-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_2437489-2600617

-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_16-snap.436-T1
Valid prediction for snap_scaffold_16-snap.438-T1
Valid prediction for GeneMark_model.66325_t
Valid prediction for snap_scaffold_16-snap.427-T1
Valid prediction for GeneMark_model.66312_t
Valid prediction for GeneMark_model.66326_t
Valid prediction for GeneMark_model.66340_t
Valid prediction for GeneMark_model.66336_t
Valid prediction for GeneMark_model.66295_t
Valid prediction for GeneMark_model.66320_t
Valid prediction for GeneMark_model.66335_t
Valid prediction for snap_scaffold_16-snap.433-T1
Valid prediction for GlimmerHMM_glimmerT_38789-T1
Valid prediction for GlimmerHMM_glimmerT_38794-T1
Valid prediction for Augustus_model.g26028.t1
Valid prediction for GeneMark_model.66309_t
Valid prediction for GeneMark_model.66304_t
Valid prediction for GlimmerHMM_glimmerT_38790-T1
Valid prediction for snap_scaffold_16-snap.424-T1
Valid prediction for GeneMark_model.66300_t
Valid prediction for GeneMark_model.66328_t
Valid prediction for snap_scaffold_16-snap.429-T1
Valid prediction for GeneMark_model.66318_t
Valid prediction for GlimmerHMM_glimmerT_38785-T1
Valid prediction for snap_scaffold_16-snap.435-T1
Valid prediction for snap_scaffold_16-snap.452-T1
Valid prediction for snap_scaffold_16-snap.441-T1
Valid prediction for GeneMark_model.66342_t
Valid prediction for GeneMark_model.66313_t
Valid prediction for GlimmerHMM_glimmerT_38802-T1
Valid prediction for GlimmerHMM_glimmerT_38798-T1
Valid prediction for snap_scaffold_16-snap.418-T1
Valid prediction for GeneMark_model.66334_t
Valid prediction for GeneMark_model.66307_t
Valid prediction for GeneMark_model.66310_t
Valid prediction for Augustus_model.g26026.t1
Valid prediction for snap_scaffold_16-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_38787-T1
Valid prediction for GlimmerHMM_glimmerT_38778-T1
Valid prediction for Augustus_model.g26036.t1
Valid prediction for GeneMark_model.66322_t
Valid prediction for GeneMark_model.66323_t
Valid prediction for snap_scaffold_16-snap.419-T1
Valid prediction for GeneMark_model.66305_t
Valid prediction for snap_scaffold_16-snap.431-T1
Valid prediction for Augustus_model.g26022.t1
Valid prediction for snap_scaffold_16-snap.421-T1
Valid prediction for Augustus_model.g26020.t1
Valid prediction for GlimmerHMM_glimmerT_38788-T1
Valid prediction for snap_scaffold_16-snap.423-T1
Valid prediction for snap_scaffold_16-snap.422-T1
Valid prediction for snap_scaffold_16-snap.447-T1
Valid prediction for GeneMark_model.66302_t
Valid prediction for GlimmerHMM_glimmerT_38783-T1
Valid prediction for GeneMark_model.66317_t
Valid prediction for GlimmerHMM_glimmerT_38792-T1
Valid prediction for snap_scaffold_16-snap.445-T1
Valid prediction for snap_scaffold_16-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_38780-T1
Valid prediction for GeneMark_model.66316_t
Valid prediction for Augustus_model.g26030.t1
Valid prediction for GeneMark_model.66332_t
Valid prediction for GlimmerHMM_glimmerT_38796-T1
Valid prediction for snap_scaffold_16-snap.443-T1
Valid prediction for Augustus_model.g26025.t1
Valid prediction for GeneMark_model.66344_t
Valid prediction for GeneMark_model.66298_t

-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.66294_t
Valid prediction for Augustus_model.g26031.t1
Valid prediction for GeneMark_model.66333_t
Valid prediction for snap_scaffold_16-snap.448-T1
Valid prediction for GeneMark_model.66301_t
Valid prediction for GlimmerHMM_glimmerT_38803-T1
Valid prediction for snap_scaffold_16-snap.450-T1
Valid prediction for GeneMark_model.66324_t
Valid prediction for GeneMark_model.66343_t
Valid prediction for GeneMark_model.66308_t
Valid prediction for snap_scaffold_16-snap.425-T1
Valid prediction for snap_scaffold_16-snap.432-T1
Valid prediction for GeneMark_model.66337_t
Valid prediction for GeneMark_model.66329_t
Valid prediction for GeneMark_model.66327_t
Valid prediction for GlimmerHMM_glimmerT_38781-T1
Valid prediction for GeneMark_model.66338_t
Valid prediction for Augustus_model.g26035.t1
Valid prediction for GeneMark_model.66299_t
Valid prediction for GlimmerHMM_glimmerT_38791-T1
Valid prediction for GlimmerHMM_glimmerT_38782-T1
Valid prediction for GlimmerHMM_glimmerT_38784-T1
Valid prediction for snap_scaffold_16-snap.444-T1
Valid prediction for snap_scaffold_16-snap.439-T1
Valid prediction for snap_scaffold_16-snap.428-T1
Valid prediction for GeneMark_model.66330_t
Valid prediction for GeneMark_model.66311_t
Valid prediction for CodingQuarry_transcript_19873-T1
Valid prediction for Augustus_model.g26023.t1
Valid prediction for GlimmerHMM_glimmerT_38800-T1
Valid prediction for snap_scaffold_16-snap.434-T1
Valid prediction for GeneMark_model.66303_t
Valid prediction for GeneMark_model.66341_t
Valid prediction for Augustus_model.g26027.t1
Valid prediction for Augustus_model.g26034.t1
Couldn't classify 36682, 36773
Sorry, prediction pasa_asmbl_16142.p1 fails validation.
(ATG)	 AA	33989-34064	GT	AGG
(GGG)	 AG	35688-35966	GT	AGG
(ATC)	 AG	36682-36773	GC	CGG
-recovered pasa_asmbl_16142.p1, initial, 33989, 34064
-recovered pasa_asmbl_16142.p1, internal, 35688, 35966
-recovered pasa_asmbl_16142.p1, internal, 36682, 36773
Valid prediction for snap_scaffold_16-snap.451-T1
Valid prediction for GeneMark_model.66296_t
Valid prediction for snap_scaffold_16-snap.417-T1
Valid prediction for snap_scaffold_16-snap.442-T1
Valid prediction for GeneMark_model.66331_t
Valid prediction for Augustus_model.g26029.t1
Valid prediction for HiQ_model.g26033.t1
Valid prediction for Augustus_model.g26021.t1
Valid prediction for Augustus_model.g26024.t1
Valid prediction for GlimmerHMM_glimmerT_38795-T1
Valid prediction for GlimmerHMM_glimmerT_38797-T1
Valid prediction for Augustus_model.g26032.t1
Valid prediction for snap_scaffold_16-snap.453-T1
Valid prediction for snap_scaffold_16-snap.449-T1
Valid prediction for GeneMark_model.66339_t
Valid prediction for GlimmerHMM_glimmerT_38801-T1
Valid prediction for snap_scaffold_16-snap.426-T1
Valid prediction for snap_scaffold_16-snap.420-T1
Valid prediction for GeneMark_model.66321_t
Valid prediction for GlimmerHMM_glimmerT_38779-T1
Valid prediction for GlimmerHMM_glimmerT_38793-T1
Valid prediction for GeneMark_model.66315_t
Valid prediction for GeneMark_model.66297_t
Valid prediction for GeneMark_model.66319_t
Valid prediction for GlimmerHMM_glimmerT_38799-T1
Valid prediction for Augustus_model.g26019.t1
Valid prediction for GeneMark_model.66306_t
Valid prediction for GlimmerHMM_glimmerT_38786-T1
Valid prediction for snap_scaffold_16-snap.430-T1
Valid prediction for snap_scaffold_16-snap.446-T1
Valid prediction for Augustus_model.g26037.t1
Couldn't classify 22369, 22384
Sorry, prediction pasa_asmbl_16145.p1 fails validation.
(GCG)	 TG	22369-22384	GT	GGG
(TCC)	 AG	24766-24888	GT	GGG
(CCC)	 AG	25748-25896	GT	AGG
(GTG)	 AG	26048-26169	GT	GGG
(GAG)	 AG	27227-27425	GT	AGG
(GCG)	 AG	27611-27738	GT	AGG
(GAT)	 AG	27912-27981	GA	GAG
-recovered pasa_asmbl_16145.p1, terminal, 27912, 27981
-recovered pasa_asmbl_16145.p1, internal, 24766, 24888
-recovered pasa_asmbl_16145.p1, internal, 25748, 25896
-recovered pasa_asmbl_16145.p1, internal, 26048, 26169
-recovered pasa_asmbl_16145.p1, internal, 27227, 27425
-recovered pasa_asmbl_16145.p1, internal, 27611, 27738

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13424, rend_intergenic: 10936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22003, rend_intergenic: 13542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26697, rend_intergenic: 23977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37232, rend_intergenic: 29895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42682, rend_intergenic: 41818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53553, rend_intergenic: 42697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60485, rend_intergenic: 53575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66336, rend_intergenic: 61197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73636, rend_intergenic: 66984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74680, rend_intergenic: 74333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91753, rend_intergenic: 74776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96545, rend_intergenic: 94635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102772, rend_intergenic: 100443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104901, rend_intergenic: 102986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116766, rend_intergenic: 112864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119676, rend_intergenic: 119208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123864, rend_intergenic: 120616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160773, rend_intergenic: 154420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163129
-exon list size: 741


building trellis

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95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 13424, rend_intergenic: 10936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22003, rend_intergenic: 13542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26697, rend_intergenic: 23977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37232, rend_intergenic: 29895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42682, rend_intergenic: 41818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53553, rend_intergenic: 42697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60485, rend_intergenic: 53575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66336, rend_intergenic: 61197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73636, rend_intergenic: 66984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74680, rend_intergenic: 74333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91753, rend_intergenic: 74776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96545, rend_intergenic: 94635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102772, rend_intergenic: 100443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104901, rend_intergenic: 102986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116766, rend_intergenic: 112864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119676, rend_intergenic: 119208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123864, rend_intergenic: 120616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160773, rend_intergenic: 154420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13196
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support