-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_2293455-2549846

-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_3-snap.538-T1
Valid prediction for GeneMark_model.10316_t
Valid prediction for GlimmerHMM_glimmerT_6296-T1
Valid prediction for snap_scaffold_3-snap.555-T1
Valid prediction for GeneMark_model.10333_t
Valid prediction for GeneMark_model.10345_t
Valid prediction for snap_scaffold_3-snap.571-T1
Valid prediction for snap_scaffold_3-snap.553-T1
Valid prediction for snap_scaffold_3-snap.539-T1
Valid prediction for Augustus_model.g4126.t1
Valid prediction for GeneMark_model.10331_t
Valid prediction for GeneMark_model.10308_t
Valid prediction for GeneMark_model.10346_t
Valid prediction for GeneMark_model.10328_t
Valid prediction for GeneMark_model.10319_t
Valid prediction for snap_scaffold_3-snap.541-T1
Valid prediction for Augustus_model.g4137.t1
Valid prediction for GlimmerHMM_glimmerT_6306-T1
Valid prediction for GlimmerHMM_glimmerT_6271-T1
Valid prediction for GlimmerHMM_glimmerT_6273-T1
Valid prediction for snap_scaffold_3-snap.536-T1
Valid prediction for Augustus_model.g4120.t1
Valid prediction for GeneMark_model.10304_t
Valid prediction for GlimmerHMM_glimmerT_6278-T1
Valid prediction for GlimmerHMM_glimmerT_6290-T1
Valid prediction for snap_scaffold_3-snap.526-T1
Valid prediction for Augustus_model.g4135.t1
Valid prediction for GeneMark_model.10336_t
Valid prediction for snap_scaffold_3-snap.556-T1
Valid prediction for snap_scaffold_3-snap.570-T1
Valid prediction for snap_scaffold_3-snap.534-T1
Valid prediction for snap_scaffold_3-snap.528-T1
Valid prediction for snap_scaffold_3-snap.568-T1
Valid prediction for GeneMark_model.10335_t
Valid prediction for snap_scaffold_3-snap.547-T1
Valid prediction for Augustus_model.g4129.t1
Valid prediction for GlimmerHMM_glimmerT_6283-T1
Valid prediction for GeneMark_model.10315_t
Valid prediction for snap_scaffold_3-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_6284-T1
Valid prediction for GeneMark_model.10302_t
Valid prediction for GlimmerHMM_glimmerT_6286-T1
Valid prediction for snap_scaffold_3-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_6274-T1
Valid prediction for GeneMark_model.10310_t
Valid prediction for GeneMark_model.10325_t
Valid prediction for GlimmerHMM_glimmerT_6303-T1
Valid prediction for snap_scaffold_3-snap.542-T1
Valid prediction for snap_scaffold_3-snap.529-T1
Valid prediction for GeneMark_model.10350_t
Valid prediction for GlimmerHMM_glimmerT_6281-T1
Valid prediction for GlimmerHMM_glimmerT_6305-T1
Valid prediction for GlimmerHMM_glimmerT_6293-T1
Valid prediction for GeneMark_model.10306_t
Valid prediction for GlimmerHMM_glimmerT_6298-T1
Valid prediction for GeneMark_model.10338_t
Valid prediction for GeneMark_model.10342_t
Valid prediction for snap_scaffold_3-snap.558-T1
Valid prediction for GeneMark_model.10349_t
Couldn't classify 32650, 32982
Sorry, prediction pasa_asmbl_38698.p1 fails validation.
(GCA)	 AG	32650-32982	CG	GAC
Valid prediction for GeneMark_model.10323_t
Valid prediction for Augustus_model.g4127.t1
Valid prediction for GlimmerHMM_glimmerT_6304-T1
Valid prediction for GlimmerHMM_glimmerT_6287-T1
Valid prediction for GlimmerHMM_glimmerT_6270-T1
Valid prediction for snap_scaffold_3-snap.567-T1
Valid prediction for Augustus_model.g4130.t1
Valid prediction for snap_scaffold_3-snap.550-T1
Valid prediction for Augustus_model.g4119.t1
Valid prediction for GlimmerHMM_glimmerT_6295-T1
Valid prediction for snap_scaffold_3-snap.532-T1
Valid prediction for GeneMark_model.10313_t
Valid prediction for GeneMark_model.10348_t
Valid prediction for GlimmerHMM_glimmerT_6282-T1
Valid prediction for GeneMark_model.10317_t
Valid prediction for snap_scaffold_3-snap.559-T1
Valid prediction for snap_scaffold_3-snap.572-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_6302-T1
Valid prediction for GeneMark_model.10332_t
Valid prediction for GeneMark_model.10347_t
Valid prediction for snap_scaffold_3-snap.544-T1
Valid prediction for GeneMark_model.10314_t
Valid prediction for snap_scaffold_3-snap.527-T1
Valid prediction for Augustus_model.g4132.t1
Valid prediction for snap_scaffold_3-snap.561-T1
Valid prediction for GeneMark_model.10321_t
Valid prediction for Augustus_model.g4128.t1
Valid prediction for snap_scaffold_3-snap.531-T1
Valid prediction for GeneMark_model.10307_t
Valid prediction for GeneMark_model.10329_t
Valid prediction for GlimmerHMM_glimmerT_6301-T1
Valid prediction for GlimmerHMM_glimmerT_6280-T1
Valid prediction for GeneMark_model.10311_t
Valid prediction for GlimmerHMM_glimmerT_6308-T1
Valid prediction for GeneMark_model.10334_t
Valid prediction for GeneMark_model.10340_t
Valid prediction for GeneMark_model.10337_t
Valid prediction for snap_scaffold_3-snap.575-T1
Valid prediction for GeneMark_model.10339_t
Valid prediction for GeneMark_model.10305_t
Valid prediction for snap_scaffold_3-snap.540-T1
Valid prediction for Augustus_model.g4123.t1
Valid prediction for GlimmerHMM_glimmerT_6292-T1
Valid prediction for Augustus_model.g4136.t1
Valid prediction for GeneMark_model.10300_t
Valid prediction for GeneMark_model.10341_t
Valid prediction for snap_scaffold_3-snap.543-T1
Valid prediction for snap_scaffold_3-snap.549-T1
Valid prediction for snap_scaffold_3-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_6275-T1
Valid prediction for snap_scaffold_3-snap.548-T1
Valid prediction for Augustus_model.g4122.t1
Valid prediction for snap_scaffold_3-snap.566-T1
Valid prediction for snap_scaffold_3-snap.569-T1
Valid prediction for snap_scaffold_3-snap.562-T1
Valid prediction for GeneMark_model.10322_t
Valid prediction for Augustus_model.g4121.t1
Valid prediction for snap_scaffold_3-snap.537-T1
Valid prediction for snap_scaffold_3-snap.560-T1
Valid prediction for snap_scaffold_3-snap.565-T1
Valid prediction for snap_scaffold_3-snap.564-T1
Valid prediction for snap_scaffold_3-snap.573-T1
Valid prediction for snap_scaffold_3-snap.552-T1
Valid prediction for GeneMark_model.10312_t
Valid prediction for GlimmerHMM_glimmerT_6276-T1
Valid prediction for GlimmerHMM_glimmerT_6294-T1
Valid prediction for GlimmerHMM_glimmerT_6291-T1
Valid prediction for snap_scaffold_3-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_6272-T1
Valid prediction for GlimmerHMM_glimmerT_6288-T1
Valid prediction for snap_scaffold_3-snap.554-T1
Couldn't classify 70858, 71884
Sorry, prediction pasa_asmbl_38700.p1 fails validation.
(TCC)	 AG	70858-71884	GT	AGG
(GTC)	 AG	72058-72071	GT	AAG
-recovered pasa_asmbl_38700.p1, terminal, 72058, 72071
-recovered pasa_asmbl_38700.p1, internal, 70858, 71884
-recovered pasa_asmbl_38700.p1, internal, 72058, 72071
Valid prediction for GeneMark_model.10309_t
Valid prediction for GlimmerHMM_glimmerT_6277-T1
Valid prediction for snap_scaffold_3-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_6300-T1
Valid prediction for GeneMark_model.10318_t
Valid prediction for snap_scaffold_3-snap.557-T1
Valid prediction for Augustus_model.g4124.t1
Valid prediction for GlimmerHMM_glimmerT_6289-T1
Valid prediction for GlimmerHMM_glimmerT_6307-T1
Valid prediction for Augustus_model.g4131.t1
Valid prediction for GeneMark_model.10343_t
Valid prediction for Augustus_model.g4125.t1
Valid prediction for snap_scaffold_3-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_6297-T1
Valid prediction for GeneMark_model.10327_t
Valid prediction for GlimmerHMM_glimmerT_6279-T1
Valid prediction for Augustus_model.g4133.t1
Valid prediction for HiQ_model.g4134.t1
Valid prediction for snap_scaffold_3-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_6285-T1
Valid prediction for GeneMark_model.10320_t
Valid prediction for Augustus_model.g4138.t1
Valid prediction for GeneMark_model.10344_t
Valid prediction for snap_scaffold_3-snap.533-T1
Valid prediction for GeneMark_model.10303_t
Valid prediction for GlimmerHMM_glimmerT_6299-T1
Valid prediction for snap_scaffold_3-snap.551-T1
Valid prediction for GeneMark_model.10326_t
Valid prediction for GeneMark_model.10301_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14863, rend_intergenic: 8607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35916, rend_intergenic: 33543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42044, rend_intergenic: 40856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45371, rend_intergenic: 42148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59521, rend_intergenic: 48254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66187, rend_intergenic: 60908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66662, rend_intergenic: 66204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71787, rend_intergenic: 67210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74756, rend_intergenic: 73180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83934, rend_intergenic: 82609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88414, rend_intergenic: 84147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100046, rend_intergenic: 90790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110693, rend_intergenic: 100229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118117, rend_intergenic: 110988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118331, rend_intergenic: 118167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122111, rend_intergenic: 118331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128286, rend_intergenic: 126513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238833, rend_intergenic: 236862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252312, rend_intergenic: 245344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254550, rend_intergenic: 252685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256392
-exon list size: 866


building trellis

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75.6    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 14863, rend_intergenic: 8607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35916, rend_intergenic: 33543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42044, rend_intergenic: 40856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45371, rend_intergenic: 42148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59521, rend_intergenic: 48254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66187, rend_intergenic: 60908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66662, rend_intergenic: 66204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71787, rend_intergenic: 67210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74756, rend_intergenic: 73180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83934, rend_intergenic: 82609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88414, rend_intergenic: 84147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100046, rend_intergenic: 90790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110693, rend_intergenic: 100229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118117, rend_intergenic: 110988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118331, rend_intergenic: 118167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122111, rend_intergenic: 118331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128286, rend_intergenic: 126513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238833, rend_intergenic: 236862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252312, rend_intergenic: 245344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254550, rend_intergenic: 252685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support