-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_8405865-8614479

-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.g38374.t1
Valid prediction for GeneMark_model.100374_t
Valid prediction for GeneMark_model.100347_t
Valid prediction for CodingQuarry_transcript_40319-T1
Valid prediction for GeneMark_model.100361_t
Valid prediction for GlimmerHMM_glimmerT_57577-T1
Valid prediction for GlimmerHMM_glimmerT_57572-T1
Valid prediction for GeneMark_model.100392_t
Valid prediction for GeneMark_model.100386_t
Valid prediction for GlimmerHMM_glimmerT_57570-T1
Valid prediction for Augustus_model.g38377.t1
Valid prediction for snap_scaffold_26-snap.1983-T1
Valid prediction for GeneMark_model.100358_t
Valid prediction for snap_scaffold_26-snap.1980-T1
Valid prediction for GeneMark_model.100381_t
Valid prediction for snap_scaffold_26-snap.1992-T1
Valid prediction for Augustus_model.g38365.t1
Valid prediction for snap_scaffold_26-snap.1955-T1
Valid prediction for GeneMark_model.100363_t
Valid prediction for snap_scaffold_26-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_57578-T1
Valid prediction for snap_scaffold_26-snap.1985-T1
Valid prediction for GeneMark_model.100383_t
Valid prediction for GlimmerHMM_glimmerT_57583-T1
Valid prediction for snap_scaffold_26-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_57591-T1
Valid prediction for pasa_asmbl_35705.p1
Valid prediction for GeneMark_model.100351_t
Valid prediction for snap_scaffold_26-snap.1989-T1
Valid prediction for GlimmerHMM_glimmerT_57593-T1
Valid prediction for GlimmerHMM_glimmerT_57586-T1
Valid prediction for GlimmerHMM_glimmerT_57576-T1
Valid prediction for snap_scaffold_26-snap.1960-T1
Valid prediction for snap_scaffold_26-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_57580-T1
Valid prediction for GeneMark_model.100384_t
Valid prediction for Augustus_model.g38367.t1
Valid prediction for GeneMark_model.100379_t
Valid prediction for GeneMark_model.100354_t
Valid prediction for Augustus_model.g38362.t1
Valid prediction for GeneMark_model.100388_t
Valid prediction for GeneMark_model.100356_t
Valid prediction for GeneMark_model.100349_t
Valid prediction for GeneMark_model.100367_t
Valid prediction for GlimmerHMM_glimmerT_57592-T1
Valid prediction for HiQ_model.g38375.t1
Valid prediction for CodingQuarry_transcript_40320-T1
Valid prediction for GeneMark_model.100375_t
Valid prediction for snap_scaffold_26-snap.1972-T1
Valid prediction for snap_scaffold_26-snap.1969-T1
Valid prediction for GeneMark_model.100352_t
Valid prediction for snap_scaffold_26-snap.1970-T1
Valid prediction for GeneMark_model.100390_t
Valid prediction for GeneMark_model.100372_t
Valid prediction for snap_scaffold_26-snap.1967-T1
Valid prediction for snap_scaffold_26-snap.1964-T1
Valid prediction for snap_scaffold_26-snap.1971-T1
Valid prediction for Augustus_model.g38360.t1
Valid prediction for CodingQuarry_transcript_40321-T1
Valid prediction for GlimmerHMM_glimmerT_57595-T1
Valid prediction for snap_scaffold_26-snap.1966-T1
Valid prediction for GeneMark_model.100377_t
Valid prediction for snap_scaffold_26-snap.1988-T1
Valid prediction for snap_scaffold_26-snap.1958-T1
Valid prediction for GeneMark_model.100369_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 GlimmerHMM_glimmerT_57587-T1
Valid prediction for GeneMark_model.100360_t
Valid prediction for GlimmerHMM_glimmerT_57588-T1
Valid prediction for GlimmerHMM_glimmerT_57598-T1
Valid prediction for GlimmerHMM_glimmerT_57584-T1
Couldn't classify 34121, 34177
Couldn't classify 35438, 35502
Sorry, prediction pasa_asmbl_35154.p1 fails validation.
(GGG)	 TG	34121-34177	GT	CAG
(GAT)	 AG	34519-34648	GT	AGG
(ATG)	 AG	35133-35201	GT	AGG
(ACT)	 AG	35284-35343	GT	TGG
(CTG)	 AG	35438-35502	GT	ATG
add_exon() Sorry, pasa_asmbl_35154.p1 35133-35201-initial-1 is invalid.
-recovered pasa_asmbl_35154.p1, initial, 35133, 35201
-recovered pasa_asmbl_35154.p1, internal, 34519, 34648
-recovered pasa_asmbl_35154.p1, internal, 35133, 35201
-recovered pasa_asmbl_35154.p1, internal, 35284, 35343
-recovered pasa_asmbl_35154.p1, internal, 35438, 35502
Valid prediction for snap_scaffold_26-snap.1968-T1
Valid prediction for Augustus_model.g38366.t1
Valid prediction for Augustus_model.g38371.t1
Valid prediction for GeneMark_model.100380_t
Valid prediction for snap_scaffold_26-snap.1979-T1
Valid prediction for snap_scaffold_26-snap.1956-T1
Couldn't classify 25528, 25671
Sorry, prediction pasa_asmbl_35007.p1 fails validation.
(CTC)	 GT	25528-25671	GT	AGG
(CAG)	 AG	25797-25928	GT	AGG
(GAG)	 AG	26419-26584	GT	GAG
(GTC)	 AG	26704-26808	GT	GGG
(TTA)	 AG	27994-28694	CC	AAC
add_exon() Sorry, pasa_asmbl_35007.p1 26419-26584-terminal-3 is invalid.
-recovered pasa_asmbl_35007.p1, terminal, 26419, 26584
-recovered pasa_asmbl_35007.p1, terminal, 27994, 28694
-recovered pasa_asmbl_35007.p1, internal, 25797, 25928
-recovered pasa_asmbl_35007.p1, internal, 26419, 26584
-recovered pasa_asmbl_35007.p1, internal, 26704, 26808
Valid prediction for GlimmerHMM_glimmerT_57575-T1
Valid prediction for Augustus_model.g38379.t1
Valid prediction for snap_scaffold_26-snap.1961-T1
Valid prediction for GeneMark_model.100378_t
Valid prediction for snap_scaffold_26-snap.1951-T1
Valid prediction for GlimmerHMM_glimmerT_57569-T1
Valid prediction for GlimmerHMM_glimmerT_57594-T1
Valid prediction for GeneMark_model.100370_t
Valid prediction for Augustus_model.g38363.t1
Valid prediction for GeneMark_model.100387_t
Valid prediction for GeneMark_model.100382_t
Valid prediction for snap_scaffold_26-snap.1977-T1
Valid prediction for GlimmerHMM_glimmerT_57573-T1
Valid prediction for Augustus_model.g38359.t1
Valid prediction for GeneMark_model.100345_t
Valid prediction for Augustus_model.g38372.t1
Couldn't classify 186045, 186111
Sorry, prediction pasa_asmbl_35001.p1 fails validation.
(CAT)	 TT	186045-186111	GT	TGG
(CGA)	 AG	186214-186335	GT	AGG
(ATG)	 AG	188196-188285	GT	AGG
(GTG)	 AG	188390-188590	GT	GAG
(GAC)	 AG	189874-189975	GT	AGG
(ACG)	 AG	190122-190271	AT	AGA
-recovered pasa_asmbl_35001.p1, initial, 188196, 188285
-recovered pasa_asmbl_35001.p1, terminal, 190122, 190271
-recovered pasa_asmbl_35001.p1, internal, 186214, 186335
-recovered pasa_asmbl_35001.p1, internal, 188196, 188285
-recovered pasa_asmbl_35001.p1, internal, 188390, 188590
-recovered pasa_asmbl_35001.p1, internal, 189874, 189975
Valid prediction for Augustus_model.g38368.t1
Valid prediction for snap_scaffold_26-snap.1986-T1
Valid prediction for GlimmerHMM_glimmerT_57571-T1
Valid prediction for snap_scaffold_26-snap.1950-T1
Valid prediction for GeneMark_model.100355_t
Valid prediction for snap_scaffold_26-snap.1984-T1
Valid prediction for snap_scaffold_26-snap.1963-T1
Valid prediction for Augustus_model.g38376.t1
Valid prediction for snap_scaffold_26-snap.1976-T1
Valid prediction for HiQ_model.g38361.t1
Valid prediction for snap_scaffold_26-snap.1949-T1
Valid prediction for GeneMark_model.100365_t
Valid prediction for snap_scaffold_26-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_57597-T1
Valid prediction for snap_scaffold_26-snap.1982-T1
Valid prediction for GeneMark_model.100357_t
Valid prediction for GeneMark_model.100346_t
Valid prediction for GeneMark_model.100350_t
Valid prediction for GlimmerHMM_glimmerT_57599-T1
Valid prediction for GlimmerHMM_glimmerT_57582-T1
Valid prediction for GeneMark_model.100376_t
Valid prediction for GeneMark_model.100385_t
Valid prediction for Augustus_model.g38373.t1
Valid prediction for GlimmerHMM_glimmerT_57596-T1
Valid prediction for snap_scaffold_26-snap.1978-T1
Valid prediction for GlimmerHMM_glimmerT_57585-T1
Valid prediction for CodingQuarry_transcript_40317-T1
Valid prediction for GlimmerHMM_glimmerT_57574-T1
Valid prediction for GeneMark_model.100348_t
Valid prediction for GeneMark_model.100389_t
Valid prediction for snap_scaffold_26-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_57589-T1
Valid prediction for snap_scaffold_26-snap.1974-T1
Valid prediction for snap_scaffold_26-snap.1957-T1
Valid prediction for GlimmerHMM_glimmerT_57579-T1
Valid prediction for snap_scaffold_26-snap.1953-T1
Valid prediction for Augustus_model.g38358.t1
Valid prediction for CodingQuarry_transcript_40318-T1
Couldn't classify 198246, 198312
Sorry, prediction pasa_asmbl_35000.p1 fails validation.
(CTC)	 TC	198246-198312	GT	AGG
(GTG)	 AG	198524-198661	GT	CGG
(ATG)	 AG	198799-198914	GT	AGG
(ATG)	 AG	199044-199261	GT	AGG
(TGC)	 AG	199392-199596	AT	GAA
add_exon() Sorry, pasa_asmbl_35000.p1 198799-198914-initial-1 is invalid.
-recovered pasa_asmbl_35000.p1, initial, 198799, 198914
-recovered pasa_asmbl_35000.p1, initial, 199044, 199261
-recovered pasa_asmbl_35000.p1, terminal, 199392, 199596
-recovered pasa_asmbl_35000.p1, internal, 198524, 198661
-recovered pasa_asmbl_35000.p1, internal, 198799, 198914
-recovered pasa_asmbl_35000.p1, internal, 199044, 199261
Valid prediction for GlimmerHMM_glimmerT_57581-T1
Valid prediction for GeneMark_model.100353_t
Valid prediction for GeneMark_model.100359_t
Valid prediction for GeneMark_model.100362_t
Valid prediction for Augustus_model.g38364.t1
Valid prediction for GeneMark_model.100391_t
Valid prediction for CodingQuarry_transcript_40322-T1
Valid prediction for GeneMark_model.100373_t
Valid prediction for Augustus_model.g38369.t1
Valid prediction for snap_scaffold_26-snap.1975-T1
Valid prediction for GeneMark_model.100364_t
Valid prediction for pasa_asmbl_35003.p1
Valid prediction for snap_scaffold_26-snap.1987-T1
Valid prediction for snap_scaffold_26-snap.1965-T1
Valid prediction for snap_scaffold_26-snap.1981-T1
Valid prediction for GeneMark_model.100371_t
Valid prediction for snap_scaffold_26-snap.1952-T1
Valid prediction for GeneMark_model.100368_t
Valid prediction for GeneMark_model.100366_t
Valid prediction for GeneMark_model.100393_t
Valid prediction for Augustus_model.g38370.t1
Valid prediction for GlimmerHMM_glimmerT_57590-T1
Couldn't classify 21048, 21250
Couldn't classify 23792, 23907
Sorry, prediction pasa_asmbl_35010.p1 fails validation.
(CAG)	 CG	21048-21250	GT	AGG
(GTC)	 AG	21414-21475	GT	AGG
(ACC)	 AG	22445-22498	GT	AGG
(AGC)	 AG	23792-23907	TT	TCT
-recovered pasa_asmbl_35010.p1, internal, 21414, 21475
-recovered pasa_asmbl_35010.p1, internal, 22445, 22498
Valid prediction for Augustus_model.g38378.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34750, rend_intergenic: 31689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69819, rend_intergenic: 66174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77923, rend_intergenic: 73969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79005, rend_intergenic: 78694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90064, rend_intergenic: 82595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110123, rend_intergenic: 105263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155910, rend_intergenic: 151766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160368, rend_intergenic: 155989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199101, rend_intergenic: 185262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208615
-exon list size: 782


building trellis

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74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 34750, rend_intergenic: 31689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69819, rend_intergenic: 66174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77923, rend_intergenic: 73969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79005, rend_intergenic: 78694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90064, rend_intergenic: 82595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110123, rend_intergenic: 105263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155910, rend_intergenic: 151766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160368, rend_intergenic: 155989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199101, rend_intergenic: 185262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support