-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_10703673-10874208

-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.56376_t
Valid prediction for Augustus_model.g22191.t1
Valid prediction for GeneMark_model.56380_t
Valid prediction for GeneMark_model.56367_t
Valid prediction for snap_scaffold_13-snap.1988-T1
Valid prediction for GeneMark_model.56360_t
Valid prediction for GeneMark_model.56378_t
Valid prediction for GeneMark_model.56384_t
Valid prediction for Augustus_model.g22200.t1
Valid prediction for Augustus_model.g22193.t1
Valid prediction for snap_scaffold_13-snap.2013-T1
Valid prediction for GeneMark_model.56379_t
Valid prediction for GeneMark_model.56387_t
Valid prediction for GeneMark_model.56372_t
Valid prediction for GeneMark_model.56370_t
Valid prediction for GeneMark_model.56363_t
Valid prediction for snap_scaffold_13-snap.2004-T1
Valid prediction for Augustus_model.g22204.t1
Valid prediction for GlimmerHMM_glimmerT_33035-T1
Valid prediction for Augustus_model.g22196.t1
Valid prediction for snap_scaffold_13-snap.1987-T1
Couldn't classify 95358, 95520
Sorry, prediction pasa_asmbl_11653.p1 fails validation.
(ACC)	 TG	95358-95520	GT	AGG
(ACC)	 AG	97888-98151	GT	AGG
(AAA)	 AG	98574-98704	GT	AGG
(GCT)	 AG	98949-99087	GT	AGG
(TGG)	 AG	99399-99550	GT	TGG
(GTG)	 AG	99889-99985	GT	GGG
(GTC)	 AG	100143-100307	GT	AGG
(GCG)	 AG	100662-100825	GT	ACG
(GGA)	 AG	101554-101640	AG	AGA
-recovered pasa_asmbl_11653.p1, terminal, 101554, 101640
-recovered pasa_asmbl_11653.p1, internal, 97888, 98151
-recovered pasa_asmbl_11653.p1, internal, 98574, 98704
-recovered pasa_asmbl_11653.p1, internal, 98949, 99087
-recovered pasa_asmbl_11653.p1, internal, 99399, 99550
-recovered pasa_asmbl_11653.p1, internal, 99889, 99985
-recovered pasa_asmbl_11653.p1, internal, 100143, 100307
-recovered pasa_asmbl_11653.p1, internal, 100662, 100825
Valid prediction for GeneMark_model.56362_t
Valid prediction for GlimmerHMM_glimmerT_33045-T1
Valid prediction for GeneMark_model.56365_t
Valid prediction for GeneMark_model.56369_t
Valid prediction for snap_scaffold_13-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_33041-T1
Valid prediction for GlimmerHMM_glimmerT_33037-T1
Valid prediction for snap_scaffold_13-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_33056-T1
Valid prediction for GeneMark_model.56382_t
Valid prediction for GlimmerHMM_glimmerT_33050-T1
Valid prediction for snap_scaffold_13-snap.1982-T1
Valid prediction for GlimmerHMM_glimmerT_33046-T1
Valid prediction for GlimmerHMM_glimmerT_33039-T1
Valid prediction for snap_scaffold_13-snap.1994-T1
Couldn't classify 87617, 88025
Couldn't classify 92026, 92114
Sorry, prediction pasa_asmbl_11236.p1 fails validation.
(GCC)	 CA	87617-88025	GT	AGG
(GTG)	 AG	88231-88605	GT	AGG
(TTC)	 AG	90742-91005	GT	AGG
(AGG)	 AG	91736-91918	GT	AGG
(GTT)	 AG	92026-92114	GG	CTG
add_exon() Sorry, pasa_asmbl_11236.p1 91736-91918-terminal-1 is invalid.
-recovered pasa_asmbl_11236.p1, terminal, 91736, 91918
-recovered pasa_asmbl_11236.p1, internal, 88231, 88605
-recovered pasa_asmbl_11236.p1, internal, 90742, 91005
-recovered pasa_asmbl_11236.p1, internal, 91736, 91918
Valid prediction for snap_scaffold_13-snap.2002-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.56394_t
Valid prediction for snap_scaffold_13-snap.2012-T1
Valid prediction for snap_scaffold_13-snap.2008-T1
Valid prediction for GeneMark_model.56371_t
Valid prediction for GeneMark_model.56359_t
Valid prediction for GeneMark_model.56377_t
Valid prediction for snap_scaffold_13-snap.1985-T1
Valid prediction for snap_scaffold_13-snap.1980-T1
Valid prediction for GeneMark_model.56390_t
Valid prediction for snap_scaffold_13-snap.1977-T1
Valid prediction for GlimmerHMM_glimmerT_33054-T1
Valid prediction for GeneMark_model.56392_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: -)Couldn't classify 155285, 155373
Couldn't classify 158400, 158549
Sorry, prediction pasa_asmbl_10021.p1 fails validation.
(CAT)	 GA	155285-155373	GT	AAG
(GTC)	 AG	157207-157340	GT	GGG
(AGA)	 AG	157619-157821	GT	TGG
(GCC)	 AG	158029-158091	GT	AGG
(GTG)	 AG	158400-158549	TA	GGT
-recovered pasa_asmbl_10021.p1, internal, 157207, 157340
-recovered pasa_asmbl_10021.p1, internal, 157619, 157821
-recovered pasa_asmbl_10021.p1, internal, 158029, 158091
Valid prediction for snap_scaffold_13-snap.2000-T1
Couldn't classify 102004, 102087
Sorry, prediction pasa_asmbl_10025.p1 fails validation.
(ATG)	 GA	100748-100966	GT	AGG
(GGT)	 AG	101802-101909	GT	AGG
(ATT)	 AG	102004-102087	AT	ACA
-recovered pasa_asmbl_10025.p1, initial, 100748, 100966
-recovered pasa_asmbl_10025.p1, internal, 101802, 101909
Valid prediction for GeneMark_model.56393_t
Valid prediction for CodingQuarry_transcript_13200-T1
Valid prediction for snap_scaffold_13-snap.1978-T1
Valid prediction for Augustus_model.g22190.t1
Valid prediction for GeneMark_model.56361_t
Valid prediction for GlimmerHMM_glimmerT_33049-T1
Valid prediction for GeneMark_model.56391_t
Valid prediction for snap_scaffold_13-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_33048-T1
Valid prediction for GeneMark_model.56375_t
Valid prediction for pasa_asmbl_10026.p1
Valid prediction for GeneMark_model.56389_t
Valid prediction for GeneMark_model.56358_t
Valid prediction for GlimmerHMM_glimmerT_33047-T1
Valid prediction for GeneMark_model.56388_t
Valid prediction for Augustus_model.g22194.t1
Valid prediction for snap_scaffold_13-snap.1991-T1
Valid prediction for Augustus_model.g22201.t1
Valid prediction for snap_scaffold_13-snap.1976-T1
Valid prediction for snap_scaffold_13-snap.2015-T1
Valid prediction for snap_scaffold_13-snap.1992-T1
Valid prediction for GeneMark_model.56383_t
Valid prediction for HiQ_model.g22199.t1
Valid prediction for snap_scaffold_13-snap.1989-T1
Valid prediction for GeneMark_model.56386_t
Valid prediction for snap_scaffold_13-snap.2014-T1
Valid prediction for snap_scaffold_13-snap.1986-T1
Valid prediction for snap_scaffold_13-snap.2011-T1
Valid prediction for snap_scaffold_13-snap.2001-T1
Valid prediction for HiQ_model.g22198.t1
Valid prediction for GeneMark_model.56364_t
Valid prediction for GeneMark_model.56374_t
Valid prediction for GeneMark_model.56381_t
Valid prediction for GeneMark_model.56368_t
Valid prediction for snap_scaffold_13-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_33057-T1
Valid prediction for snap_scaffold_13-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_33051-T1
Couldn't classify 102696, 102739
Couldn't classify 103473, 103526
Sorry, prediction pasa_asmbl_10024.p1 fails validation.
(TTT)	 AC	102696-102739	GT	AAG
(AAC)	 AG	102849-102944	GT	ATG
(GTA)	 AG	103155-103353	GT	AGG
(GGT)	 AG	103473-103526	CA	TCC
-recovered pasa_asmbl_10024.p1, internal, 102849, 102944
-recovered pasa_asmbl_10024.p1, internal, 103155, 103353
Valid prediction for GlimmerHMM_glimmerT_33052-T1
Valid prediction for Augustus_model.g22202.t1
Valid prediction for GlimmerHMM_glimmerT_33036-T1
Valid prediction for GeneMark_model.56366_t
Valid prediction for GlimmerHMM_glimmerT_33040-T1
Valid prediction for GlimmerHMM_glimmerT_33058-T1
Valid prediction for snap_scaffold_13-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_33044-T1
Valid prediction for snap_scaffold_13-snap.1983-T1
Valid prediction for Augustus_model.g22205.t1
Valid prediction for snap_scaffold_13-snap.1990-T1
Valid prediction for Augustus_model.g22192.t1
Valid prediction for snap_scaffold_13-snap.2006-T1
Valid prediction for snap_scaffold_13-snap.1998-T1
Valid prediction for CodingQuarry_transcript_13199-T1
Valid prediction for snap_scaffold_13-snap.1981-T1
Valid prediction for snap_scaffold_13-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_33038-T1
Valid prediction for Augustus_model.g22195.t1
Valid prediction for GlimmerHMM_glimmerT_33053-T1
Valid prediction for snap_scaffold_13-snap.1995-T1
Valid prediction for snap_scaffold_13-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_33055-T1
Valid prediction for GeneMark_model.56373_t
Couldn't classify 94673, 94753
Sorry, prediction pasa_asmbl_10027.p1 fails validation.
(CTT)	 AC	94673-94753	GT	AGG
(GCT)	 AG	95008-95172	GT	AGG
(GAA)	 AG	95587-95769	TG	GAT
-recovered pasa_asmbl_10027.p1, terminal, 95587, 95769
-recovered pasa_asmbl_10027.p1, internal, 95008, 95172
Valid prediction for GlimmerHMM_glimmerT_33059-T1
Valid prediction for Augustus_model.g22206.t1
Valid prediction for GeneMark_model.56385_t
Valid prediction for Augustus_model.g22203.t1
Valid prediction for snap_scaffold_13-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_33043-T1
Valid prediction for snap_scaffold_13-snap.2007-T1
Valid prediction for snap_scaffold_13-snap.1999-T1
Valid prediction for Augustus_model.g22197.t1
Valid prediction for GlimmerHMM_glimmerT_33042-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10098, rend_intergenic: 5429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12964, rend_intergenic: 11013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22549, rend_intergenic: 18512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27699, rend_intergenic: 24447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37962, rend_intergenic: 37629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45037, rend_intergenic: 40297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93250, rend_intergenic: 91684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97972, rend_intergenic: 96616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132179, rend_intergenic: 130758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141185, rend_intergenic: 140157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145813, rend_intergenic: 142316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170536
-exon list size: 491


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10098, rend_intergenic: 5429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12964, rend_intergenic: 11013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22549, rend_intergenic: 18512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27699, rend_intergenic: 24447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37962, rend_intergenic: 37629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45037, rend_intergenic: 40297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93250, rend_intergenic: 91684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97972, rend_intergenic: 96616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132179, rend_intergenic: 130758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141185, rend_intergenic: 140157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145813, rend_intergenic: 142316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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