-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_3037390-3230245

-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 GlimmerHMM_glimmerT_51952-T1
Valid prediction for Augustus_model.g34920.t1
Valid prediction for GeneMark_model.90225_t
Valid prediction for snap_scaffold_23-snap.617-T1
Valid prediction for snap_scaffold_23-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_51976-T1
Valid prediction for GeneMark_model.90223_t
Valid prediction for GlimmerHMM_glimmerT_51960-T1
Valid prediction for Augustus_model.g34921.t1
Valid prediction for GeneMark_model.90263_t
Valid prediction for snap_scaffold_23-snap.622-T1
Valid prediction for Augustus_model.g34917.t1
Valid prediction for snap_scaffold_23-snap.600-T1
Valid prediction for GlimmerHMM_glimmerT_51966-T1
Valid prediction for GlimmerHMM_glimmerT_51980-T1
Valid prediction for GeneMark_model.90246_t
Valid prediction for GeneMark_model.90220_t
Valid prediction for snap_scaffold_23-snap.624-T1
Valid prediction for GeneMark_model.90232_t
Valid prediction for GeneMark_model.90255_t
Valid prediction for snap_scaffold_23-snap.613-T1
Valid prediction for GeneMark_model.90265_t
Valid prediction for Augustus_model.g34932.t1
Valid prediction for GlimmerHMM_glimmerT_51958-T1
Valid prediction for GeneMark_model.90261_t
Valid prediction for snap_scaffold_23-snap.601-T1
Valid prediction for snap_scaffold_23-snap.618-T1
Valid prediction for GeneMark_model.90230_t
Valid prediction for GeneMark_model.90229_t
Valid prediction for snap_scaffold_23-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_51967-T1
Valid prediction for GeneMark_model.90281_t
Valid prediction for GeneMark_model.90239_t
Valid prediction for GeneMark_model.90244_t
Valid prediction for GlimmerHMM_glimmerT_51977-T1
Valid prediction for snap_scaffold_23-snap.604-T1
Valid prediction for GeneMark_model.90269_t
Valid prediction for GlimmerHMM_glimmerT_51954-T1
Valid prediction for Augustus_model.g34922.t1
Valid prediction for Augustus_model.g34924.t1
Valid prediction for GeneMark_model.90276_t
Valid prediction for GeneMark_model.90282_t
Valid prediction for GlimmerHMM_glimmerT_51978-T1
Valid prediction for Augustus_model.g34926.t1
Valid prediction for GeneMark_model.90257_t
Valid prediction for Augustus_model.g34936.t1
Valid prediction for GeneMark_model.90241_t
Valid prediction for GeneMark_model.90240_t
Valid prediction for GlimmerHMM_glimmerT_51961-T1
Valid prediction for GeneMark_model.90251_t
Valid prediction for GlimmerHMM_glimmerT_51965-T1
Valid prediction for snap_scaffold_23-snap.587-T1
Valid prediction for snap_scaffold_23-snap.608-T1
Valid prediction for GeneMark_model.90237_t
Valid prediction for GlimmerHMM_glimmerT_51982-T1
Valid prediction for Augustus_model.g34928.t1
Valid prediction for GlimmerHMM_glimmerT_51963-T1
Valid prediction for GeneMark_model.90274_t
Valid prediction for GeneMark_model.90253_t
Valid prediction for snap_scaffold_23-snap.627-T1
Valid prediction for GeneMark_model.90242_t
Valid prediction for snap_scaffold_23-snap.626-T1
Valid prediction for GeneMark_model.90278_t
Valid prediction for GeneMark_model.90283_t
Valid prediction for GlimmerHMM_glimmerT_51981-T1
Valid prediction for GeneMark_model.90235_t
Valid prediction for GlimmerHMM_glimmerT_51983-T1
Valid prediction for GeneMark_model.90272_t
Valid prediction for snap_scaffold_23-snap.599-T1
Valid prediction for GeneMark_model.90260_t
Valid prediction for GeneMark_model.90227_t
Valid prediction for GeneMark_model.90248_t
Valid prediction for snap_scaffold_23-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_51970-T1
Valid prediction for snap_scaffold_23-snap.597-T1
Valid prediction for Augustus_model.g34930.t1
Valid prediction for GeneMark_model.90267_t
Valid prediction for GlimmerHMM_glimmerT_51955-T1
Valid prediction for snap_scaffold_23-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_51969-T1
Valid prediction for snap_scaffold_23-snap.628-T1
Valid prediction for GlimmerHMM_glimmerT_51984-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_23-snap.584-T1
Valid prediction for snap_scaffold_23-snap.593-T1
Valid prediction for snap_scaffold_23-snap.594-T1
Valid prediction for snap_scaffold_23-snap.621-T1
Valid prediction for snap_scaffold_23-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_51979-T1
Valid prediction for GeneMark_model.90226_t
Valid prediction for GeneMark_model.90245_t
Valid prediction for Augustus_model.g34927.t1
Valid prediction for GeneMark_model.90268_t
Valid prediction for GeneMark_model.90231_t
Valid prediction for GeneMark_model.90250_t
Valid prediction for GeneMark_model.90254_t
Valid prediction for snap_scaffold_23-snap.623-T1
Valid prediction for GeneMark_model.90271_t
Valid prediction for snap_scaffold_23-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_51986-T1
Valid prediction for GlimmerHMM_glimmerT_51959-T1
Valid prediction for Augustus_model.g34935.t1
Valid prediction for GeneMark_model.90221_t
Valid prediction for GlimmerHMM_glimmerT_51964-T1
Valid prediction for Augustus_model.g34937.t1
Valid prediction for GeneMark_model.90256_t
Valid prediction for snap_scaffold_23-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_51971-T1
Valid prediction for GeneMark_model.90266_t
Valid prediction for GlimmerHMM_glimmerT_51953-T1
Valid prediction for snap_scaffold_23-snap.591-T1
Valid prediction for GeneMark_model.90234_t
Valid prediction for GlimmerHMM_glimmerT_51956-T1
Valid prediction for GeneMark_model.90262_t
Valid prediction for Augustus_model.g34923.t1
Valid prediction for GeneMark_model.90264_t
Valid prediction for snap_scaffold_23-snap.589-T1
Valid prediction for GeneMark_model.90284_t
Valid prediction for GlimmerHMM_glimmerT_51974-T1
Valid prediction for GlimmerHMM_glimmerT_51968-T1
Valid prediction for GeneMark_model.90233_t
Valid prediction for GeneMark_model.90259_t
Valid prediction for Augustus_model.g34915.t1
Valid prediction for GeneMark_model.90275_t
Valid prediction for GeneMark_model.90279_t
Valid prediction for GeneMark_model.90243_t
Valid prediction for GeneMark_model.90238_t
Valid prediction for snap_scaffold_23-snap.619-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.616-T1
Valid prediction for snap_scaffold_23-snap.595-T1
Valid prediction for GeneMark_model.90249_t
Valid prediction for GlimmerHMM_glimmerT_51957-T1
Valid prediction for Augustus_model.g34933.t1
Valid prediction for GeneMark_model.90236_t
Valid prediction for GeneMark_model.90277_t
Valid prediction for GeneMark_model.90270_t
Valid prediction for snap_scaffold_23-snap.620-T1
Valid prediction for GeneMark_model.90222_t
Valid prediction for GeneMark_model.90219_t
Valid prediction for GeneMark_model.90273_t
Valid prediction for GeneMark_model.90280_t
Valid prediction for GeneMark_model.90252_t
Valid prediction for GlimmerHMM_glimmerT_51985-T1
Valid prediction for GlimmerHMM_glimmerT_51975-T1
Valid prediction for GeneMark_model.90228_t
Valid prediction for snap_scaffold_23-snap.630-T1
Valid prediction for snap_scaffold_23-snap.603-T1
Couldn't classify 158737, 158784
Couldn't classify 163080, 163271
Sorry, prediction pasa_asmbl_31506.p1 fails validation.
(GCA)	 CA	158737-158784	GT	CGG
(ATC)	 AG	158918-158996	GT	AAG
(CTG)	 AG	161539-161618	GT	TGG
(CAG)	 AG	163080-163271	CA	GGC
-recovered pasa_asmbl_31506.p1, internal, 158918, 158996
-recovered pasa_asmbl_31506.p1, internal, 161539, 161618
Valid prediction for snap_scaffold_23-snap.598-T1
Valid prediction for Augustus_model.g34934.t1
Valid prediction for snap_scaffold_23-snap.607-T1
Valid prediction for GeneMark_model.90247_t
Valid prediction for snap_scaffold_23-snap.609-T1
Valid prediction for GeneMark_model.90218_t
Valid prediction for GlimmerHMM_glimmerT_51962-T1
Valid prediction for snap_scaffold_23-snap.605-T1
Valid prediction for Augustus_model.g34919.t1
Valid prediction for snap_scaffold_23-snap.585-T1
Valid prediction for GeneMark_model.90258_t
Valid prediction for snap_scaffold_23-snap.615-T1
Valid prediction for Augustus_model.g34925.t1
Valid prediction for Augustus_model.g34916.t1
Valid prediction for Augustus_model.g34918.t1
Valid prediction for snap_scaffold_23-snap.611-T1
Valid prediction for snap_scaffold_23-snap.629-T1
Valid prediction for snap_scaffold_23-snap.610-T1
Valid prediction for snap_scaffold_23-snap.614-T1
Valid prediction for Augustus_model.g34929.t1
Valid prediction for GlimmerHMM_glimmerT_51973-T1
Valid prediction for GlimmerHMM_glimmerT_51972-T1
Valid prediction for snap_scaffold_23-snap.602-T1
Valid prediction for snap_scaffold_23-snap.625-T1
Valid prediction for Augustus_model.g34931.t1
Couldn't classify 174415, 174550
Sorry, prediction pasa_asmbl_31505.p1 fails validation.
(GTG)	 AG	174415-174550	GT	GGG
(CTC)	 AG	176526-176670	GT	AGG
(CAA)	 AG	177431-177660	GT	AGG
(AGA)	 AG	178174-178306	GT	ATG
(GTC)	 AG	179483-179531	CA	GAC
add_exon() Sorry, pasa_asmbl_31505.p1 176526-176670-terminal-3 is invalid.
-recovered pasa_asmbl_31505.p1, terminal, 176526, 176670
-recovered pasa_asmbl_31505.p1, terminal, 179483, 179531
-recovered pasa_asmbl_31505.p1, internal, 174415, 174550
-recovered pasa_asmbl_31505.p1, internal, 176526, 176670
-recovered pasa_asmbl_31505.p1, internal, 177431, 177660
-recovered pasa_asmbl_31505.p1, internal, 178174, 178306
Valid prediction for snap_scaffold_23-snap.612-T1
Valid prediction for GeneMark_model.90224_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20243, rend_intergenic: 13872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26199, rend_intergenic: 25347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29078, rend_intergenic: 27332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32132, rend_intergenic: 29099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36996, rend_intergenic: 36201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59619, rend_intergenic: 58200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66125, rend_intergenic: 63553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68055, rend_intergenic: 66688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77920, rend_intergenic: 74512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104546, rend_intergenic: 98045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123441, rend_intergenic: 121586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141582, rend_intergenic: 138182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162950, rend_intergenic: 158207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192856
-exon list size: 834


building trellis

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75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
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    
79.1    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
95.9    
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    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 20243, rend_intergenic: 13872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26199, rend_intergenic: 25347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29078, rend_intergenic: 27332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32132, rend_intergenic: 29099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36996, rend_intergenic: 36201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59619, rend_intergenic: 58200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66125, rend_intergenic: 63553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68055, rend_intergenic: 66688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77920, rend_intergenic: 74512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104546, rend_intergenic: 98045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123441, rend_intergenic: 121586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141582, rend_intergenic: 138182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162950, rend_intergenic: 158207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12171
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 397 - 12171
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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