-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_8611431-8782817

-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_57616-T1
Valid prediction for Augustus_model.g38392.t1
Valid prediction for HiQ_model.g38383.t1
Valid prediction for GeneMark_model.100437_t
Valid prediction for GlimmerHMM_glimmerT_57604-T1
Valid prediction for Augustus_model.g38384.t1
Valid prediction for snap_scaffold_26-snap.2012-T1
Valid prediction for snap_scaffold_26-snap.2023-T1
Valid prediction for snap_scaffold_26-snap.2015-T1
Valid prediction for snap_scaffold_26-snap.2016-T1
Valid prediction for snap_scaffold_26-snap.2022-T1
Valid prediction for GeneMark_model.100397_t
Valid prediction for GeneMark_model.100412_t
Valid prediction for GlimmerHMM_glimmerT_57617-T1
Valid prediction for GlimmerHMM_glimmerT_57611-T1
Valid prediction for snap_scaffold_26-snap.2008-T1
Valid prediction for GeneMark_model.100415_t
Valid prediction for GeneMark_model.100401_t
Valid prediction for GeneMark_model.100435_t
Valid prediction for GlimmerHMM_glimmerT_57602-T1
Valid prediction for GlimmerHMM_glimmerT_57615-T1
Valid prediction for snap_scaffold_26-snap.2019-T1
Valid prediction for Augustus_model.g38393.t1
Valid prediction for GeneMark_model.100408_t
Valid prediction for GeneMark_model.100405_t
Valid prediction for snap_scaffold_26-snap.2018-T1
Valid prediction for snap_scaffold_26-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_57609-T1
Valid prediction for snap_scaffold_26-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_57619-T1
Valid prediction for GeneMark_model.100430_t
Valid prediction for GeneMark_model.100419_t
Valid prediction for snap_scaffold_26-snap.1995-T1
Valid prediction for GeneMark_model.100395_t
Valid prediction for GeneMark_model.100417_t
Valid prediction for GeneMark_model.100429_t
Valid prediction for Augustus_model.g38381.t1
Valid prediction for snap_scaffold_26-snap.1998-T1
Valid prediction for GeneMark_model.100426_t
Valid prediction for GeneMark_model.100423_t
Valid prediction for snap_scaffold_26-snap.2007-T1
Valid prediction for GeneMark_model.100394_t
Couldn't classify 24536, 24589
Sorry, prediction pasa_asmbl_35709.p1 fails validation.
(ATG)	 AA	23587-23678	GT	GGG
(GAA)	 AG	23850-23956	GT	TGG
(TCA)	 AG	24224-24292	GT	AGG
(AAT)	 AG	24393-24436	GT	CAG
(CTC)	 AG	24536-24589	CA	ACC
-recovered pasa_asmbl_35709.p1, initial, 23587, 23678
-recovered pasa_asmbl_35709.p1, internal, 23850, 23956
-recovered pasa_asmbl_35709.p1, internal, 24224, 24292
-recovered pasa_asmbl_35709.p1, internal, 24393, 24436
Valid prediction for snap_scaffold_26-snap.2002-T1
Valid prediction for GeneMark_model.100410_t
Valid prediction for snap_scaffold_26-snap.1996-T1
Valid prediction for snap_scaffold_26-snap.2005-T1
Valid prediction for snap_scaffold_26-snap.1999-T1
Valid prediction for snap_scaffold_26-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_57600-T1
Valid prediction for GeneMark_model.100432_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.g38397.t1
Valid prediction for GlimmerHMM_glimmerT_57603-T1
Valid prediction for snap_scaffold_26-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_57620-T1
Valid prediction for GeneMark_model.100414_t
Valid prediction for GlimmerHMM_glimmerT_57618-T1
Valid prediction for GeneMark_model.100406_t
Valid prediction for GeneMark_model.100407_t
Valid prediction for GlimmerHMM_glimmerT_57625-T1
Valid prediction for GlimmerHMM_glimmerT_57612-T1
Valid prediction for GlimmerHMM_glimmerT_57621-T1
Valid prediction for GlimmerHMM_glimmerT_57626-T1
Valid prediction for snap_scaffold_26-snap.2000-T1
Couldn't classify 139429, 139512
Sorry, prediction pasa_asmbl_35017.p1 fails validation.
(CGG)	 CA	139429-139512	GT	AGG
(GTC)	 AG	139674-139868	GT	AGG
(GTG)	 AG	139989-140528	GA	GAG
-recovered pasa_asmbl_35017.p1, terminal, 139989, 140528
-recovered pasa_asmbl_35017.p1, internal, 139674, 139868
Valid prediction for Augustus_model.g38395.t1
Valid prediction for snap_scaffold_26-snap.1997-T1
Valid prediction for CodingQuarry_transcript_40324-T1
Valid prediction for snap_scaffold_26-snap.2001-T1
Valid prediction for GeneMark_model.100402_t
Valid prediction for Augustus_model.g38385.t1
Valid prediction for GlimmerHMM_glimmerT_57623-T1
Valid prediction for GeneMark_model.100421_t
Valid prediction for snap_scaffold_26-snap.2020-T1
Valid prediction for GeneMark_model.100433_t
Valid prediction for GeneMark_model.100418_t
Valid prediction for snap_scaffold_26-snap.2014-T1
Valid prediction for GeneMark_model.100396_t
Valid prediction for snap_scaffold_26-snap.2017-T1
Valid prediction for GeneMark_model.100420_t
Valid prediction for Augustus_model.g38399.t1
Valid prediction for GeneMark_model.100431_t
Valid prediction for GeneMark_model.100427_t
Valid prediction for GlimmerHMM_glimmerT_57613-T1
Valid prediction for snap_scaffold_26-snap.2004-T1
Valid prediction for GeneMark_model.100424_t
Valid prediction for GeneMark_model.100399_t
Valid prediction for GlimmerHMM_glimmerT_57628-T1
Valid prediction for snap_scaffold_26-snap.2003-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g38388.t1
Valid prediction for GeneMark_model.100434_t
Valid prediction for GlimmerHMM_glimmerT_57627-T1
Valid prediction for HiQ_model.g38394.t1
Valid prediction for Augustus_model.g38380.t1
Valid prediction for snap_scaffold_26-snap.2011-T1
Valid prediction for GeneMark_model.100404_t
Valid prediction for HiQ_model.g38382.t1
Valid prediction for GlimmerHMM_glimmerT_57614-T1
Valid prediction for snap_scaffold_26-snap.2027-T1
Valid prediction for snap_scaffold_26-snap.2010-T1
Valid prediction for GeneMark_model.100436_t
Valid prediction for Augustus_model.g38387.t1
Couldn't classify 147975, 148121
Sorry, prediction pasa_asmbl_35015.p1 fails validation.
(GTT)	 AC	147975-148121	GT	ATG
(AGT)	 AG	148400-148471	GT	AGG
(ACT)	 AG	148612-148728	GT	AGG
(TGG)	 AG	148839-149030	GT	TGG
(GTC)	 AG	149153-149341	GT	CGG
(GGT)	 AG	149507-149581	GT	CGG
(ATG)	 AG	149855-149962	GT	TGG
(GGT)	 AG	150077-150133	CC	GAC
-recovered pasa_asmbl_35015.p1, initial, 149855, 149962
-recovered pasa_asmbl_35015.p1, terminal, 150077, 150133
-recovered pasa_asmbl_35015.p1, internal, 148400, 148471
-recovered pasa_asmbl_35015.p1, internal, 148612, 148728
-recovered pasa_asmbl_35015.p1, internal, 148839, 149030
-recovered pasa_asmbl_35015.p1, internal, 149153, 149341
-recovered pasa_asmbl_35015.p1, internal, 149507, 149581
-recovered pasa_asmbl_35015.p1, internal, 149855, 149962
Valid prediction for Augustus_model.g38398.t1
Valid prediction for Augustus_model.g38396.t1
Valid prediction for snap_scaffold_26-snap.2024-T1
Valid prediction for snap_scaffold_26-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_57624-T1
Valid prediction for GlimmerHMM_glimmerT_57606-T1
Valid prediction for GlimmerHMM_glimmerT_57610-T1
Valid prediction for snap_scaffold_26-snap.1993-T1
Valid prediction for GeneMark_model.100425_t
Valid prediction for GlimmerHMM_glimmerT_57607-T1
Valid prediction for pasa_asmbl_35019.p1
Valid prediction for Augustus_model.g38389.t1
Valid prediction for GlimmerHMM_glimmerT_57608-T1
Valid prediction for GlimmerHMM_glimmerT_57601-T1
Valid prediction for snap_scaffold_26-snap.2013-T1
Valid prediction for GeneMark_model.100398_t
Valid prediction for GeneMark_model.100411_t
Valid prediction for GlimmerHMM_glimmerT_57622-T1
Valid prediction for GeneMark_model.100422_t
Valid prediction for GeneMark_model.100400_t
Valid prediction for GeneMark_model.100413_t
Valid prediction for Augustus_model.g38386.t1
Valid prediction for Augustus_model.g38390.t1
Valid prediction for GeneMark_model.100403_t
Valid prediction for GeneMark_model.100428_t
Valid prediction for Augustus_model.g38391.t1
Valid prediction for snap_scaffold_26-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_57605-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16055, rend_intergenic: 7551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45952, rend_intergenic: 44516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155464, rend_intergenic: 133667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166787, rend_intergenic: 157663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171387
-exon list size: 527


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 16055, rend_intergenic: 7551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45952, rend_intergenic: 44516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155464, rend_intergenic: 133667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166787, rend_intergenic: 157663  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 20 predictions persist after filtering for low support