-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_3111703-3266041

-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: +)Couldn't classify 68708, 69127
Sorry, prediction pasa_asmbl_6226.p2 fails validation.
(ATG)	 GC	68708-69127	CT	GGC
Valid prediction for GeneMark_model.47229_t
Valid prediction for GeneMark_model.47195_t
Valid prediction for GlimmerHMM_glimmerT_27333-T1
Valid prediction for GlimmerHMM_glimmerT_27322-T1
Valid prediction for GlimmerHMM_glimmerT_27347-T1
Valid prediction for GeneMark_model.47222_t
Valid prediction for GeneMark_model.47209_t
Valid prediction for Augustus_model.g18239.t1
Valid prediction for GeneMark_model.47203_t
Valid prediction for HiQ_model.g18240.t1
Valid prediction for snap_scaffold_11-snap.810-T1
Valid prediction for snap_scaffold_11-snap.816-T1
Valid prediction for snap_scaffold_11-snap.799-T1
Valid prediction for GeneMark_model.47193_t
Couldn't classify 70758, 70833
Couldn't classify 71683, 71703
Sorry, prediction pasa_asmbl_6241.p1 fails validation.
(AGC)	 CC	70758-70833	GT	AGG
(TGT)	 AG	71045-71145	GT	TGG
(GTG)	 AG	71278-71400	GT	TGG
(GTG)	 AG	71683-71703	CT	GGC
-recovered pasa_asmbl_6241.p1, internal, 71045, 71145
-recovered pasa_asmbl_6241.p1, internal, 71278, 71400
Valid prediction for GlimmerHMM_glimmerT_27334-T1
Valid prediction for snap_scaffold_11-snap.793-T1
Valid prediction for snap_scaffold_11-snap.800-T1
Couldn't classify 71899, 72043
Sorry, prediction pasa_asmbl_5369.p1 fails validation.
(TTC)	 TC	71899-72043	GT	GGG
(GGT)	 AG	74433-74536	GT	AGG
(GGG)	 AG	74663-75160	GT	TGG
(CCT)	 AG	75272-75753	GT	AGG
(GTT)	 AG	75870-76056	GT	TGG
(GGC)	 AG	76262-76513	CC	GAC
-recovered pasa_asmbl_5369.p1, terminal, 76262, 76513
-recovered pasa_asmbl_5369.p1, internal, 74433, 74536
-recovered pasa_asmbl_5369.p1, internal, 74663, 75160
-recovered pasa_asmbl_5369.p1, internal, 75272, 75753
-recovered pasa_asmbl_5369.p1, internal, 75870, 76056
Valid prediction for GlimmerHMM_glimmerT_27348-T1
Valid prediction for snap_scaffold_11-snap.801-T1
Valid prediction for snap_scaffold_11-snap.814-T1
Valid prediction for HiQ_model.g18243.t1
Valid prediction for Augustus_model.g18238.t1
Valid prediction for snap_scaffold_11-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_27323-T1
Valid prediction for Augustus_model.g18233.t1
Valid prediction for GeneMark_model.47199_t
Valid prediction for GeneMark_model.47205_t
Couldn't classify 398, 616
Couldn't classify 3077, 3208
Sorry, prediction pasa_asmbl_5364.p1 fails validation.
(ACT)	 AC	398-616	GT	AGG
(TTG)	 AG	838-933	GT	AGG
(ACA)	 AG	1130-1294	GT	AGG
(GCC)	 AG	1773-1867	GT	GGG
(TGC)	 AG	2523-2589	GT	AGG
(AGC)	 AG	2725-2762	GT	AGG
(ATT)	 AG	2854-2986	GT	AGG
(GAA)	 AG	3077-3208	GT	AGG
-recovered pasa_asmbl_5364.p1, internal, 838, 933
-recovered pasa_asmbl_5364.p1, internal, 1130, 1294
-recovered pasa_asmbl_5364.p1, internal, 1773, 1867
-recovered pasa_asmbl_5364.p1, internal, 2523, 2589
-recovered pasa_asmbl_5364.p1, internal, 2725, 2762
-recovered pasa_asmbl_5364.p1, internal, 2854, 2986
-recovered pasa_asmbl_5364.p1, internal, 3077, 3208
Valid prediction for snap_scaffold_11-snap.789-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27325-T1
Couldn't classify 69278, 69405
Couldn't classify 69881, 70124
Sorry, prediction pasa_asmbl_5367.p1 fails validation.
(GAG)	 CA	69278-69405	GT	AGG
(GTT)	 AG	69881-70124	CG	CCC
Valid prediction for GeneMark_model.47213_t
Valid prediction for GlimmerHMM_glimmerT_27330-T1
Valid prediction for GeneMark_model.47217_t
Valid prediction for snap_scaffold_11-snap.822-T1
Valid prediction for GeneMark_model.47197_t
Valid prediction for CodingQuarry_transcript_7982-T1
Valid prediction for GeneMark_model.47211_t
Valid prediction for GeneMark_model.47207_t
Valid prediction for CodingQuarry_transcript_7980-T1
Valid prediction for snap_scaffold_11-snap.805-T1
Valid prediction for GeneMark_model.47215_t
Valid prediction for GeneMark_model.47201_t
Valid prediction for GlimmerHMM_glimmerT_27324-T1
Valid prediction for snap_scaffold_11-snap.812-T1
Valid prediction for Augustus_model.g18245.t1
Valid prediction for GlimmerHMM_glimmerT_27341-T1
Valid prediction for GlimmerHMM_glimmerT_27344-T1
Valid prediction for snap_scaffold_11-snap.795-T1
Valid prediction for GeneMark_model.47227_t
Valid prediction for snap_scaffold_11-snap.807-T1
Valid prediction for snap_scaffold_11-snap.808-T1
Valid prediction for snap_scaffold_11-snap.797-T1
Valid prediction for GeneMark_model.47221_t
Valid prediction for GlimmerHMM_glimmerT_27331-T1
Valid prediction for snap_scaffold_11-snap.819-T1
Valid prediction for Augustus_model.g18234.t1
Valid prediction for GlimmerHMM_glimmerT_27336-T1
Valid prediction for snap_scaffold_11-snap.804-T1
Valid prediction for GeneMark_model.47219_t
Valid prediction for HiQ_model.g18242.t1
Valid prediction for GlimmerHMM_glimmerT_27338-T1
Valid prediction for GeneMark_model.47224_t
Valid prediction for pasa_asmbl_6301.p1

-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_11-snap.813-T1
Valid prediction for GeneMark_model.47194_t
Valid prediction for Augustus_model.g18247.t1
Valid prediction for GeneMark_model.47225_t
Valid prediction for GlimmerHMM_glimmerT_27335-T1
Couldn't classify 115566, 116241
Couldn't classify 116519, 116949
Sorry, prediction pasa_asmbl_6512.p1 fails validation.
(GAC)	 AT	115566-116241	GT	AGG
(AGA)	 AG	116519-116949	AT	GCA
Valid prediction for Augustus_model.g18237.t1
Valid prediction for snap_scaffold_11-snap.811-T1
Valid prediction for Augustus_model.g18231.t1
Valid prediction for snap_scaffold_11-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_27327-T1
Valid prediction for GlimmerHMM_glimmerT_27329-T1
Valid prediction for GlimmerHMM_glimmerT_27328-T1
Valid prediction for GeneMark_model.47198_t
Valid prediction for GeneMark_model.47216_t
Valid prediction for snap_scaffold_11-snap.796-T1
Valid prediction for HiQ_model.g18246.t1
Valid prediction for GeneMark_model.47226_t
Valid prediction for snap_scaffold_11-snap.809-T1
Valid prediction for GeneMark_model.47212_t
Valid prediction for snap_scaffold_11-snap.806-T1
Valid prediction for GeneMark_model.47228_t
Valid prediction for snap_scaffold_11-snap.790-T1
Valid prediction for pasa_asmbl_6523.p1
Valid prediction for GeneMark_model.47204_t
Valid prediction for snap_scaffold_11-snap.788-T1
Valid prediction for GeneMark_model.47230_t
Valid prediction for snap_scaffold_11-snap.798-T1
Valid prediction for snap_scaffold_11-snap.821-T1
Valid prediction for pasa_asmbl_6515.p1
Valid prediction for snap_scaffold_11-snap.820-T1
Valid prediction for GeneMark_model.47206_t
Valid prediction for Augustus_model.g18232.t1
Valid prediction for GlimmerHMM_glimmerT_27340-T1
Valid prediction for GeneMark_model.47223_t
Valid prediction for CodingQuarry_transcript_7979-T1
Valid prediction for snap_scaffold_11-snap.791-T1
Valid prediction for snap_scaffold_11-snap.815-T1
Valid prediction for GeneMark_model.47208_t
Valid prediction for Augustus_model.g18236.t1
Valid prediction for GlimmerHMM_glimmerT_27342-T1
Valid prediction for pasa_asmbl_6521.p1
Valid prediction for GeneMark_model.47202_t
Valid prediction for GlimmerHMM_glimmerT_27326-T1
Valid prediction for GlimmerHMM_glimmerT_27345-T1
Valid prediction for snap_scaffold_11-snap.802-T1
Valid prediction for snap_scaffold_11-snap.803-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.47218_t
Valid prediction for GlimmerHMM_glimmerT_27346-T1
Valid prediction for GeneMark_model.47196_t
Valid prediction for GeneMark_model.47200_t
Valid prediction for GlimmerHMM_glimmerT_27320-T1
Valid prediction for CodingQuarry_transcript_7983-T1
Valid prediction for pasa_asmbl_6507.p1
Valid prediction for GeneMark_model.47210_t
Valid prediction for CodingQuarry_transcript_7984-T1
Valid prediction for HiQ_model.g18241.t1
Valid prediction for GlimmerHMM_glimmerT_27339-T1
Valid prediction for GlimmerHMM_glimmerT_27332-T1
Valid prediction for snap_scaffold_11-snap.818-T1
Valid prediction for snap_scaffold_11-snap.794-T1
Valid prediction for Augustus_model.g18235.t1
Valid prediction for HiQ_model.g18244.t1
Valid prediction for GeneMark_model.47220_t
Valid prediction for CodingQuarry_transcript_7981-T1
Valid prediction for GlimmerHMM_glimmerT_27321-T1
Valid prediction for GlimmerHMM_glimmerT_27343-T1
Valid prediction for GlimmerHMM_glimmerT_27337-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14104, rend_intergenic: 8227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16038, rend_intergenic: 14242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29273, rend_intergenic: 25711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31072, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41745, rend_intergenic: 32365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64734, rend_intergenic: 59447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110665, rend_intergenic: 106637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152746, rend_intergenic: 148427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154339
-exon list size: 478


building trellis

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99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 14104, rend_intergenic: 8227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16038, rend_intergenic: 14242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29273, rend_intergenic: 25711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31072, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41745, rend_intergenic: 32365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64734, rend_intergenic: 59447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110665, rend_intergenic: 106637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152746, rend_intergenic: 148427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support