-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_7685229-7866773

-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.100219_t
Valid prediction for GeneMark_model.100221_t
Valid prediction for Augustus_model.g38294.t1
Valid prediction for snap_scaffold_26-snap.1833-T1
Valid prediction for Augustus_model.g38305.t1
Valid prediction for snap_scaffold_26-snap.1831-T1
Valid prediction for snap_scaffold_26-snap.1840-T1
Valid prediction for snap_scaffold_26-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_57493-T1
Valid prediction for Augustus_model.g38303.t1
Valid prediction for Augustus_model.g38295.t1
Valid prediction for GeneMark_model.100209_t
Valid prediction for GeneMark_model.100211_t
Couldn't classify 101990, 102119
Couldn't classify 103020, 103212
Sorry, prediction pasa_asmbl_35675.p1 fails validation.
(AAC)	 AG	101990-102119	GT	AGG
(AAT)	 AG	102629-102764	GT	GGG
(AAA)	 AG	103020-103212	AG	TGA
-recovered pasa_asmbl_35675.p1, internal, 101990, 102119
-recovered pasa_asmbl_35675.p1, internal, 102629, 102764
Valid prediction for GlimmerHMM_glimmerT_57482-T1
Couldn't classify 89257, 89463
Couldn't classify 93273, 93319
Sorry, prediction pasa_asmbl_35673.p1 fails validation.
(CCC)	 CC	89257-89463	GT	CAG
(CAG)	 AG	92351-92531	GT	AGG
(GTG)	 AG	93273-93319	GG	CTG
-recovered pasa_asmbl_35673.p1, internal, 92351, 92531
Valid prediction for GeneMark_model.100236_t
Valid prediction for GlimmerHMM_glimmerT_57475-T1
Valid prediction for GeneMark_model.100250_t
Valid prediction for GeneMark_model.100246_t
Valid prediction for GeneMark_model.100242_t
Valid prediction for snap_scaffold_26-snap.1823-T1
Valid prediction for snap_scaffold_26-snap.1854-T1
Valid prediction for snap_scaffold_26-snap.1821-T1
Valid prediction for Augustus_model.g38308.t1
Valid prediction for snap_scaffold_26-snap.1841-T1
Couldn't classify 174328, 174422
Couldn't classify 178223, 178318
Sorry, prediction pasa_asmbl_35677.p1 fails validation.
(TAC)	 TG	174328-174422	GT	ATG
(CAA)	 AG	176459-176610	GT	AGG
(GTT)	 AG	176720-176780	GT	CAG
(GGG)	 AG	176911-177051	GT	CAG
(GAC)	 AG	177464-177577	GT	CTG
(GAT)	 AG	177910-178084	GT	TGG
(GTG)	 AG	178223-178318	GG	TAG
-recovered pasa_asmbl_35677.p1, internal, 176459, 176610
-recovered pasa_asmbl_35677.p1, internal, 176720, 176780
-recovered pasa_asmbl_35677.p1, internal, 176911, 177051
-recovered pasa_asmbl_35677.p1, internal, 177464, 177577
-recovered pasa_asmbl_35677.p1, internal, 177910, 178084
Valid prediction for snap_scaffold_26-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_57491-T1
Valid prediction for Augustus_model.g38296.t1
Valid prediction for GeneMark_model.100215_t
Valid prediction for GeneMark_model.100214_t
Valid prediction for snap_scaffold_26-snap.1814-T1
Valid prediction for snap_scaffold_26-snap.1844-T1
Valid prediction for GeneMark_model.100230_t
Valid prediction for GlimmerHMM_glimmerT_57465-T1
Valid prediction for GeneMark_model.100248_t
Valid prediction for GlimmerHMM_glimmerT_57479-T1
Valid prediction for snap_scaffold_26-snap.1847-T1
Valid prediction for snap_scaffold_26-snap.1845-T1
Valid prediction for GeneMark_model.100217_t
Valid prediction for GeneMark_model.100222_t
Valid prediction for GlimmerHMM_glimmerT_57481-T1
Valid prediction for Augustus_model.g38299.t1
Valid prediction for GeneMark_model.100238_t
Valid prediction for GlimmerHMM_glimmerT_57471-T1
Valid prediction for GlimmerHMM_glimmerT_57486-T1
Valid prediction for Augustus_model.g38301.t1
Valid prediction for snap_scaffold_26-snap.1816-T1
Valid prediction for GeneMark_model.100244_t
Valid prediction for snap_scaffold_26-snap.1818-T1
Valid prediction for GeneMark_model.100224_t
Valid prediction for GlimmerHMM_glimmerT_57468-T1
Valid prediction for snap_scaffold_26-snap.1837-T1
Valid prediction for snap_scaffold_26-snap.1836-T1
Valid prediction for GeneMark_model.100231_t
Valid prediction for GlimmerHMM_glimmerT_57472-T1
Valid prediction for snap_scaffold_26-snap.1812-T1
Valid prediction for snap_scaffold_26-snap.1853-T1
Valid prediction for GeneMark_model.100254_t
Valid prediction for snap_scaffold_26-snap.1832-T1
Valid prediction for snap_scaffold_26-snap.1826-T1
Valid prediction for CodingQuarry_transcript_40311-T1
Valid prediction for GlimmerHMM_glimmerT_57487-T1
Valid prediction for Augustus_model.g38309.t1
Valid prediction for snap_scaffold_26-snap.1843-T1
Valid prediction for snap_scaffold_26-snap.1839-T1
Valid prediction for Augustus_model.g38306.t1
Valid prediction for GlimmerHMM_glimmerT_57488-T1
Valid prediction for GlimmerHMM_glimmerT_57492-T1
Valid prediction for GeneMark_model.100255_t
Valid prediction for GeneMark_model.100252_t
Valid prediction for GeneMark_model.100233_t
Valid prediction for snap_scaffold_26-snap.1849-T1
Valid prediction for GeneMark_model.100245_t
Valid prediction for GeneMark_model.100235_t
Valid prediction for GlimmerHMM_glimmerT_57473-T1
Valid prediction for GeneMark_model.100240_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.100210_t
Valid prediction for snap_scaffold_26-snap.1846-T1
Valid prediction for GeneMark_model.100237_t
Valid prediction for GeneMark_model.100212_t
Valid prediction for snap_scaffold_26-snap.1828-T1
Valid prediction for Augustus_model.g38300.t1
Valid prediction for Augustus_model.g38302.t1
Valid prediction for GlimmerHMM_glimmerT_57480-T1
Valid prediction for snap_scaffold_26-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_57477-T1
Valid prediction for snap_scaffold_26-snap.1811-T1
Valid prediction for snap_scaffold_26-snap.1825-T1
Valid prediction for snap_scaffold_26-snap.1822-T1
Valid prediction for GeneMark_model.100216_t
Valid prediction for snap_scaffold_26-snap.1835-T1
Valid prediction for GeneMark_model.100220_t
Valid prediction for GeneMark_model.100208_t
Valid prediction for GeneMark_model.100213_t
Valid prediction for Augustus_model.g38310.t1
Couldn't classify 140053, 140400
Sorry, prediction pasa_asmbl_35664.p1 fails validation.
(ACT)	 AA	140053-140400	TG	AGT
Valid prediction for GeneMark_model.100241_t
Valid prediction for snap_scaffold_26-snap.1850-T1
Valid prediction for GeneMark_model.100256_t
Valid prediction for GlimmerHMM_glimmerT_57476-T1
Valid prediction for GeneMark_model.100251_t
Valid prediction for snap_scaffold_26-snap.1827-T1
Valid prediction for GeneMark_model.100229_t
Valid prediction for GlimmerHMM_glimmerT_57467-T1
Valid prediction for GeneMark_model.100228_t
Valid prediction for GlimmerHMM_glimmerT_57478-T1
Valid prediction for snap_scaffold_26-snap.1824-T1
Valid prediction for Augustus_model.g38304.t1
Valid prediction for snap_scaffold_26-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_57489-T1
Valid prediction for snap_scaffold_26-snap.1851-T1
Valid prediction for GeneMark_model.100249_t
Valid prediction for GeneMark_model.100226_t
Valid prediction for GeneMark_model.100253_t
Valid prediction for GeneMark_model.100247_t
Valid prediction for GlimmerHMM_glimmerT_57485-T1
Valid prediction for GeneMark_model.100234_t
Valid prediction for snap_scaffold_26-snap.1829-T1
Valid prediction for GeneMark_model.100227_t
Valid prediction for snap_scaffold_26-snap.1830-T1
Valid prediction for snap_scaffold_26-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_57470-T1
Valid prediction for Augustus_model.g38307.t1
Valid prediction for GeneMark_model.100223_t
Valid prediction for snap_scaffold_26-snap.1820-T1
Valid prediction for GeneMark_model.100232_t
Valid prediction for Augustus_model.g38297.t1
Valid prediction for GeneMark_model.100239_t
Valid prediction for Augustus_model.g38298.t1
Valid prediction for GeneMark_model.100218_t
Valid prediction for GeneMark_model.100225_t
Valid prediction for GlimmerHMM_glimmerT_57484-T1
Valid prediction for snap_scaffold_26-snap.1842-T1
Valid prediction for snap_scaffold_26-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_57466-T1
Valid prediction for GlimmerHMM_glimmerT_57490-T1
Valid prediction for GlimmerHMM_glimmerT_57483-T1
Valid prediction for GlimmerHMM_glimmerT_57474-T1
Valid prediction for GlimmerHMM_glimmerT_57469-T1
Valid prediction for GeneMark_model.100243_t
Valid prediction for snap_scaffold_26-snap.1852-T1
Valid prediction for snap_scaffold_26-snap.1848-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4847, rend_intergenic: 3131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6974, rend_intergenic: 4967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54547, rend_intergenic: 49575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69243, rend_intergenic: 59628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83522, rend_intergenic: 71583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85495, rend_intergenic: 83571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88499, rend_intergenic: 86846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98634, rend_intergenic: 92207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132204, rend_intergenic: 128831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148832, rend_intergenic: 142706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156386, rend_intergenic: 149480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179977, rend_intergenic: 171544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181545
-exon list size: 727


building trellis

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96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 4847, rend_intergenic: 3131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6974, rend_intergenic: 4967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54547, rend_intergenic: 49575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69243, rend_intergenic: 59628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83522, rend_intergenic: 71583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85495, rend_intergenic: 83571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88499, rend_intergenic: 86846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98634, rend_intergenic: 92207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132204, rend_intergenic: 128831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148832, rend_intergenic: 142706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156386, rend_intergenic: 149480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179977, rend_intergenic: 171544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support