-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_10693345-10896646

-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_13-snap.1982-T1
Valid prediction for snap_scaffold_13-snap.2002-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32305-T1
Valid prediction for snap_scaffold_13-snap.2013-T1
Couldn't classify 105686, 105848
Sorry, prediction pasa_asmbl_11647.p1 fails validation.
(ACC)	 TG	105686-105848	GT	AGG
(ACC)	 AG	108216-108479	GT	AGG
(AAA)	 AG	108902-109032	GT	AGG
(GCT)	 AG	109277-109415	GT	AGG
(TGG)	 AG	109727-109878	GT	TGG
(GTG)	 AG	110217-110313	GT	GGG
(GTC)	 AG	110471-110635	GT	AGG
(GCG)	 AG	110990-111153	GT	ACG
(GGA)	 AG	111882-111968	AG	AGA
-recovered pasa_asmbl_11647.p1, terminal, 111882, 111968
-recovered pasa_asmbl_11647.p1, internal, 108216, 108479
-recovered pasa_asmbl_11647.p1, internal, 108902, 109032
-recovered pasa_asmbl_11647.p1, internal, 109277, 109415
-recovered pasa_asmbl_11647.p1, internal, 109727, 109878
-recovered pasa_asmbl_11647.p1, internal, 110217, 110313
-recovered pasa_asmbl_11647.p1, internal, 110471, 110635
-recovered pasa_asmbl_11647.p1, internal, 110990, 111153
Couldn't classify 97945, 98353
Couldn't classify 102354, 102442
Sorry, prediction pasa_asmbl_11250.p1 fails validation.
(GCC)	 CA	97945-98353	GT	AGG
(GTG)	 AG	98559-98933	GT	AGG
(TTC)	 AG	101070-101333	GT	AGG
(AGG)	 AG	102064-102246	GT	AGG
(GTT)	 AG	102354-102442	GG	CTG
add_exon() Sorry, pasa_asmbl_11250.p1 102064-102246-terminal-1 is invalid.
-recovered pasa_asmbl_11250.p1, terminal, 102064, 102246
-recovered pasa_asmbl_11250.p1, internal, 98559, 98933
-recovered pasa_asmbl_11250.p1, internal, 101070, 101333
-recovered pasa_asmbl_11250.p1, internal, 102064, 102246
Valid prediction for GlimmerHMM_glimmerT_32318-T1
Valid prediction for snap_scaffold_13-snap.1984-T1
Valid prediction for snap_scaffold_13-snap.2018-T1
Valid prediction for Augustus_model.g21578.t1
Valid prediction for snap_scaffold_13-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_32326-T1
Valid prediction for GlimmerHMM_glimmerT_32314-T1
Valid prediction for GlimmerHMM_glimmerT_32311-T1
Valid prediction for snap_scaffold_13-snap.1990-T1
Valid prediction for snap_scaffold_13-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_32307-T1
Valid prediction for snap_scaffold_13-snap.1995-T1
Valid prediction for snap_scaffold_13-snap.1989-T1
Valid prediction for Augustus_model.g21570.t1
Valid prediction for GlimmerHMM_glimmerT_32320-T1
Valid prediction for snap_scaffold_13-snap.2004-T1
Valid prediction for Augustus_model.g21574.t1
Valid prediction for snap_scaffold_13-snap.2016-T1
Valid prediction for Augustus_model.g21565.t1
Valid prediction for snap_scaffold_13-snap.1987-T1
Valid prediction for Augustus_model.g21567.t1
Valid prediction for snap_scaffold_13-snap.1998-T1
Valid prediction for snap_scaffold_13-snap.1978-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2017-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: -)Couldn't classify 125134, 125177
Couldn't classify 125911, 125964
Sorry, prediction pasa_asmbl_10064.p1 fails validation.
(TTT)	 AC	125134-125177	GT	AAG
(AAC)	 AG	125287-125382	GT	ATG
(GTA)	 AG	125593-125791	GT	AGG
(GGT)	 AG	125911-125964	CA	TCC
-recovered pasa_asmbl_10064.p1, internal, 125287, 125382
-recovered pasa_asmbl_10064.p1, internal, 125593, 125791
Valid prediction for snap_scaffold_13-snap.2011-T1
Valid prediction for HiQ_model.g21572.t1
Valid prediction for Augustus_model.g21566.t1
Valid prediction for GlimmerHMM_glimmerT_32316-T1
Valid prediction for snap_scaffold_13-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_32325-T1
Valid prediction for snap_scaffold_13-snap.1981-T1
Valid prediction for snap_scaffold_13-snap.2009-T1
Valid prediction for snap_scaffold_13-snap.2015-T1
Valid prediction for Augustus_model.g21569.t1
Valid prediction for Augustus_model.g21580.t1
Couldn't classify 124442, 124525
Sorry, prediction pasa_asmbl_10065.p1 fails validation.
(ATG)	 GA	123186-123404	GT	AGG
(GGT)	 AG	124240-124347	GT	AGG
(ATT)	 AG	124442-124525	AT	ACA
-recovered pasa_asmbl_10065.p1, initial, 123186, 123404
-recovered pasa_asmbl_10065.p1, internal, 124240, 124347
Valid prediction for snap_scaffold_13-snap.2006-T1
Valid prediction for snap_scaffold_13-snap.1979-T1
Valid prediction for Augustus_model.g21575.t1
Valid prediction for snap_scaffold_13-snap.1980-T1
Valid prediction for pasa_asmbl_10066.p1
Couldn't classify 177723, 177811
Couldn't classify 180838, 180987
Sorry, prediction pasa_asmbl_10061.p1 fails validation.
(CAT)	 GA	177723-177811	GT	AAG
(GTC)	 AG	179645-179778	GT	GGG
(AGA)	 AG	180057-180259	GT	TGG
(GCC)	 AG	180467-180529	GT	AGG
(GTG)	 AG	180838-180987	TA	GGT
-recovered pasa_asmbl_10061.p1, internal, 179645, 179778
-recovered pasa_asmbl_10061.p1, internal, 180057, 180259
-recovered pasa_asmbl_10061.p1, internal, 180467, 180529
Valid prediction for snap_scaffold_13-snap.1996-T1
Valid prediction for HiQ_model.g21573.t1
Valid prediction for Augustus_model.g21576.t1
Valid prediction for snap_scaffold_13-snap.1999-T1
Valid prediction for Augustus_model.g21563.t1
Valid prediction for snap_scaffold_13-snap.1986-T1
Valid prediction for snap_scaffold_13-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_32319-T1
Valid prediction for CodingQuarry_transcript_13231-T1
Valid prediction for GlimmerHMM_glimmerT_32308-T1
Valid prediction for snap_scaffold_13-snap.1997-T1
Valid prediction for snap_scaffold_13-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_32323-T1
Valid prediction for snap_scaffold_13-snap.2000-T1
Valid prediction for CodingQuarry_transcript_13232-T1
Valid prediction for snap_scaffold_13-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_32303-T1
Valid prediction for GlimmerHMM_glimmerT_32313-T1
Couldn't classify 117111, 117191
Sorry, prediction pasa_asmbl_10067.p1 fails validation.
(CTT)	 AC	117111-117191	GT	AGG
(GCT)	 AG	117446-117610	GT	AGG
(GAA)	 AG	118025-118207	TG	GAT
-recovered pasa_asmbl_10067.p1, terminal, 118025, 118207
-recovered pasa_asmbl_10067.p1, internal, 117446, 117610
Valid prediction for Augustus_model.g21568.t1
Valid prediction for GlimmerHMM_glimmerT_32304-T1
Valid prediction for Augustus_model.g21564.t1
Valid prediction for Augustus_model.g21579.t1
Valid prediction for GlimmerHMM_glimmerT_32322-T1
Valid prediction for GlimmerHMM_glimmerT_32306-T1
Valid prediction for snap_scaffold_13-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_32309-T1
Valid prediction for GlimmerHMM_glimmerT_32324-T1
Valid prediction for GlimmerHMM_glimmerT_32317-T1
Valid prediction for GlimmerHMM_glimmerT_32310-T1
Valid prediction for Augustus_model.g21577.t1
Valid prediction for snap_scaffold_13-snap.1994-T1
Valid prediction for snap_scaffold_13-snap.2003-T1
Valid prediction for snap_scaffold_13-snap.1977-T1
Valid prediction for snap_scaffold_13-snap.2014-T1
Valid prediction for snap_scaffold_13-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_32315-T1
Valid prediction for snap_scaffold_13-snap.1993-T1
Valid prediction for Augustus_model.g21571.t1
Valid prediction for GlimmerHMM_glimmerT_32312-T1
Valid prediction for snap_scaffold_13-snap.1988-T1
Valid prediction for Augustus_model.g21581.t1
Valid prediction for snap_scaffold_13-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_32321-T1
Valid prediction for snap_scaffold_13-snap.1991-T1
Valid prediction for snap_scaffold_13-snap.1983-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15065, rend_intergenic: 12087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23292, rend_intergenic: 15237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32533, rend_intergenic: 28840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38027, rend_intergenic: 34775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44277, rend_intergenic: 41260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48290, rend_intergenic: 47957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53478, rend_intergenic: 50625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103578, rend_intergenic: 102012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108300, rend_intergenic: 105587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142507, rend_intergenic: 140329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151513, rend_intergenic: 150485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156141, rend_intergenic: 152644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203302
-exon list size: 320


building trellis

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42.5    
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43.5    
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44.4    
44.7    
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45.3    
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46.6    
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48.4    
48.8    
49.1    
49.4    
49.7    
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50.6    
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64.3    
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86.6    
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89.4    
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94.4    
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95.0    
95.3    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 15065, rend_intergenic: 12087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23292, rend_intergenic: 15237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32533, rend_intergenic: 28840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38027, rend_intergenic: 34775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44277, rend_intergenic: 41260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48290, rend_intergenic: 47957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53478, rend_intergenic: 50625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103578, rend_intergenic: 102012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108300, rend_intergenic: 105587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142507, rend_intergenic: 140329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151513, rend_intergenic: 150485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156141, rend_intergenic: 152644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 192760 - 203302
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support