-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_8841891-9053609

-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 snap_scaffold_4-snap.1868-T1
Valid prediction for snap_scaffold_4-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_10038-T1
Valid prediction for GeneMark_model.16329_t
Valid prediction for snap_scaffold_4-snap.1882-T1
Valid prediction for Augustus_model.g6597.t1
Valid prediction for GlimmerHMM_glimmerT_10037-T1
Valid prediction for snap_scaffold_4-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_10049-T1
Valid prediction for GeneMark_model.16324_t
Valid prediction for GlimmerHMM_glimmerT_10059-T1
Valid prediction for GlimmerHMM_glimmerT_10054-T1
Valid prediction for Augustus_model.g6587.t1
Valid prediction for GeneMark_model.16304_t
Couldn't classify 101816, 101923
Couldn't classify 105153, 105317
Sorry, prediction pasa_asmbl_42928.p1 fails validation.
(ACC)	 GA	101816-101923	GT	AGG
(CCA)	 AG	104310-104378	GT	AGG
(ACC)	 AG	105153-105317	AG	CCA
-recovered pasa_asmbl_42928.p1, internal, 104310, 104378
Valid prediction for GeneMark_model.16307_t
Valid prediction for GeneMark_model.16334_t
Valid prediction for snap_scaffold_4-snap.1867-T1
Valid prediction for snap_scaffold_4-snap.1877-T1
Valid prediction for snap_scaffold_4-snap.1892-T1
Valid prediction for CodingQuarry_transcript_48987-T1
Valid prediction for GlimmerHMM_glimmerT_10060-T1
Valid prediction for snap_scaffold_4-snap.1848-T1
Valid prediction for pasa_asmbl_42921.p1
Valid prediction for GeneMark_model.16301_t
Valid prediction for GeneMark_model.16315_t
Valid prediction for GeneMark_model.16303_t
Valid prediction for Augustus_model.g6601.t1
Valid prediction for snap_scaffold_4-snap.1864-T1
Couldn't classify 26769, 26808
Sorry, prediction pasa_asmbl_42925.p1 fails validation.
(TCT)	 AC	26769-26808	GT	AGG
(GCC)	 AG	26953-27136	GT	AGG
(GCT)	 AG	27475-27643	GT	AGG
(GTG)	 AG	28011-28149	GT	TAG
(GCC)	 AG	28470-28681	CG	GAC
-recovered pasa_asmbl_42925.p1, terminal, 28470, 28681
-recovered pasa_asmbl_42925.p1, internal, 26953, 27136
-recovered pasa_asmbl_42925.p1, internal, 27475, 27643
-recovered pasa_asmbl_42925.p1, internal, 28011, 28149
Valid prediction for snap_scaffold_4-snap.1873-T1
Valid prediction for CodingQuarry_transcript_48988-T1
Valid prediction for snap_scaffold_4-snap.1891-T1
Valid prediction for Augustus_model.g6595.t1
Valid prediction for Augustus_model.g6588.t1
Valid prediction for snap_scaffold_4-snap.1875-T1
Valid prediction for Augustus_model.g6594.t1
Valid prediction for snap_scaffold_4-snap.1872-T1
Valid prediction for GeneMark_model.16332_t
Valid prediction for pasa_asmbl_42932.p1
Valid prediction for Augustus_model.g6585.t1
Valid prediction for Augustus_model.g6584.t1
Valid prediction for Augustus_model.g6600.t1
Valid prediction for GeneMark_model.16323_t
Valid prediction for snap_scaffold_4-snap.1852-T1
Valid prediction for GeneMark_model.16335_t
Valid prediction for GlimmerHMM_glimmerT_10058-T1
Valid prediction for GlimmerHMM_glimmerT_10055-T1
Valid prediction for snap_scaffold_4-snap.1857-T1
Valid prediction for snap_scaffold_4-snap.1853-T1
Valid prediction for snap_scaffold_4-snap.1886-T1
Valid prediction for GeneMark_model.16314_t
Valid prediction for snap_scaffold_4-snap.1889-T1
Valid prediction for GeneMark_model.16333_t
Valid prediction for GlimmerHMM_glimmerT_10043-T1
Valid prediction for GeneMark_model.16319_t
Valid prediction for GeneMark_model.16338_t
Valid prediction for GeneMark_model.16321_t
Valid prediction for snap_scaffold_4-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_10046-T1
Valid prediction for GeneMark_model.16302_t
Valid prediction for snap_scaffold_4-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_10048-T1
Valid prediction for GeneMark_model.16327_t
Valid prediction for GeneMark_model.16313_t
Valid prediction for GlimmerHMM_glimmerT_10047-T1
Valid prediction for snap_scaffold_4-snap.1863-T1
Couldn't classify 99392, 99498
Couldn't classify 100305, 100325
Sorry, prediction pasa_asmbl_43591.p1 fails validation.
(GCC)	 AT	99392-99498	GT	TCG
(GGA)	 AG	99670-99865	GT	AGG
(GCC)	 AG	99988-100065	GT	GGG
(GTT)	 AG	100305-100325	TG	ACT
-recovered pasa_asmbl_43591.p1, internal, 99670, 99865
-recovered pasa_asmbl_43591.p1, internal, 99988, 100065
Valid prediction for GeneMark_model.16316_t
Valid prediction for GlimmerHMM_glimmerT_10035-T1
Valid prediction for snap_scaffold_4-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_10056-T1
Valid prediction for Augustus_model.g6593.t1
Valid prediction for GlimmerHMM_glimmerT_10044-T1
Valid prediction for GlimmerHMM_glimmerT_10045-T1
Valid prediction for HiQ_model.g6596.t1
Valid prediction for CodingQuarry_transcript_48989-T1
Couldn't classify 139555, 139714
Couldn't classify 142433, 142554
Sorry, prediction pasa_asmbl_42933.p1 fails validation.
(GGT)	 CA	139555-139714	GT	TGG
(TCA)	 AG	139836-139990	GT	AGG
(GGT)	 AG	140102-140230	GT	GAG
(CTG)	 AG	140379-140573	GT	AGG
(GAA)	 AG	141601-141730	GT	AGG
(GAG)	 AG	142094-142267	GT	CGG
(CCC)	 AG	142433-142554	AG	GCA
-recovered pasa_asmbl_42933.p1, internal, 139836, 139990
-recovered pasa_asmbl_42933.p1, internal, 140102, 140230
-recovered pasa_asmbl_42933.p1, internal, 140379, 140573
-recovered pasa_asmbl_42933.p1, internal, 141601, 141730
-recovered pasa_asmbl_42933.p1, internal, 142094, 142267
Valid prediction for Augustus_model.g6586.t1
Valid prediction for GlimmerHMM_glimmerT_10050-T1
Valid prediction for GeneMark_model.16308_t
Valid prediction for Augustus_model.g6589.t1
Valid prediction for GeneMark_model.16325_t
Valid prediction for GeneMark_model.16306_t
Valid prediction for snap_scaffold_4-snap.1847-T1
Valid prediction for snap_scaffold_4-snap.1854-T1
Valid prediction for snap_scaffold_4-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_10057-T1
Valid prediction for snap_scaffold_4-snap.1865-T1
Couldn't classify 24640, 24763
Couldn't classify 25524, 25708
Sorry, prediction pasa_asmbl_42924.p2 fails validation.
(TGG)	 GC	24640-24763	GT	TGG
(TTG)	 AG	25350-25373	GT	AGG
(GCC)	 AG	25524-25708	GG	CAG
-recovered pasa_asmbl_42924.p2, internal, 25350, 25373
Valid prediction for GeneMark_model.16331_t
Valid prediction for CodingQuarry_transcript_48984-T1
Valid prediction for GlimmerHMM_glimmerT_10034-T1
Valid prediction for snap_scaffold_4-snap.1851-T1
Valid prediction for Augustus_model.g6602.t1
Valid prediction for GeneMark_model.16336_t
Valid prediction for GeneMark_model.16311_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 Augustus_model.g6592.t1
Valid prediction for Augustus_model.g6604.t1
Valid prediction for snap_scaffold_4-snap.1866-T1
Valid prediction for Augustus_model.g6603.t1
Valid prediction for snap_scaffold_4-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_10051-T1
Valid prediction for snap_scaffold_4-snap.1876-T1
Valid prediction for GeneMark_model.16326_t
Valid prediction for pasa_asmbl_41534.p1
Valid prediction for snap_scaffold_4-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_10041-T1
Valid prediction for GlimmerHMM_glimmerT_10053-T1
Valid prediction for snap_scaffold_4-snap.1870-T1
Valid prediction for GeneMark_model.16337_t
Valid prediction for CodingQuarry_transcript_48985-T1
Valid prediction for snap_scaffold_4-snap.1883-T1
Valid prediction for snap_scaffold_4-snap.1895-T1
Valid prediction for snap_scaffold_4-snap.1884-T1
Valid prediction for snap_scaffold_4-snap.1885-T1
Valid prediction for GeneMark_model.16312_t
Valid prediction for GeneMark_model.16305_t
Valid prediction for Augustus_model.g6598.t1
Valid prediction for snap_scaffold_4-snap.1893-T1
Valid prediction for GeneMark_model.16317_t
Valid prediction for GlimmerHMM_glimmerT_10040-T1
Valid prediction for GlimmerHMM_glimmerT_10061-T1
Valid prediction for GeneMark_model.16318_t
Valid prediction for GlimmerHMM_glimmerT_10042-T1
Valid prediction for GlimmerHMM_glimmerT_10039-T1
Valid prediction for GeneMark_model.16320_t
Valid prediction for snap_scaffold_4-snap.1860-T1
Valid prediction for snap_scaffold_4-snap.1888-T1
Valid prediction for snap_scaffold_4-snap.1879-T1
Valid prediction for pasa_asmbl_41535.p1
Valid prediction for HiQ_model.g6591.t1
Valid prediction for snap_scaffold_4-snap.1861-T1
Valid prediction for snap_scaffold_4-snap.1880-T1
Valid prediction for Augustus_model.g6599.t1
Valid prediction for Augustus_model.g6590.t1
Valid prediction for snap_scaffold_4-snap.1858-T1
Valid prediction for CodingQuarry_transcript_48986-T1
Valid prediction for GeneMark_model.16322_t
Valid prediction for GlimmerHMM_glimmerT_10036-T1
Valid prediction for GlimmerHMM_glimmerT_10052-T1
Valid prediction for snap_scaffold_4-snap.1881-T1
Valid prediction for GeneMark_model.16310_t
Valid prediction for GeneMark_model.16328_t
Valid prediction for GeneMark_model.16330_t
Valid prediction for GeneMark_model.16309_t
Valid prediction for snap_scaffold_4-snap.1859-T1
Valid prediction for snap_scaffold_4-snap.1850-T1
Valid prediction for snap_scaffold_4-snap.1874-T1
Valid prediction for snap_scaffold_4-snap.1887-T1
Valid prediction for snap_scaffold_4-snap.1856-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24553, rend_intergenic: 22167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52805, rend_intergenic: 51297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75015, rend_intergenic: 71204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89875, rend_intergenic: 85509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123110, rend_intergenic: 119013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133895, rend_intergenic: 129503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 139570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164017, rend_intergenic: 159099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211719
-exon list size: 607


building trellis

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99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 24553, rend_intergenic: 22167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52805, rend_intergenic: 51297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75015, rend_intergenic: 71204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89875, rend_intergenic: 85509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123110, rend_intergenic: 119013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133895, rend_intergenic: 129503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 139570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164017, rend_intergenic: 159099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support