-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_16312244-16467271

-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 Augustus_model.g16152.t1
Valid prediction for snap_scaffold_9-snap.3344-T1
Valid prediction for snap_scaffold_9-snap.3345-T1
Couldn't classify 82221, 82359
Sorry, prediction CodingQuarry_transcript_62271-T1 fails validation.
(ATG)	 AA	82043-82080	GT	CAG
(GCG)	 CG	82221-82359	GG	GAG
-recovered CodingQuarry_transcript_62271-T1, initial, 82043, 82080
Valid prediction for snap_scaffold_9-snap.3332-T1
Valid prediction for GeneMark_model.41407_t
Valid prediction for snap_scaffold_9-snap.3334-T1
Valid prediction for snap_scaffold_9-snap.3354-T1
Valid prediction for snap_scaffold_9-snap.3350-T1
Valid prediction for GeneMark_model.41409_t
Valid prediction for Augustus_model.g16142.t1
Valid prediction for GlimmerHMM_glimmerT_24129-T1
Valid prediction for GeneMark_model.41416_t
Valid prediction for GlimmerHMM_glimmerT_24126-T1
Valid prediction for GeneMark_model.41399_t
Valid prediction for GeneMark_model.41404_t
Valid prediction for GeneMark_model.41397_t
Valid prediction for GeneMark_model.41395_t
Valid prediction for Augustus_model.g16151.t1
Valid prediction for snap_scaffold_9-snap.3363-T1
Valid prediction for snap_scaffold_9-snap.3335-T1
Valid prediction for GlimmerHMM_glimmerT_24131-T1
Valid prediction for snap_scaffold_9-snap.3343-T1
Valid prediction for GlimmerHMM_glimmerT_24120-T1
Valid prediction for GeneMark_model.41419_t
Valid prediction for snap_scaffold_9-snap.3361-T1
Valid prediction for snap_scaffold_9-snap.3358-T1
Valid prediction for Augustus_model.g16144.t1
Valid prediction for GlimmerHMM_glimmerT_24121-T1
Valid prediction for GlimmerHMM_glimmerT_24112-T1
Valid prediction for snap_scaffold_9-snap.3353-T1
Valid prediction for pasa_asmbl_54570.p1
Valid prediction for Augustus_model.g16155.t1
Valid prediction for Augustus_model.g16156.t1
Valid prediction for GeneMark_model.41415_t
Valid prediction for snap_scaffold_9-snap.3366-T1
Valid prediction for GlimmerHMM_glimmerT_24128-T1
Valid prediction for Augustus_model.g16141.t1
Valid prediction for CodingQuarry_transcript_62270-T1
Valid prediction for GlimmerHMM_glimmerT_24119-T1
Valid prediction for GeneMark_model.41425_t
Valid prediction for GeneMark_model.41414_t
Valid prediction for GlimmerHMM_glimmerT_24130-T1
Valid prediction for GlimmerHMM_glimmerT_24114-T1
Valid prediction for GlimmerHMM_glimmerT_24117-T1
Valid prediction for snap_scaffold_9-snap.3356-T1
Valid prediction for GeneMark_model.41428_t
Valid prediction for GeneMark_model.41423_t
Valid prediction for snap_scaffold_9-snap.3337-T1
Valid prediction for GeneMark_model.41401_t
Valid prediction for GlimmerHMM_glimmerT_24127-T1
Valid prediction for GeneMark_model.41402_t
Valid prediction for Augustus_model.g16154.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.41413_t
Valid prediction for snap_scaffold_9-snap.3362-T1
Valid prediction for GeneMark_model.41403_t
Valid prediction for GlimmerHMM_glimmerT_24113-T1
Valid prediction for GeneMark_model.41420_t
Valid prediction for snap_scaffold_9-snap.3336-T1
Valid prediction for snap_scaffold_9-snap.3346-T1
Valid prediction for snap_scaffold_9-snap.3338-T1
Valid prediction for pasa_asmbl_55531.p1
Valid prediction for GlimmerHMM_glimmerT_24115-T1
Valid prediction for snap_scaffold_9-snap.3351-T1
Couldn't classify 100196, 100420
Couldn't classify 102435, 102568
Sorry, prediction pasa_asmbl_55536.p1 fails validation.
(TCC)	 GT	100196-100420	GT	AAG
(AGG)	 AG	100553-100734	GT	GCG
(AGA)	 AG	101047-101279	GT	AGG
(AGT)	 AG	102435-102568	AA	TCA
-recovered pasa_asmbl_55536.p1, internal, 100553, 100734
-recovered pasa_asmbl_55536.p1, internal, 101047, 101279
Valid prediction for pasa_asmbl_55533.p1
Valid prediction for GeneMark_model.41424_t
Valid prediction for snap_scaffold_9-snap.3333-T1
Valid prediction for Augustus_model.g16153.t1
Valid prediction for snap_scaffold_9-snap.3359-T1
Valid prediction for Augustus_model.g16148.t1
Valid prediction for GeneMark_model.41408_t
Valid prediction for GlimmerHMM_glimmerT_24132-T1
Couldn't classify 109492, 109583
Sorry, prediction pasa_asmbl_55535.p1 fails validation.
(GGC)	 CA	109492-109583	GT	CCG
(GTA)	 AG	109666-109868	GT	GGG
(GGA)	 AG	110115-110236	CT	GAC
-recovered pasa_asmbl_55535.p1, terminal, 110115, 110236
-recovered pasa_asmbl_55535.p1, internal, 109666, 109868
Valid prediction for GeneMark_model.41426_t
Valid prediction for GlimmerHMM_glimmerT_24124-T1
Valid prediction for snap_scaffold_9-snap.3355-T1
Couldn't classify 69851, 70007
Sorry, prediction pasa_asmbl_55537.p1 fails validation.
(CCA)	 AA	69851-70007	GT	AGG
(TGA)	 AG	70223-70467	CT	GAC
-recovered pasa_asmbl_55537.p1, terminal, 70223, 70467
Valid prediction for Augustus_model.g16149.t1
Valid prediction for snap_scaffold_9-snap.3340-T1
Valid prediction for GeneMark_model.41405_t
Valid prediction for snap_scaffold_9-snap.3339-T1
Valid prediction for snap_scaffold_9-snap.3347-T1
Valid prediction for GlimmerHMM_glimmerT_24123-T1
Valid prediction for Augustus_model.g16143.t1
Valid prediction for snap_scaffold_9-snap.3360-T1
Valid prediction for GeneMark_model.41417_t
Valid prediction for snap_scaffold_9-snap.3364-T1
Couldn't classify 66176, 66246
Couldn't classify 67628, 67792
Sorry, prediction pasa_asmbl_55538.p1 fails validation.
(ACA)	 AC	66176-66246	GT	CTG
(CTC)	 AG	66571-66787	GT	GGG
(CCT)	 AG	67628-67792	GG	GGG
-recovered pasa_asmbl_55538.p1, internal, 66571, 66787
Valid prediction for snap_scaffold_9-snap.3348-T1
Valid prediction for snap_scaffold_9-snap.3357-T1
Valid prediction for GeneMark_model.41400_t
Valid prediction for GeneMark_model.41418_t
Valid prediction for GlimmerHMM_glimmerT_24116-T1
Valid prediction for snap_scaffold_9-snap.3341-T1
Valid prediction for GlimmerHMM_glimmerT_24125-T1
Valid prediction for GeneMark_model.41421_t
Valid prediction for snap_scaffold_9-snap.3352-T1
Valid prediction for GeneMark_model.41412_t
Valid prediction for snap_scaffold_9-snap.3365-T1
Valid prediction for Augustus_model.g16147.t1
Valid prediction for GeneMark_model.41406_t
Valid prediction for GeneMark_model.41422_t
Valid prediction for GeneMark_model.41411_t
Valid prediction for GeneMark_model.41398_t
Valid prediction for CodingQuarry_transcript_62267-T1
Valid prediction for HiQ_model.g16145.t1
Valid prediction for GlimmerHMM_glimmerT_24111-T1
Valid prediction for snap_scaffold_9-snap.3342-T1
Valid prediction for GeneMark_model.41427_t
Valid prediction for GeneMark_model.41396_t
Valid prediction for GlimmerHMM_glimmerT_24118-T1
Valid prediction for Augustus_model.g16146.t1
Valid prediction for GlimmerHMM_glimmerT_24122-T1
Valid prediction for snap_scaffold_9-snap.3349-T1
Valid prediction for CodingQuarry_transcript_62268-T1
Valid prediction for GeneMark_model.41410_t
Valid prediction for Augustus_model.g16150.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 6451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55090, rend_intergenic: 50397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77941, rend_intergenic: 76421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108344, rend_intergenic: 106761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116859, rend_intergenic: 115247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119647, rend_intergenic: 118220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131104, rend_intergenic: 128278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137587, rend_intergenic: 132608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155028
-exon list size: 580


building trellis

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88.1    
88.3    
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88.8    
89.0    
89.2    
89.3    
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90.9    
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91.9    
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92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
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96.4    
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98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 6451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55090, rend_intergenic: 50397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77941, rend_intergenic: 76421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108344, rend_intergenic: 106761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116859, rend_intergenic: 115247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119647, rend_intergenic: 118220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131104, rend_intergenic: 128278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137587, rend_intergenic: 132608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support