-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_10567328-10821667

-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.21697_t
Valid prediction for GeneMark_model.21740_t
Valid prediction for snap_scaffold_5-snap.1998-T1
Valid prediction for Augustus_model.g8547.t1
Valid prediction for Augustus_model.g8551.t1
Valid prediction for snap_scaffold_5-snap.2018-T1
Valid prediction for snap_scaffold_5-snap.1995-T1
Valid prediction for Augustus_model.g8565.t1
Valid prediction for Augustus_model.g8546.t1
Valid prediction for snap_scaffold_5-snap.1999-T1
Valid prediction for snap_scaffold_5-snap.1991-T1
Valid prediction for GeneMark_model.21736_t
Valid prediction for GeneMark_model.21712_t
Valid prediction for GeneMark_model.21739_t
Valid prediction for GeneMark_model.21708_t
Valid prediction for snap_scaffold_5-snap.1986-T1
Valid prediction for GeneMark_model.21709_t
Couldn't classify 249417, 249508
Sorry, prediction pasa_asmbl_45113.p1 fails validation.
(ATG)	 GG	248532-248642	GT	CGG
(GAG)	 AG	248814-248941	GT	TGG
(GCG)	 AG	249242-249300	GT	GGG
(TTC)	 AG	249417-249508	GT	CTG
-recovered pasa_asmbl_45113.p1, initial, 248532, 248642
-recovered pasa_asmbl_45113.p1, internal, 248814, 248941
-recovered pasa_asmbl_45113.p1, internal, 249242, 249300
-recovered pasa_asmbl_45113.p1, internal, 249417, 249508
Valid prediction for snap_scaffold_5-snap.1992-T1
Valid prediction for Augustus_model.g8554.t1
Valid prediction for Augustus_model.g8553.t1
Valid prediction for Augustus_model.g8555.t1
Valid prediction for Augustus_model.g8540.t1
Valid prediction for GeneMark_model.21706_t
Valid prediction for GlimmerHMM_glimmerT_12860-T1
Valid prediction for snap_scaffold_5-snap.1990-T1
Valid prediction for CodingQuarry_transcript_52102-T1
Valid prediction for GlimmerHMM_glimmerT_12846-T1
Valid prediction for pasa_asmbl_44363.p1
Valid prediction for CodingQuarry_transcript_52103-T1
Valid prediction for snap_scaffold_5-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_12862-T1
Couldn't classify 249868, 249878
Sorry, prediction pasa_asmbl_44365.p1 fails validation.
(AAC)	 AC	249868-249878	GT	AGG
(CGC)	 AG	250076-250219	GT	AGG
(GCC)	 AG	250334-250454	GT	TGG
(GTG)	 AG	250648-250772	GT	AGG
(GGT)	 AG	250897-250957	GT	AGG
(TCA)	 AG	251045-251135	GT	AGG
(GGG)	 AG	251268-251361	GT	GTG
(AGT)	 AG	251477-251544	GT	AGG
(GTT)	 AG	251641-251722	GT	TGG
(TGG)	 AG	251840-251924	GT	TGG
(TGC)	 AG	252134-252289	CC	AAC
-recovered pasa_asmbl_44365.p1, terminal, 252134, 252289
-recovered pasa_asmbl_44365.p1, internal, 250076, 250219
-recovered pasa_asmbl_44365.p1, internal, 250334, 250454
-recovered pasa_asmbl_44365.p1, internal, 250648, 250772
-recovered pasa_asmbl_44365.p1, internal, 250897, 250957
-recovered pasa_asmbl_44365.p1, internal, 251045, 251135
-recovered pasa_asmbl_44365.p1, internal, 251268, 251361
-recovered pasa_asmbl_44365.p1, internal, 251477, 251544
-recovered pasa_asmbl_44365.p1, internal, 251641, 251722
-recovered pasa_asmbl_44365.p1, internal, 251840, 251924
Valid prediction for Augustus_model.g8544.t1
Valid prediction for GlimmerHMM_glimmerT_12844-T1
Valid prediction for GlimmerHMM_glimmerT_12853-T1
Couldn't classify 80888, 80914
Sorry, prediction pasa_asmbl_44353.p1 fails validation.
(TTT)	 TC	80888-80914	GT	ATG
(TAT)	 AG	80997-81068	GT	GGG
(AGG)	 AG	81194-81280	GT	AGG
(AAC)	 AG	81672-81809	GT	TGG
(AAC)	 AG	83202-83384	GT	GGG
(GTG)	 AG	84689-84783	GT	AAG
(TTG)	 AG	86751-86754	CT	GAC
-recovered pasa_asmbl_44353.p1, terminal, 84689, 84783
-recovered pasa_asmbl_44353.p1, terminal, 86751, 86754
-recovered pasa_asmbl_44353.p1, internal, 80997, 81068
-recovered pasa_asmbl_44353.p1, internal, 81194, 81280
-recovered pasa_asmbl_44353.p1, internal, 81672, 81809
-recovered pasa_asmbl_44353.p1, internal, 83202, 83384
-recovered pasa_asmbl_44353.p1, internal, 84689, 84783
Valid prediction for GeneMark_model.21714_t
Valid prediction for snap_scaffold_5-snap.2016-T1
Valid prediction for GeneMark_model.21725_t
Valid prediction for snap_scaffold_5-snap.1987-T1
Valid prediction for snap_scaffold_5-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_12839-T1
Valid prediction for snap_scaffold_5-snap.1980-T1
Valid prediction for HiQ_model.g8563.t1
Valid prediction for GeneMark_model.21733_t
Valid prediction for GeneMark_model.21723_t
Valid prediction for GlimmerHMM_glimmerT_12863-T1
Valid prediction for GeneMark_model.21719_t
Valid prediction for snap_scaffold_5-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_12848-T1
Valid prediction for GlimmerHMM_glimmerT_12854-T1
Valid prediction for Augustus_model.g8550.t1
Valid prediction for Augustus_model.g8561.t1
Valid prediction for GeneMark_model.21738_t
Valid prediction for snap_scaffold_5-snap.1983-T1
Valid prediction for snap_scaffold_5-snap.2002-T1
Valid prediction for snap_scaffold_5-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_12841-T1
Valid prediction for GeneMark_model.21704_t
Valid prediction for GlimmerHMM_glimmerT_12852-T1
Valid prediction for GlimmerHMM_glimmerT_12843-T1
Valid prediction for Augustus_model.g8562.t1
Valid prediction for GlimmerHMM_glimmerT_12850-T1
Valid prediction for Augustus_model.g8542.t1
Valid prediction for snap_scaffold_5-snap.2000-T1
Valid prediction for GeneMark_model.21716_t
Valid prediction for snap_scaffold_5-snap.2012-T1
Valid prediction for GeneMark_model.21699_t
Valid prediction for snap_scaffold_5-snap.2014-T1
Valid prediction for GeneMark_model.21702_t
Valid prediction for snap_scaffold_5-snap.1993-T1
Valid prediction for snap_scaffold_5-snap.1994-T1
Valid prediction for snap_scaffold_5-snap.1985-T1
Valid prediction for GeneMark_model.21727_t
Valid prediction for GeneMark_model.21743_t
Valid prediction for GeneMark_model.21711_t
Valid prediction for Augustus_model.g8548.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_5-snap.1996-T1
Valid prediction for Augustus_model.g8552.t1
Valid prediction for snap_scaffold_5-snap.1984-T1
Valid prediction for snap_scaffold_5-snap.1981-T1
Valid prediction for Augustus_model.g8559.t1
Valid prediction for snap_scaffold_5-snap.2015-T1
Valid prediction for snap_scaffold_5-snap.2011-T1
Valid prediction for GeneMark_model.21724_t
Valid prediction for snap_scaffold_5-snap.1977-T1
Valid prediction for GeneMark_model.21717_t
Valid prediction for Augustus_model.g8538.t1
Valid prediction for GlimmerHMM_glimmerT_12858-T1
Valid prediction for Augustus_model.g8549.t1
Valid prediction for HiQ_model.g8539.t1
Valid prediction for snap_scaffold_5-snap.2004-T1
Valid prediction for GeneMark_model.21730_t
Valid prediction for CodingQuarry_transcript_52100-T1
Valid prediction for HiQ_model.g8541.t1
Valid prediction for GeneMark_model.21707_t
Valid prediction for GlimmerHMM_glimmerT_12837-T1
Valid prediction for GeneMark_model.21722_t
Valid prediction for snap_scaffold_5-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_12845-T1
Valid prediction for GeneMark_model.21701_t
Valid prediction for Augustus_model.g8558.t1
Valid prediction for pasa_asmbl_45754.p1
Valid prediction for snap_scaffold_5-snap.1997-T1
Couldn't classify 72945, 73034
Sorry, prediction pasa_asmbl_45761.p1 fails validation.
(CAG)	 CC	72945-73034	GT	AGG
(GTG)	 AG	73133-73221	GT	CCG
(ACT)	 AG	74073-74503	GT	GGG
(TGT)	 AG	75257-75348	GT	TGG
(AAC)	 AG	75546-75698	GT	AGG
(GAG)	 AG	75807-76031	GA	GAG
-recovered pasa_asmbl_45761.p1, terminal, 75807, 76031
-recovered pasa_asmbl_45761.p1, internal, 73133, 73221
-recovered pasa_asmbl_45761.p1, internal, 74073, 74503
-recovered pasa_asmbl_45761.p1, internal, 75257, 75348
-recovered pasa_asmbl_45761.p1, internal, 75546, 75698
Valid prediction for snap_scaffold_5-snap.1982-T1
Valid prediction for GeneMark_model.21715_t
Valid prediction for snap_scaffold_5-snap.2017-T1
Valid prediction for snap_scaffold_5-snap.1978-T1
Valid prediction for snap_scaffold_5-snap.2007-T1
Valid prediction for snap_scaffold_5-snap.2006-T1
Valid prediction for Augustus_model.g8564.t1
Valid prediction for snap_scaffold_5-snap.2005-T1
Valid prediction for snap_scaffold_5-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_12838-T1
Valid prediction for GlimmerHMM_glimmerT_12855-T1
Valid prediction for Augustus_model.g8560.t1
Valid prediction for GeneMark_model.21703_t
Valid prediction for GeneMark_model.21710_t
Valid prediction for GlimmerHMM_glimmerT_12861-T1
Valid prediction for snap_scaffold_5-snap.2013-T1
Valid prediction for GeneMark_model.21695_t
Valid prediction for GeneMark_model.21726_t
Valid prediction for Augustus_model.g8557.t1
Valid prediction for GeneMark_model.21718_t
Valid prediction for snap_scaffold_5-snap.2008-T1
Valid prediction for GeneMark_model.21713_t
Valid prediction for GlimmerHMM_glimmerT_12859-T1
Valid prediction for CodingQuarry_transcript_52099-T1
Valid prediction for snap_scaffold_5-snap.1989-T1
Valid prediction for Augustus_model.g8545.t1
Valid prediction for GlimmerHMM_glimmerT_12842-T1
Valid prediction for GeneMark_model.21720_t
Valid prediction for GlimmerHMM_glimmerT_12847-T1
Valid prediction for GeneMark_model.21742_t
Valid prediction for GeneMark_model.21705_t
Valid prediction for GlimmerHMM_glimmerT_12840-T1
Valid prediction for pasa_asmbl_45752.p1
Valid prediction for pasa_asmbl_45756.p1
Valid prediction for GeneMark_model.21741_t
Valid prediction for GeneMark_model.21734_t
Valid prediction for GlimmerHMM_glimmerT_12856-T1
Couldn't classify 87213, 87281
Sorry, prediction pasa_asmbl_46334.p1 fails validation.
(ATG)	 TC	85032-85122	GT	AGG
(ATG)	 AG	86093-86155	GT	TGG
(GCT)	 AG	86463-86527	GT	TAG
(CAG)	 AG	87213-87281	AG	CCA
-recovered pasa_asmbl_46334.p1, initial, 85032, 85122
add_exon() Sorry, pasa_asmbl_46334.p1 86093-86155-initial-1 is invalid.
-recovered pasa_asmbl_46334.p1, initial, 86093, 86155
-recovered pasa_asmbl_46334.p1, internal, 86093, 86155
-recovered pasa_asmbl_46334.p1, internal, 86463, 86527
Valid prediction for GlimmerHMM_glimmerT_12857-T1
Couldn't classify 82945, 82980
Sorry, prediction pasa_asmbl_45759.p1 fails validation.
(ATG)	 TC	80556-80643	GT	CTG
(CAT)	 AG	81548-81673	GT	GGG
(TGT)	 AG	82087-82183	GT	AAG
(ACA)	 AG	82664-82730	GT	CTG
(GTT)	 AG	82945-82980	AA	GAA
-recovered pasa_asmbl_45759.p1, initial, 80556, 80643
-recovered pasa_asmbl_45759.p1, internal, 81548, 81673
-recovered pasa_asmbl_45759.p1, internal, 82087, 82183
-recovered pasa_asmbl_45759.p1, internal, 82664, 82730
Valid prediction for GeneMark_model.21735_t
Valid prediction for GeneMark_model.21694_t
Valid prediction for snap_scaffold_5-snap.2003-T1
Valid prediction for GeneMark_model.21737_t
Valid prediction for GeneMark_model.21731_t
Valid prediction for GeneMark_model.21732_t
Valid prediction for GeneMark_model.21700_t
Valid prediction for CodingQuarry_transcript_52101-T1
Valid prediction for GeneMark_model.21721_t
Valid prediction for Augustus_model.g8537.t1
Valid prediction for GeneMark_model.21728_t
Valid prediction for GlimmerHMM_glimmerT_12849-T1
Valid prediction for GeneMark_model.21698_t
Valid prediction for GeneMark_model.21729_t
Valid prediction for Augustus_model.g8543.t1
Valid prediction for GlimmerHMM_glimmerT_12851-T1
Valid prediction for snap_scaffold_5-snap.2009-T1
Valid prediction for GeneMark_model.21696_t
Valid prediction for HiQ_model.g8556.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 240534, rend_intergenic: 240531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44469, rend_intergenic: 42145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55230, rend_intergenic: 45283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87110, rend_intergenic: 76658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133884, rend_intergenic: 121234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201686, rend_intergenic: 194757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220347, rend_intergenic: 216668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254340
-exon list size: 696


building trellis

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73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 240534, rend_intergenic: 240531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44469, rend_intergenic: 42145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55230, rend_intergenic: 45283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87110, rend_intergenic: 76658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133884, rend_intergenic: 121234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201686, rend_intergenic: 194757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220347, rend_intergenic: 216668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support