355_t
Valid prediction for Augustus_model.g19785.t1
Valid prediction for snap_scaffold_12-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_29730-T1
Valid prediction for GlimmerHMM_glimmerT_29725-T1
Valid prediction for GeneMark_model.51378_t
Valid prediction for GeneMark_model.51397_t
Valid prediction for GeneMark_model.51391_t
Valid prediction for Augustus_model.g19786.t1
Valid prediction for GeneMark_model.51361_t
Valid prediction for GlimmerHMM_glimmerT_29741-T1
Valid prediction for Augustus_model.g19791.t1
Valid prediction for GeneMark_model.51392_t
Couldn't classify 80840, 81313
Sorry, prediction pasa_asmbl_7509.p1 fails validation.
(CTC)	 GT	80840-81313	TG	GAT
Valid prediction for CodingQuarry_transcript_10138-T1
Valid prediction for snap_scaffold_12-snap.795-T1
Valid prediction for HiQ_model.g19794.t1
Valid prediction for GeneMark_model.51381_t
Valid prediction for GeneMark_model.51394_t
Valid prediction for snap_scaffold_12-snap.792-T1
Valid prediction for GeneMark_model.51357_t
Valid prediction for snap_scaffold_12-snap.788-T1
Valid prediction for snap_scaffold_12-snap.778-T1
Valid prediction for snap_scaffold_12-snap.790-T1
Valid prediction for GeneMark_model.51384_t
Valid prediction for snap_scaffold_12-snap.763-T1
Valid prediction for Augustus_model.g19787.t1
Valid prediction for GeneMark_model.51367_t
Valid prediction for Augustus_model.g19798.t1
Valid prediction for GlimmerHMM_glimmerT_29724-T1
Valid prediction for GlimmerHMM_glimmerT_29723-T1
Valid prediction for snap_scaffold_12-snap.777-T1
Valid prediction for snap_scaffold_12-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_29742-T1
Valid prediction for Augustus_model.g19790.t1
Valid prediction for GeneMark_model.51393_t
Valid prediction for GeneMark_model.51365_t
Valid prediction for GlimmerHMM_glimmerT_29735-T1
Valid prediction for snap_scaffold_12-snap.770-T1
Valid prediction for GeneMark_model.51363_t
Valid prediction for GeneMark_model.51386_t
Valid prediction for GeneMark_model.51380_t
Valid prediction for Augustus_model.g19799.t1
Couldn't classify 111402, 111602
Sorry, prediction pasa_asmbl_7502.p1 fails validation.
(GCA)	 GG	111402-111602	GT	AGG
(GGT)	 AG	112823-112876	GT	AGG
(GTG)	 AG	113356-113435	GT	GGG
(GTC)	 AG	115608-115839	CT	AGC
-recovered pasa_asmbl_7502.p1, terminal, 115608, 115839
-recovered pasa_asmbl_7502.p1, internal, 112823, 112876
-recovered pasa_asmbl_7502.p1, internal, 113356, 113435
Valid prediction for snap_scaffold_12-snap.781-T1
Valid prediction for GeneMark_model.51371_t
Valid prediction for GeneMark_model.51374_t
Valid prediction for snap_scaffold_12-snap.782-T1
Valid prediction for snap_scaffold_12-snap.784-T1
Valid prediction for GeneMark_model.51359_t
Valid prediction for GlimmerHMM_glimmerT_29739-T1
Valid prediction for GlimmerHMM_glimmerT_29736-T1
Valid prediction for snap_scaffold_12-snap.761-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6224, rend_intergenic: 5010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13687, rend_intergenic: 6236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28268, rend_intergenic: 22665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42521, rend_intergenic: 34973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51690, rend_intergenic: 44364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65518, rend_intergenic: 59962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69403, rend_intergenic: 67211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70684, rend_intergenic: 69889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80936, rend_intergenic: 70721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131489, rend_intergenic: 128055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149257, rend_intergenic: 146469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186546
-exon list size: 657


building trellis

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-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 6224, rend_intergenic: 5010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13687, rend_intergenic: 6236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28268, rend_intergenic: 22665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42521, rend_intergenic: 34973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51690, rend_intergenic: 44364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65518, rend_intergenic: 59962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69403, rend_intergenic: 67211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70684, rend_intergenic: 69889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80936, rend_intergenic: 70721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131489, rend_intergenic: 128055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149257, rend_intergenic: 146469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support