-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_11228984-11447816

-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 GeneMark_model.44426_t
Valid prediction for Augustus_model.g17392.t1
Valid prediction for snap_scaffold_10-snap.2209-T1
Valid prediction for snap_scaffold_10-snap.2207-T1
Valid prediction for GlimmerHMM_glimmerT_25931-T1
Valid prediction for GlimmerHMM_glimmerT_25933-T1
Valid prediction for snap_scaffold_10-snap.2235-T1
Valid prediction for GeneMark_model.44392_t
Valid prediction for GlimmerHMM_glimmerT_25927-T1
Valid prediction for GeneMark_model.44412_t
Valid prediction for GeneMark_model.44416_t
Valid prediction for snap_scaffold_10-snap.2231-T1
Valid prediction for snap_scaffold_10-snap.2193-T1
Valid prediction for GeneMark_model.44419_t
Valid prediction for snap_scaffold_10-snap.2185-T1
Valid prediction for GeneMark_model.44394_t
Valid prediction for snap_scaffold_10-snap.2189-T1
Valid prediction for snap_scaffold_10-snap.2216-T1
Valid prediction for GeneMark_model.44408_t
Valid prediction for Augustus_model.g17388.t1
Valid prediction for GeneMark_model.44390_t
Valid prediction for GeneMark_model.44431_t
Valid prediction for GeneMark_model.44420_t
Valid prediction for GeneMark_model.44417_t
Valid prediction for GeneMark_model.44403_t
Valid prediction for GeneMark_model.44440_t
Valid prediction for GeneMark_model.44438_t
Valid prediction for snap_scaffold_10-snap.2221-T1
Valid prediction for GeneMark_model.44386_t
Valid prediction for Augustus_model.g17387.t1
Valid prediction for snap_scaffold_10-snap.2204-T1
Valid prediction for snap_scaffold_10-snap.2214-T1
Valid prediction for snap_scaffold_10-snap.2225-T1
Valid prediction for GeneMark_model.44441_t
Valid prediction for snap_scaffold_10-snap.2238-T1
Valid prediction for GeneMark_model.44443_t
Valid prediction for snap_scaffold_10-snap.2195-T1
Valid prediction for GlimmerHMM_glimmerT_25935-T1
Valid prediction for snap_scaffold_10-snap.2211-T1
Valid prediction for GlimmerHMM_glimmerT_25916-T1
Valid prediction for snap_scaffold_10-snap.2202-T1
Valid prediction for GeneMark_model.44436_t
Valid prediction for GlimmerHMM_glimmerT_25925-T1
Valid prediction for snap_scaffold_10-snap.2230-T1
Valid prediction for snap_scaffold_10-snap.2198-T1
Valid prediction for GeneMark_model.44400_t
Valid prediction for GeneMark_model.44422_t
Valid prediction for GeneMark_model.44380_t
Valid prediction for Augustus_model.g17402.t1
Valid prediction for GeneMark_model.44424_t
Valid prediction for Augustus_model.g17397.t1
Valid prediction for GeneMark_model.44442_t
Valid prediction for snap_scaffold_10-snap.2232-T1
Valid prediction for GeneMark_model.44405_t
Valid prediction for Augustus_model.g17396.t1
Valid prediction for GeneMark_model.44428_t
Valid prediction for GeneMark_model.44407_t
Valid prediction for snap_scaffold_10-snap.2227-T1
Valid prediction for GeneMark_model.44396_t
Valid prediction for snap_scaffold_10-snap.2234-T1
Valid prediction for snap_scaffold_10-snap.2203-T1
Valid prediction for GeneMark_model.44399_t
Valid prediction for GeneMark_model.44383_t
Valid prediction for GeneMark_model.44414_t
Valid prediction for snap_scaffold_10-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_25923-T1
Valid prediction for snap_scaffold_10-snap.2196-T1
Valid prediction for snap_scaffold_10-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_25930-T1
Valid prediction for snap_scaffold_10-snap.2184-T1
Valid prediction for snap_scaffold_10-snap.2218-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 GeneMark_model.44387_t
Valid prediction for GlimmerHMM_glimmerT_25924-T1
Valid prediction for snap_scaffold_10-snap.2217-T1
Valid prediction for snap_scaffold_10-snap.2205-T1
Valid prediction for GeneMark_model.44423_t
Valid prediction for GeneMark_model.44429_t
Valid prediction for snap_scaffold_10-snap.2237-T1
Valid prediction for snap_scaffold_10-snap.2220-T1
Valid prediction for GeneMark_model.44402_t
Valid prediction for snap_scaffold_10-snap.2236-T1
Valid prediction for Augustus_model.g17400.t1
Valid prediction for GeneMark_model.44384_t
Valid prediction for GeneMark_model.44389_t
Valid prediction for GeneMark_model.44391_t
Valid prediction for snap_scaffold_10-snap.2192-T1
Valid prediction for GeneMark_model.44398_t
Valid prediction for GlimmerHMM_glimmerT_25920-T1
Valid prediction for GlimmerHMM_glimmerT_25918-T1
Valid prediction for snap_scaffold_10-snap.2194-T1
Valid prediction for GlimmerHMM_glimmerT_25926-T1
Valid prediction for snap_scaffold_10-snap.2186-T1
Valid prediction for Augustus_model.g17391.t1
Valid prediction for snap_scaffold_10-snap.2206-T1
Valid prediction for snap_scaffold_10-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_25919-T1
Valid prediction for GlimmerHMM_glimmerT_25937-T1
Valid prediction for GlimmerHMM_glimmerT_25929-T1
Valid prediction for GeneMark_model.44410_t
Valid prediction for GeneMark_model.44418_t
Valid prediction for snap_scaffold_10-snap.2188-T1
Valid prediction for CodingQuarry_transcript_5557-T1
Valid prediction for GeneMark_model.44415_t
Valid prediction for GeneMark_model.44432_t
Valid prediction for Augustus_model.g17395.t1
Valid prediction for GeneMark_model.44395_t
Valid prediction for GeneMark_model.44404_t
Valid prediction for Augustus_model.g17394.t1
Valid prediction for GeneMark_model.44401_t
Valid prediction for snap_scaffold_10-snap.2226-T1
Valid prediction for GeneMark_model.44427_t
Valid prediction for snap_scaffold_10-snap.2219-T1
Valid prediction for HiQ_model.g17389.t1
Valid prediction for snap_scaffold_10-snap.2210-T1
Valid prediction for GeneMark_model.44425_t
Valid prediction for GlimmerHMM_glimmerT_25915-T1
Valid prediction for snap_scaffold_10-snap.2215-T1
Valid prediction for snap_scaffold_10-snap.2222-T1
Valid prediction for GeneMark_model.44382_t
Valid prediction for Augustus_model.g17386.t1
Valid prediction for Augustus_model.g17393.t1
Valid prediction for GeneMark_model.44388_t
Valid prediction for snap_scaffold_10-snap.2213-T1
Couldn't classify 177870, 177969
Couldn't classify 178122, 178318
Sorry, prediction pasa_asmbl_4011.p1 fails validation.
(GAG)	 CA	177870-177969	GT	AGG
(AGG)	 AG	178122-178318	GT	AGG
-recovered pasa_asmbl_4011.p1, internal, 178122, 178318
Valid prediction for snap_scaffold_10-snap.2197-T1
Valid prediction for GeneMark_model.44439_t
Valid prediction for GlimmerHMM_glimmerT_25917-T1
Valid prediction for GeneMark_model.44435_t
Valid prediction for GeneMark_model.44433_t
Valid prediction for GlimmerHMM_glimmerT_25922-T1
Valid prediction for GeneMark_model.44406_t
Valid prediction for Augustus_model.g17390.t1
Valid prediction for snap_scaffold_10-snap.2200-T1
Valid prediction for GeneMark_model.44434_t
Valid prediction for GlimmerHMM_glimmerT_25928-T1
Couldn't classify 136246, 136336
Couldn't classify 138745, 138833
Sorry, prediction pasa_asmbl_4010.p1 fails validation.
(GGT)	 AT	136246-136336	GT	GAG
(CTG)	 AG	136607-136709	GT	AGG
(GCG)	 AG	138355-138470	GT	TGG
(GTC)	 AG	138745-138833	AG	CCA
-recovered pasa_asmbl_4010.p1, internal, 136607, 136709
-recovered pasa_asmbl_4010.p1, internal, 138355, 138470
Valid prediction for snap_scaffold_10-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_25921-T1
Valid prediction for GeneMark_model.44437_t
Valid prediction for snap_scaffold_10-snap.2212-T1
Valid prediction for Augustus_model.g17399.t1
Valid prediction for GeneMark_model.44385_t
Valid prediction for GeneMark_model.44411_t
Valid prediction for GeneMark_model.44421_t
Valid prediction for snap_scaffold_10-snap.2201-T1
Valid prediction for GeneMark_model.44393_t
Valid prediction for snap_scaffold_10-snap.2191-T1
Valid prediction for snap_scaffold_10-snap.2190-T1
Valid prediction for snap_scaffold_10-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_25934-T1
Valid prediction for snap_scaffold_10-snap.2187-T1
Valid prediction for snap_scaffold_10-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_25936-T1
Valid prediction for Augustus_model.g17401.t1
Couldn't classify 52619, 53401
Couldn't classify 54033, 54102
Sorry, prediction pasa_asmbl_3680.p1 fails validation.
(ACC)	 AG	52619-53401	GT	GTG
(GAT)	 AG	53606-53796	GT	AGG
(CCA)	 AG	54033-54102	CA	TGC
-recovered pasa_asmbl_3680.p1, internal, 52619, 53401
-recovered pasa_asmbl_3680.p1, internal, 53606, 53796
Valid prediction for Augustus_model.g17398.t1
Valid prediction for snap_scaffold_10-snap.2233-T1
Valid prediction for GeneMark_model.44397_t
Valid prediction for GeneMark_model.44413_t
Valid prediction for GeneMark_model.44381_t
Valid prediction for GeneMark_model.44430_t
Valid prediction for GlimmerHMM_glimmerT_25932-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25117, rend_intergenic: 9268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33402, rend_intergenic: 26953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39888, rend_intergenic: 36767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40594, rend_intergenic: 39956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56944, rend_intergenic: 40601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67443, rend_intergenic: 58535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70235, rend_intergenic: 67563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88073, rend_intergenic: 73683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95191, rend_intergenic: 92367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127030, rend_intergenic: 122626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133319, rend_intergenic: 131298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140529, rend_intergenic: 136229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154558, rend_intergenic: 142686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161128, rend_intergenic: 154671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165255, rend_intergenic: 162725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171363, rend_intergenic: 168722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175435, rend_intergenic: 172597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193973, rend_intergenic: 179779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203838, rend_intergenic: 194195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215994, rend_intergenic: 210873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218833
-exon list size: 788


building trellis

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79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
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    
85.4    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
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: 25117, rend_intergenic: 9268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33402, rend_intergenic: 26953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39888, rend_intergenic: 36767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40594, rend_intergenic: 39956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56944, rend_intergenic: 40601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67443, rend_intergenic: 58535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70235, rend_intergenic: 67563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88073, rend_intergenic: 73683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95191, rend_intergenic: 92367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127030, rend_intergenic: 122626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133319, rend_intergenic: 131298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140529, rend_intergenic: 136229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154558, rend_intergenic: 142686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161128, rend_intergenic: 154671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165255, rend_intergenic: 162725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171363, rend_intergenic: 168722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175435, rend_intergenic: 172597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193973, rend_intergenic: 179779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203838, rend_intergenic: 194195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215994, rend_intergenic: 210873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support