-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_2734081-2908249

-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.10423_t
Valid prediction for GeneMark_model.10426_t
Valid prediction for GeneMark_model.10417_t
Valid prediction for GeneMark_model.10434_t
Valid prediction for snap_scaffold_3-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_6347-T1
Valid prediction for GeneMark_model.10407_t
Valid prediction for GeneMark_model.10402_t
Valid prediction for GlimmerHMM_glimmerT_6343-T1
Valid prediction for GeneMark_model.10435_t
Valid prediction for HiQ_model.g4161.t1
Valid prediction for snap_scaffold_3-snap.655-T1
Valid prediction for snap_scaffold_3-snap.633-T1
Valid prediction for snap_scaffold_3-snap.654-T1
Valid prediction for GeneMark_model.10430_t
Valid prediction for snap_scaffold_3-snap.631-T1
Valid prediction for Augustus_model.g4157.t1
Valid prediction for GlimmerHMM_glimmerT_6351-T1
Valid prediction for snap_scaffold_3-snap.623-T1
Valid prediction for Augustus_model.g4156.t1
Valid prediction for GlimmerHMM_glimmerT_6355-T1
Valid prediction for GeneMark_model.10419_t
Valid prediction for snap_scaffold_3-snap.650-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.642-T1
Valid prediction for snap_scaffold_3-snap.640-T1
Valid prediction for snap_scaffold_3-snap.636-T1
Valid prediction for snap_scaffold_3-snap.641-T1
Valid prediction for GlimmerHMM_glimmerT_6364-T1
Valid prediction for GlimmerHMM_glimmerT_6354-T1
Valid prediction for GeneMark_model.10420_t
Valid prediction for snap_scaffold_3-snap.629-T1
Valid prediction for snap_scaffold_3-snap.625-T1
Valid prediction for GeneMark_model.10406_t
Valid prediction for GeneMark_model.10422_t
Valid prediction for snap_scaffold_3-snap.622-T1
Valid prediction for snap_scaffold_3-snap.644-T1
Valid prediction for GlimmerHMM_glimmerT_6360-T1
Valid prediction for snap_scaffold_3-snap.634-T1
Valid prediction for snap_scaffold_3-snap.646-T1
Valid prediction for GeneMark_model.10416_t
Valid prediction for pasa_asmbl_39878.p1
Valid prediction for Augustus_model.g4155.t1
Valid prediction for GeneMark_model.10429_t
Valid prediction for snap_scaffold_3-snap.639-T1
Valid prediction for GeneMark_model.10413_t
Valid prediction for GeneMark_model.10432_t
Valid prediction for GeneMark_model.10421_t
Valid prediction for snap_scaffold_3-snap.626-T1
Valid prediction for GeneMark_model.10410_t
Valid prediction for Augustus_model.g4152.t1
Valid prediction for snap_scaffold_3-snap.645-T1
Valid prediction for snap_scaffold_3-snap.649-T1
Valid prediction for GlimmerHMM_glimmerT_6362-T1
Valid prediction for GeneMark_model.10404_t
Valid prediction for snap_scaffold_3-snap.656-T1
Valid prediction for GlimmerHMM_glimmerT_6346-T1
Couldn't classify 102540, 102758
Sorry, prediction pasa_asmbl_39874.p1 fails validation.
(GAT)	 CA	102540-102758	GT	TTG
(GGT)	 AG	102923-103042	GT	AGG
(TGC)	 AG	103341-103472	AG	GAA
-recovered pasa_asmbl_39874.p1, terminal, 103341, 103472
-recovered pasa_asmbl_39874.p1, internal, 102923, 103042
Valid prediction for CodingQuarry_transcript_45987-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_3-snap.647-T1
Valid prediction for snap_scaffold_3-snap.638-T1
Valid prediction for Augustus_model.g4160.t1
Valid prediction for GeneMark_model.10408_t
Valid prediction for snap_scaffold_3-snap.630-T1
Valid prediction for snap_scaffold_3-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_6365-T1
Valid prediction for Augustus_model.g4153.t1
Valid prediction for GlimmerHMM_glimmerT_6356-T1
Valid prediction for GeneMark_model.10415_t
Valid prediction for Augustus_model.g4158.t1
Valid prediction for snap_scaffold_3-snap.628-T1
Valid prediction for GeneMark_model.10412_t
Valid prediction for snap_scaffold_3-snap.637-T1
Valid prediction for Augustus_model.g4159.t1
Valid prediction for Augustus_model.g4162.t1
Valid prediction for GeneMark_model.10411_t
Valid prediction for GlimmerHMM_glimmerT_6363-T1
Valid prediction for GlimmerHMM_glimmerT_6352-T1
Valid prediction for GlimmerHMM_glimmerT_6358-T1
Couldn't classify 33015, 33350
Sorry, prediction pasa_asmbl_39662.p1 fails validation.
(CTC)	 TG	33015-33350	CT	AGC
Couldn't classify 32820, 32858
Couldn't classify 32888, 33104
Couldn't classify 33131, 33189
Sorry, prediction CodingQuarry_transcript_45988-T1 fails validation.
(ATG)	 AA	32820-32858	AA	GGA
(CCC)	 GG	32888-33104	GC	CTG
(ACT)	 CT	33131-33189	TC	AAT
Valid prediction for GeneMark_model.10436_t
Valid prediction for GlimmerHMM_glimmerT_6345-T1
Valid prediction for CodingQuarry_transcript_45989-T1
Valid prediction for snap_scaffold_3-snap.652-T1
Couldn't classify 20541, 20684
Couldn't classify 21435, 21593
Sorry, prediction pasa_asmbl_39737.p1 fails validation.
(CAC)	 GT	20541-20684	GT	AGG
(GTG)	 AG	21435-21593	CT	AGC
Valid prediction for GeneMark_model.10403_t
Valid prediction for GlimmerHMM_glimmerT_6348-T1
Valid prediction for snap_scaffold_3-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_6342-T1
Valid prediction for Augustus_model.g4154.t1
Valid prediction for GeneMark_model.10409_t
Valid prediction for GeneMark_model.10433_t
Valid prediction for GlimmerHMM_glimmerT_6350-T1
Valid prediction for GlimmerHMM_glimmerT_6357-T1
Valid prediction for GlimmerHMM_glimmerT_6344-T1
Valid prediction for snap_scaffold_3-snap.632-T1
Valid prediction for GeneMark_model.10424_t
Valid prediction for GeneMark_model.10418_t
Valid prediction for GlimmerHMM_glimmerT_6361-T1
Valid prediction for GeneMark_model.10431_t
Couldn't classify 29317, 29323
Sorry, prediction pasa_asmbl_38701.p1 fails validation.
(CTT)	 TG	29317-29323	GT	GGG
(GAA)	 AG	29584-29753	GT	AGG
(GTG)	 AG	30066-30239	GT	CGG
(CTG)	 AG	30577-30654	TA	AGT
-recovered pasa_asmbl_38701.p1, terminal, 30577, 30654
-recovered pasa_asmbl_38701.p1, internal, 29584, 29753
-recovered pasa_asmbl_38701.p1, internal, 30066, 30239
Valid prediction for GeneMark_model.10427_t
Valid prediction for GeneMark_model.10405_t
Valid prediction for GlimmerHMM_glimmerT_6353-T1
Valid prediction for snap_scaffold_3-snap.635-T1
Valid prediction for GeneMark_model.10425_t
Valid prediction for snap_scaffold_3-snap.651-T1
Valid prediction for Augustus_model.g4163.t1
Valid prediction for snap_scaffold_3-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_6359-T1
Valid prediction for GeneMark_model.10414_t
Valid prediction for GeneMark_model.10428_t
Valid prediction for GeneMark_model.10437_t
Valid prediction for GlimmerHMM_glimmerT_6349-T1
Valid prediction for GeneMark_model.10401_t
Couldn't classify 26507, 26618
Couldn't classify 27584, 27709
Sorry, prediction pasa_asmbl_38702.p1 fails validation.
(CCT)	 AC	26507-26618	GT	GGG
(GAG)	 AG	26774-26922	GT	AGG
(TTC)	 AG	27157-27351	GT	AGG
(GTG)	 AG	27584-27709	CT	CCC
-recovered pasa_asmbl_38702.p1, internal, 26774, 26922
-recovered pasa_asmbl_38702.p1, internal, 27157, 27351
Valid prediction for snap_scaffold_3-snap.653-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22035, rend_intergenic: 17283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28621, rend_intergenic: 27132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35639, rend_intergenic: 31882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50116, rend_intergenic: 48485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126453, rend_intergenic: 108396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128469, rend_intergenic: 127104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129799, rend_intergenic: 128990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164097, rend_intergenic: 157132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174169
-exon list size: 474


building trellis

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98.1    
98.3    
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98.9    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 22035, rend_intergenic: 17283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28621, rend_intergenic: 27132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35639, rend_intergenic: 31882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50116, rend_intergenic: 48485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126453, rend_intergenic: 108396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128469, rend_intergenic: 127104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129799, rend_intergenic: 128990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164097, rend_intergenic: 157132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support