-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_10834042-11016245

-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_45892-T1
Valid prediction for GeneMark_model.80009_t
Valid prediction for GeneMark_model.79979_t
Valid prediction for GeneMark_model.80000_t
Valid prediction for GlimmerHMM_glimmerT_45895-T1
Valid prediction for GlimmerHMM_glimmerT_45884-T1
Valid prediction for snap_scaffold_19-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_45863-T1
Valid prediction for snap_scaffold_19-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_45897-T1
Valid prediction for Augustus_model.g30603.t1
Valid prediction for Augustus_model.g30600.t1
Valid prediction for GlimmerHMM_glimmerT_45885-T1
Valid prediction for GlimmerHMM_glimmerT_45879-T1
Couldn't classify 170931, 170984
Sorry, prediction GeneMark_model.80023_t fails validation.
(ATG)	 GC	170117-170142	GT	GTG
(AAA)	 AG	170251-170259	GT	GTG
(AGA)	 AG	170283-170309	GT	GTG
(GAC)	 AG	170487-170525	GT	CGG
(ATG)	 AG	170587-170663	GT	AGG
(GAG)	 AG	170931-170984	GC	CGG
-recovered GeneMark_model.80023_t, initial, 170117, 170142
-recovered GeneMark_model.80023_t, initial, 170587, 170663
-recovered GeneMark_model.80023_t, internal, 170251, 170259
-recovered GeneMark_model.80023_t, internal, 170283, 170309
-recovered GeneMark_model.80023_t, internal, 170487, 170525
-recovered GeneMark_model.80023_t, internal, 170587, 170663
-recovered GeneMark_model.80023_t, internal, 170931, 170984
Valid prediction for Augustus_model.g30592.t1
Valid prediction for snap_scaffold_19-snap.2110-T1
Valid prediction for GeneMark_model.80027_t
Valid prediction for snap_scaffold_19-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_45877-T1
Valid prediction for Augustus_model.g30602.t1
Valid prediction for GlimmerHMM_glimmerT_45872-T1
Valid prediction for snap_scaffold_19-snap.2126-T1
Valid prediction for GeneMark_model.79995_t
Valid prediction for snap_scaffold_19-snap.2123-T1
Valid prediction for GlimmerHMM_glimmerT_45866-T1
Valid prediction for GlimmerHMM_glimmerT_45891-T1
Valid prediction for GeneMark_model.79983_t
Valid prediction for GeneMark_model.79987_t
Valid prediction for GeneMark_model.79998_t
Valid prediction for GeneMark_model.80004_t
Valid prediction for GeneMark_model.80028_t
Valid prediction for GeneMark_model.79976_t
Valid prediction for snap_scaffold_19-snap.2107-T1
Valid prediction for Augustus_model.g30593.t1
Valid prediction for Augustus_model.g30591.t1
Valid prediction for GeneMark_model.80024_t
Valid prediction for GlimmerHMM_glimmerT_45886-T1
Valid prediction for GlimmerHMM_glimmerT_45871-T1
Valid prediction for snap_scaffold_19-snap.2111-T1
Valid prediction for GlimmerHMM_glimmerT_45864-T1
Valid prediction for GlimmerHMM_glimmerT_45888-T1
Valid prediction for GeneMark_model.80020_t
Valid prediction for Augustus_model.g30601.t1
Valid prediction for GlimmerHMM_glimmerT_45896-T1
Valid prediction for GeneMark_model.79978_t
Valid prediction for Augustus_model.g30597.t1
Valid prediction for Augustus_model.g30589.t1
Valid prediction for snap_scaffold_19-snap.2105-T1
Valid prediction for GeneMark_model.80002_t
Valid prediction for GeneMark_model.80013_t
Valid prediction for snap_scaffold_19-snap.2121-T1
Valid prediction for GeneMark_model.79981_t
Valid prediction for snap_scaffold_19-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_45870-T1
Valid prediction for Augustus_model.g30598.t1
Valid prediction for GlimmerHMM_glimmerT_45875-T1
Valid prediction for GeneMark_model.79991_t
Valid prediction for Augustus_model.g30587.t1
Valid prediction for GlimmerHMM_glimmerT_45882-T1
Valid prediction for GeneMark_model.80017_t
Valid prediction for GlimmerHMM_glimmerT_45874-T1
Valid prediction for snap_scaffold_19-snap.2102-T1
Valid prediction for snap_scaffold_19-snap.2096-T1
Valid prediction for Augustus_model.g30594.t1
Valid prediction for GeneMark_model.79973_t
Valid prediction for Augustus_model.g30599.t1
Valid prediction for GlimmerHMM_glimmerT_45868-T1
Valid prediction for snap_scaffold_19-snap.2104-T1
Valid prediction for GeneMark_model.80007_t
Valid prediction for snap_scaffold_19-snap.2098-T1
Valid prediction for snap_scaffold_19-snap.2113-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_19-snap.2095-T1
Valid prediction for Augustus_model.g30596.t1
Valid prediction for GeneMark_model.79975_t
Valid prediction for snap_scaffold_19-snap.2094-T1
Valid prediction for snap_scaffold_19-snap.2115-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.79977_t
Valid prediction for GeneMark_model.79986_t
Valid prediction for GlimmerHMM_glimmerT_45876-T1
Valid prediction for GeneMark_model.80010_t
Valid prediction for snap_scaffold_19-snap.2118-T1
Valid prediction for GlimmerHMM_glimmerT_45878-T1
Valid prediction for snap_scaffold_19-snap.2106-T1
Valid prediction for GeneMark_model.80012_t
Valid prediction for snap_scaffold_19-snap.2124-T1
Valid prediction for GeneMark_model.79984_t
Valid prediction for GeneMark_model.79980_t
Valid prediction for GeneMark_model.80015_t
Valid prediction for GeneMark_model.79997_t
Valid prediction for GlimmerHMM_glimmerT_45889-T1
Couldn't classify 157638, 157802
Couldn't classify 159035, 159295
Sorry, prediction pasa_asmbl_21573.p1 fails validation.
(GGT)	 AG	157638-157802	GT	TGG
(CAG)	 AG	158169-158369	GT	AGG
(GTG)	 AG	159035-159295	AG	TGA
-recovered pasa_asmbl_21573.p1, internal, 157638, 157802
-recovered pasa_asmbl_21573.p1, internal, 158169, 158369
Valid prediction for GlimmerHMM_glimmerT_45865-T1
Valid prediction for snap_scaffold_19-snap.2117-T1
Valid prediction for GeneMark_model.80019_t
Valid prediction for Augustus_model.g30586.t1
Valid prediction for GeneMark_model.80008_t
Valid prediction for snap_scaffold_19-snap.2093-T1
Valid prediction for GeneMark_model.79994_t
Valid prediction for snap_scaffold_19-snap.2109-T1
Valid prediction for GeneMark_model.79993_t
Valid prediction for Augustus_model.g30595.t1
Valid prediction for GeneMark_model.79989_t
Valid prediction for GlimmerHMM_glimmerT_45894-T1
Valid prediction for GeneMark_model.80021_t
Valid prediction for GlimmerHMM_glimmerT_45862-T1
Valid prediction for snap_scaffold_19-snap.2108-T1
Valid prediction for GeneMark_model.79992_t
Valid prediction for snap_scaffold_19-snap.2112-T1
Valid prediction for GlimmerHMM_glimmerT_45880-T1
Valid prediction for GlimmerHMM_glimmerT_45861-T1
Valid prediction for GeneMark_model.79990_t
Valid prediction for GeneMark_model.80022_t
Valid prediction for snap_scaffold_19-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_45873-T1
Valid prediction for GeneMark_model.79996_t
Valid prediction for GlimmerHMM_glimmerT_45867-T1
Valid prediction for GeneMark_model.80025_t
Valid prediction for GeneMark_model.79985_t
Valid prediction for snap_scaffold_19-snap.2101-T1
Valid prediction for GeneMark_model.80016_t
Valid prediction for GlimmerHMM_glimmerT_45887-T1
Couldn't classify 105937, 105986
Sorry, prediction pasa_asmbl_21577.p1 fails validation.
(CCC)	 TC	105937-105986	GT	GGG
(GTG)	 AG	106079-106173	GT	AGG
(ACC)	 AG	106262-106390	GT	AGG
(GAA)	 AG	106627-106769	GC	GAG
-recovered pasa_asmbl_21577.p1, terminal, 106627, 106769
-recovered pasa_asmbl_21577.p1, internal, 106079, 106173
-recovered pasa_asmbl_21577.p1, internal, 106262, 106390
-recovered pasa_asmbl_21577.p1, internal, 106627, 106769
Valid prediction for GlimmerHMM_glimmerT_45890-T1
Valid prediction for GeneMark_model.80026_t
Valid prediction for GeneMark_model.80018_t
Valid prediction for snap_scaffold_19-snap.2120-T1
Valid prediction for GeneMark_model.80003_t
Valid prediction for GeneMark_model.80011_t
Valid prediction for snap_scaffold_19-snap.2099-T1
Valid prediction for Augustus_model.g30590.t1
Valid prediction for GlimmerHMM_glimmerT_45893-T1
Valid prediction for Augustus_model.g30588.t1
Valid prediction for GeneMark_model.79974_t
Valid prediction for GeneMark_model.79999_t
Valid prediction for snap_scaffold_19-snap.2100-T1
Valid prediction for snap_scaffold_19-snap.2114-T1
Valid prediction for GlimmerHMM_glimmerT_45883-T1
Valid prediction for GlimmerHMM_glimmerT_45860-T1
Valid prediction for GlimmerHMM_glimmerT_45881-T1
Valid prediction for GeneMark_model.80001_t
Valid prediction for GeneMark_model.80005_t
Valid prediction for GeneMark_model.79982_t
Valid prediction for GlimmerHMM_glimmerT_45869-T1
Valid prediction for GeneMark_model.80014_t
Valid prediction for GeneMark_model.80006_t
Valid prediction for snap_scaffold_19-snap.2122-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27001, rend_intergenic: 13285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31606, rend_intergenic: 27062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67546, rend_intergenic: 66808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74839, rend_intergenic: 67554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81471, rend_intergenic: 78124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142534, rend_intergenic: 97354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142597, rend_intergenic: 142563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145225, rend_intergenic: 144735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149566, rend_intergenic: 145274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167877, rend_intergenic: 150349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172495, rend_intergenic: 167939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175618, rend_intergenic: 172928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182204
-exon list size: 902


building trellis

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75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
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    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
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    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.6    
99.7    
99.8    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 27001, rend_intergenic: 13285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31606, rend_intergenic: 27062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67546, rend_intergenic: 66808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74839, rend_intergenic: 67554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81471, rend_intergenic: 78124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142534, rend_intergenic: 97354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142597, rend_intergenic: 142563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145225, rend_intergenic: 144735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149566, rend_intergenic: 145274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167877, rend_intergenic: 150349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172495, rend_intergenic: 167939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175618, rend_intergenic: 172928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support