-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_8780799-9015905

-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.100468_t
Valid prediction for GlimmerHMM_glimmerT_57629-T1
Valid prediction for GlimmerHMM_glimmerT_57636-T1
Valid prediction for snap_scaffold_26-snap.2039-T1
Valid prediction for snap_scaffold_26-snap.2062-T1
Valid prediction for GeneMark_model.100473_t
Valid prediction for GeneMark_model.100464_t
Valid prediction for CodingQuarry_transcript_40327-T1
Valid prediction for snap_scaffold_26-snap.2037-T1
Valid prediction for GeneMark_model.100467_t
Valid prediction for GeneMark_model.100472_t
Valid prediction for snap_scaffold_26-snap.2054-T1
Valid prediction for GeneMark_model.100446_t
Valid prediction for GlimmerHMM_glimmerT_57630-T1
Valid prediction for GeneMark_model.100448_t
Valid prediction for GeneMark_model.100466_t
Valid prediction for snap_scaffold_26-snap.2061-T1
Valid prediction for GeneMark_model.100450_t
Valid prediction for GeneMark_model.100458_t
Valid prediction for GlimmerHMM_glimmerT_57647-T1
Valid prediction for Augustus_model.g38400.t1
Valid prediction for GeneMark_model.100462_t
Valid prediction for snap_scaffold_26-snap.2055-T1
Valid prediction for CodingQuarry_transcript_40328-T1
Valid prediction for snap_scaffold_26-snap.2029-T1
Valid prediction for Augustus_model.g38407.t1
Valid prediction for GeneMark_model.100443_t
Valid prediction for GlimmerHMM_glimmerT_57639-T1
Valid prediction for GeneMark_model.100457_t
Valid prediction for pasa_asmbl_35714.p1
Valid prediction for snap_scaffold_26-snap.2040-T1
Valid prediction for HiQ_model.g38412.t1
Valid prediction for snap_scaffold_26-snap.2028-T1
Valid prediction for pasa_asmbl_35716.p1
Valid prediction for Augustus_model.g38411.t1
Valid prediction for GlimmerHMM_glimmerT_57652-T1
Valid prediction for GlimmerHMM_glimmerT_57649-T1
Valid prediction for GlimmerHMM_glimmerT_57631-T1
Valid prediction for snap_scaffold_26-snap.2057-T1
Valid prediction for GeneMark_model.100440_t
Valid prediction for GlimmerHMM_glimmerT_57656-T1
Valid prediction for snap_scaffold_26-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_57653-T1
Valid prediction for GlimmerHMM_glimmerT_57633-T1
Valid prediction for Augustus_model.g38402.t1
Valid prediction for snap_scaffold_26-snap.2035-T1
Valid prediction for Augustus_model.g38409.t1
Valid prediction for snap_scaffold_26-snap.2044-T1
Valid prediction for HiQ_model.g38410.t1
Valid prediction for snap_scaffold_26-snap.2056-T1
Valid prediction for GeneMark_model.100452_t
Valid prediction for GeneMark_model.100445_t
Valid prediction for snap_scaffold_26-snap.2033-T1
Valid prediction for GlimmerHMM_glimmerT_57637-T1
Valid prediction for snap_scaffold_26-snap.2060-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_26-snap.2065-T1
Valid prediction for Augustus_model.g38413.t1
Valid prediction for snap_scaffold_26-snap.2046-T1
Valid prediction for pasa_asmbl_35023.p1
Valid prediction for snap_scaffold_26-snap.2049-T1
Valid prediction for GeneMark_model.100454_t
Valid prediction for GlimmerHMM_glimmerT_57638-T1
Valid prediction for GeneMark_model.100438_t
Valid prediction for snap_scaffold_26-snap.2063-T1
Valid prediction for CodingQuarry_transcript_40330-T1
Valid prediction for snap_scaffold_26-snap.2047-T1
Valid prediction for snap_scaffold_26-snap.2048-T1
Valid prediction for Augustus_model.g38415.t1
Valid prediction for GlimmerHMM_glimmerT_57645-T1
Valid prediction for Augustus_model.g38414.t1
Valid prediction for Augustus_model.g38403.t1
Valid prediction for Augustus_model.g38401.t1
Valid prediction for GlimmerHMM_glimmerT_57640-T1
Valid prediction for GeneMark_model.100447_t
Valid prediction for GeneMark_model.100455_t
Valid prediction for GeneMark_model.100453_t
Valid prediction for snap_scaffold_26-snap.2058-T1
Valid prediction for GlimmerHMM_glimmerT_57646-T1
Valid prediction for snap_scaffold_26-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_57651-T1
Valid prediction for GeneMark_model.100456_t
Valid prediction for GeneMark_model.100449_t
Valid prediction for GeneMark_model.100444_t
Valid prediction for GeneMark_model.100463_t
Valid prediction for Augustus_model.g38405.t1
Valid prediction for Augustus_model.g38404.t1
Valid prediction for snap_scaffold_26-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_57654-T1
Valid prediction for snap_scaffold_26-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_57635-T1
Valid prediction for CodingQuarry_transcript_40329-T1
Couldn't classify 14336, 14349
Couldn't classify 15175, 15297
Sorry, prediction pasa_asmbl_35026.p1 fails validation.
(GCG)	 CG	14336-14349	GT	GAG
(CTA)	 AG	14529-14575	GT	CAG
(ACA)	 AG	14930-15048	GT	TGG
(GCG)	 AG	15175-15297	AG	ACA
-recovered pasa_asmbl_35026.p1, internal, 14529, 14575
-recovered pasa_asmbl_35026.p1, internal, 14930, 15048
Valid prediction for GlimmerHMM_glimmerT_57644-T1
Valid prediction for Augustus_model.g38406.t1
Valid prediction for snap_scaffold_26-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_57632-T1
Valid prediction for snap_scaffold_26-snap.2043-T1
Valid prediction for snap_scaffold_26-snap.2041-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.2052-T1
Valid prediction for GeneMark_model.100451_t
Valid prediction for GlimmerHMM_glimmerT_57650-T1
Valid prediction for GeneMark_model.100441_t
Valid prediction for GlimmerHMM_glimmerT_57648-T1
Valid prediction for GeneMark_model.100461_t
Valid prediction for GlimmerHMM_glimmerT_57641-T1
Valid prediction for snap_scaffold_26-snap.2045-T1
Valid prediction for snap_scaffold_26-snap.2036-T1
Valid prediction for GeneMark_model.100459_t
Valid prediction for snap_scaffold_26-snap.2038-T1
Valid prediction for GeneMark_model.100471_t
Valid prediction for GlimmerHMM_glimmerT_57643-T1
Valid prediction for GeneMark_model.100442_t
Valid prediction for snap_scaffold_26-snap.2059-T1
Valid prediction for snap_scaffold_26-snap.2067-T1
Valid prediction for Augustus_model.g38408.t1
Valid prediction for snap_scaffold_26-snap.2064-T1
Valid prediction for GeneMark_model.100465_t
Couldn't classify 6846, 6923
Sorry, prediction pasa_asmbl_35027.p1 fails validation.
(CCA)	 TG	6846-6923	GT	TGG
(CTT)	 AG	7303-7411	GT	TGG
(ACA)	 AG	7615-7698	GT	GGG
(GTG)	 AG	7795-7904	GT	AGG
(GAG)	 AG	7995-8127	GT	AGG
(ATG)	 AG	8205-8359	GT	GGG
(GTG)	 AG	8436-8530	GT	AGG
(ACA)	 AG	8647-8720	GT	ATG
(TGT)	 AG	8820-8932	TG	AGT
add_exon() Sorry, pasa_asmbl_35027.p1 8205-8359-initial-1 is invalid.
-recovered pasa_asmbl_35027.p1, initial, 8205, 8359
-recovered pasa_asmbl_35027.p1, terminal, 8820, 8932
-recovered pasa_asmbl_35027.p1, internal, 7303, 7411
-recovered pasa_asmbl_35027.p1, internal, 7615, 7698
-recovered pasa_asmbl_35027.p1, internal, 7795, 7904
-recovered pasa_asmbl_35027.p1, internal, 7995, 8127
-recovered pasa_asmbl_35027.p1, internal, 8205, 8359
-recovered pasa_asmbl_35027.p1, internal, 8436, 8530
-recovered pasa_asmbl_35027.p1, internal, 8647, 8720
Valid prediction for snap_scaffold_26-snap.2042-T1
Valid prediction for CodingQuarry_transcript_40326-T1
Valid prediction for GeneMark_model.100470_t
Valid prediction for snap_scaffold_26-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_57642-T1
Valid prediction for GeneMark_model.100460_t
Valid prediction for snap_scaffold_26-snap.2032-T1
Valid prediction for GlimmerHMM_glimmerT_57655-T1
Valid prediction for snap_scaffold_26-snap.2053-T1
Valid prediction for GeneMark_model.100469_t
Valid prediction for GlimmerHMM_glimmerT_57634-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11083, rend_intergenic: 8681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20475, rend_intergenic: 17932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31296, rend_intergenic: 31182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36499, rend_intergenic: 35202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38095, rend_intergenic: 36803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235107
-exon list size: 475


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11083, rend_intergenic: 8681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20475, rend_intergenic: 17932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31296, rend_intergenic: 31182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36499, rend_intergenic: 35202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38095, rend_intergenic: 36803  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