-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_2701523-2924240

-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 Augustus_model.g36593.t1
Valid prediction for snap_scaffold_26-snap.586-T1
Valid prediction for snap_scaffold_26-snap.567-T1
Valid prediction for Augustus_model.g36584.t1
Valid prediction for snap_scaffold_26-snap.537-T1
Valid prediction for Augustus_model.g36589.t1
Valid prediction for Augustus_model.g36587.t1
Valid prediction for pasa_asmbl_34756.p1
Valid prediction for GlimmerHMM_glimmerT_55248-T1
Valid prediction for GlimmerHMM_glimmerT_55260-T1
Valid prediction for GlimmerHMM_glimmerT_55244-T1
Valid prediction for Augustus_model.g36582.t1
Valid prediction for snap_scaffold_26-snap.547-T1
Valid prediction for snap_scaffold_26-snap.539-T1
Valid prediction for GlimmerHMM_glimmerT_55240-T1
Valid prediction for Augustus_model.g36586.t1
Valid prediction for snap_scaffold_26-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_55242-T1
Valid prediction for snap_scaffold_26-snap.574-T1
Valid prediction for snap_scaffold_26-snap.546-T1
Valid prediction for snap_scaffold_26-snap.555-T1
Valid prediction for GlimmerHMM_glimmerT_55256-T1
Valid prediction for GlimmerHMM_glimmerT_55262-T1
Valid prediction for snap_scaffold_26-snap.575-T1
Valid prediction for Augustus_model.g36583.t1
Valid prediction for snap_scaffold_26-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_55239-T1
Valid prediction for Augustus_model.g36585.t1
Valid prediction for GlimmerHMM_glimmerT_55258-T1
Valid prediction for snap_scaffold_26-snap.576-T1
Valid prediction for snap_scaffold_26-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_55245-T1
Valid prediction for snap_scaffold_26-snap.573-T1
Valid prediction for snap_scaffold_26-snap.557-T1
Valid prediction for snap_scaffold_26-snap.563-T1
Valid prediction for Augustus_model.g36592.t1
Couldn't classify 81187, 81355
Sorry, prediction pasa_asmbl_34754.p1 fails validation.
(ATG)	 CC	76694-76794	GT	AGG
(GGG)	 AG	78403-78436	GT	CGG
(GTT)	 AG	78757-78816	GT	TGG
(GGA)	 AG	79277-79348	GT	AGG
(TGT)	 AG	79586-79736	GT	AGG
(TCT)	 AG	80417-80431	GT	AGG
(ACA)	 AG	80645-80769	GT	TGG
(TCT)	 AG	80880-80971	GT	ACG
(GGT)	 AG	81187-81355	GA	GGG
-recovered pasa_asmbl_34754.p1, initial, 76694, 76794
-recovered pasa_asmbl_34754.p1, internal, 78403, 78436
-recovered pasa_asmbl_34754.p1, internal, 78757, 78816
-recovered pasa_asmbl_34754.p1, internal, 79277, 79348
-recovered pasa_asmbl_34754.p1, internal, 79586, 79736
-recovered pasa_asmbl_34754.p1, internal, 80417, 80431
-recovered pasa_asmbl_34754.p1, internal, 80645, 80769
-recovered pasa_asmbl_34754.p1, internal, 80880, 80971
Valid prediction for snap_scaffold_26-snap.549-T1
Couldn't classify 53402, 53465
Couldn't classify 53841, 53987
Sorry, prediction pasa_asmbl_34752.p1 fails validation.
(CTG)	 CT	53402-53465	GT	ATG
(ATG)	 AG	53602-53723	GT	CAG
(GTG)	 AG	53841-53987	AT	GCA
add_exon() Sorry, pasa_asmbl_34752.p1 53602-53723-initial-1 is invalid.
-recovered pasa_asmbl_34752.p1, initial, 53602, 53723
-recovered pasa_asmbl_34752.p1, internal, 53602, 53723
Valid prediction for GlimmerHMM_glimmerT_55243-T1
Valid prediction for Augustus_model.g36588.t1
Valid prediction for GlimmerHMM_glimmerT_55246-T1
Valid prediction for snap_scaffold_26-snap.570-T1
Valid prediction for snap_scaffold_26-snap.583-T1
Valid prediction for snap_scaffold_26-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_55274-T1
Valid prediction for GlimmerHMM_glimmerT_55257-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 Augustus_model.g36604.t1
Valid prediction for GlimmerHMM_glimmerT_55259-T1
Valid prediction for GlimmerHMM_glimmerT_55273-T1
Valid prediction for Augustus_model.g36596.t1
Valid prediction for snap_scaffold_26-snap.578-T1
Valid prediction for Augustus_model.g36601.t1
Valid prediction for snap_scaffold_26-snap.554-T1
Valid prediction for Augustus_model.g36603.t1
Valid prediction for GlimmerHMM_glimmerT_55250-T1
Valid prediction for GlimmerHMM_glimmerT_55241-T1
Valid prediction for snap_scaffold_26-snap.564-T1
Couldn't classify 125255, 125281
Sorry, prediction CodingQuarry_transcript_40261-T1 fails validation.
(ATG)	 AC	125031-125141	GT	CAG
(TGT)	 TG	125255-125281	GT	AGG
-recovered CodingQuarry_transcript_40261-T1, initial, 125031, 125141
Couldn't classify 64693, 64774
Sorry, prediction Augustus_model.g36599.t1 fails validation.
(ATG)	 AC	52785-52836	GT	AGG
(TTT)	 AG	53111-53156	GT	AAG
(GTC)	 AG	55786-55932	GT	CGG
(GGC)	 AG	56284-56374	GT	AGG
(GAG)	 AG	58345-58440	GT	TTG
(ATA)	 AG	58663-58740	GT	TGG
(GAG)	 AG	59144-59259	GT	CGG
(GGA)	 AG	60188-60256	GT	CAG
(GAC)	 AG	60468-60546	GT	AGG
(CGT)	 AG	61169-61242	GT	AGG
(ATA)	 AG	62799-63087	GT	AGG
(ATA)	 AG	63646-63783	GT	AGG
(GAG)	 AG	64036-64183	GT	GGG
(GTG)	 AG	64693-64774	GT	AGG
-recovered Augustus_model.g36599.t1, initial, 52785, 52836
-recovered Augustus_model.g36599.t1, internal, 53111, 53156
-recovered Augustus_model.g36599.t1, internal, 55786, 55932
-recovered Augustus_model.g36599.t1, internal, 56284, 56374
-recovered Augustus_model.g36599.t1, internal, 58345, 58440
-recovered Augustus_model.g36599.t1, internal, 58663, 58740
-recovered Augustus_model.g36599.t1, internal, 59144, 59259
-recovered Augustus_model.g36599.t1, internal, 60188, 60256
-recovered Augustus_model.g36599.t1, internal, 60468, 60546
-recovered Augustus_model.g36599.t1, internal, 61169, 61242
-recovered Augustus_model.g36599.t1, internal, 62799, 63087
-recovered Augustus_model.g36599.t1, internal, 63646, 63783
-recovered Augustus_model.g36599.t1, internal, 64036, 64183
-recovered Augustus_model.g36599.t1, internal, 64693, 64774
Valid prediction for GlimmerHMM_glimmerT_55254-T1
Valid prediction for GlimmerHMM_glimmerT_55267-T1
Valid prediction for GlimmerHMM_glimmerT_55263-T1
Valid prediction for GlimmerHMM_glimmerT_55272-T1
Valid prediction for snap_scaffold_26-snap.558-T1
Valid prediction for snap_scaffold_26-snap.559-T1
Valid prediction for snap_scaffold_26-snap.572-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.551-T1
Valid prediction for GlimmerHMM_glimmerT_55249-T1
Valid prediction for GlimmerHMM_glimmerT_55270-T1
Valid prediction for snap_scaffold_26-snap.548-T1
Valid prediction for snap_scaffold_26-snap.571-T1
Valid prediction for snap_scaffold_26-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_55268-T1
Valid prediction for GlimmerHMM_glimmerT_55264-T1
Valid prediction for GlimmerHMM_glimmerT_55251-T1
Valid prediction for snap_scaffold_26-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_55247-T1
Valid prediction for snap_scaffold_26-snap.550-T1
Valid prediction for Augustus_model.g36600.t1
Valid prediction for snap_scaffold_26-snap.584-T1
Valid prediction for Augustus_model.g36595.t1
Valid prediction for snap_scaffold_26-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_55261-T1
Couldn't classify 108757, 108813
Sorry, prediction pasa_asmbl_35447.p1 fails validation.
(CCT)	 CT	108757-108813	GT	TGG
(GTG)	 AG	109261-109337	GT	CCG
(GGC)	 AG	109807-110056	GT	TGG
(AAC)	 AG	110363-110610	GT	AGG
(GCA)	 AG	111663-111810	GT	AGG
(ATC)	 AG	112582-112732	GT	TGG
(GTA)	 AG	113370-113446	GT	AGG
(TCT)	 AG	114794-114901	CG	AAC
-recovered pasa_asmbl_35447.p1, terminal, 114794, 114901
-recovered pasa_asmbl_35447.p1, internal, 109261, 109337
-recovered pasa_asmbl_35447.p1, internal, 109807, 110056
-recovered pasa_asmbl_35447.p1, internal, 110363, 110610
-recovered pasa_asmbl_35447.p1, internal, 111663, 111810
-recovered pasa_asmbl_35447.p1, internal, 112582, 112732
-recovered pasa_asmbl_35447.p1, internal, 113370, 113446
Valid prediction for snap_scaffold_26-snap.581-T1
Valid prediction for snap_scaffold_26-snap.553-T1
Valid prediction for Augustus_model.g36594.t1
Valid prediction for snap_scaffold_26-snap.565-T1
Valid prediction for snap_scaffold_26-snap.552-T1
Valid prediction for Augustus_model.g36591.t1
Couldn't classify 124878, 124917
Couldn't classify 125282, 125428
Sorry, prediction pasa_asmbl_35837.p1 fails validation.
(GCC)	 AT	124878-124917	GT	ATG
(ATG)	 AG	125020-125141	GT	CAG
(GTG)	 AG	125282-125428	AT	GCA
add_exon() Sorry, pasa_asmbl_35837.p1 125020-125141-initial-1 is invalid.
-recovered pasa_asmbl_35837.p1, initial, 125020, 125141
-recovered pasa_asmbl_35837.p1, internal, 125020, 125141
Valid prediction for snap_scaffold_26-snap.577-T1
Valid prediction for snap_scaffold_26-snap.541-T1
Valid prediction for Augustus_model.g36602.t1
Valid prediction for snap_scaffold_26-snap.568-T1
Couldn't classify 108623, 108684
Sorry, prediction pasa_asmbl_35448.p1 fails validation.
(ATG)	 CG	95358-95381	GT	CGG
(ACG)	 AG	95802-95899	GT	AGG
(TCT)	 AG	97058-97121	GT	TGG
(TAC)	 AG	97415-97459	GT	AGG
(ACT)	 AG	100432-100494	GT	AGG
(CAC)	 AG	100710-100814	GT	GCG
(CAA)	 AG	103334-103520	GT	AGG
(AGC)	 AG	103978-103994	GT	CAG
(AGT)	 AG	106400-106507	GT	ACG
(GAC)	 AG	106635-106688	GT	AGG
(GAC)	 AG	106829-106981	GT	TGG
(CGT)	 AG	108321-108459	GT	TAG
(CCG)	 AG	108623-108684	CC	TGC
-recovered pasa_asmbl_35448.p1, initial, 95358, 95381
-recovered pasa_asmbl_35448.p1, internal, 95802, 95899
-recovered pasa_asmbl_35448.p1, internal, 97058, 97121
-recovered pasa_asmbl_35448.p1, internal, 97415, 97459
-recovered pasa_asmbl_35448.p1, internal, 100432, 100494
-recovered pasa_asmbl_35448.p1, internal, 100710, 100814
-recovered pasa_asmbl_35448.p1, internal, 103334, 103520
-recovered pasa_asmbl_35448.p1, internal, 103978, 103994
-recovered pasa_asmbl_35448.p1, internal, 106400, 106507
-recovered pasa_asmbl_35448.p1, internal, 106635, 106688
-recovered pasa_asmbl_35448.p1, internal, 106829, 106981
-recovered pasa_asmbl_35448.p1, internal, 108321, 108459
Valid prediction for pasa_asmbl_35444.p1
Valid prediction for Augustus_model.g36597.t1
Valid prediction for GlimmerHMM_glimmerT_55252-T1
Valid prediction for GlimmerHMM_glimmerT_55253-T1
Valid prediction for snap_scaffold_26-snap.540-T1
Valid prediction for Augustus_model.g36598.t1
Valid prediction for GlimmerHMM_glimmerT_55269-T1
Valid prediction for snap_scaffold_26-snap.542-T1
Valid prediction for snap_scaffold_26-snap.561-T1
Valid prediction for snap_scaffold_26-snap.556-T1
Valid prediction for CodingQuarry_transcript_40260-T1
Valid prediction for snap_scaffold_26-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_55266-T1
Valid prediction for snap_scaffold_26-snap.545-T1
Valid prediction for snap_scaffold_26-snap.585-T1
Valid prediction for Augustus_model.g36590.t1
Valid prediction for GlimmerHMM_glimmerT_55271-T1
Valid prediction for snap_scaffold_26-snap.562-T1
Valid prediction for snap_scaffold_26-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_55265-T1
Valid prediction for GlimmerHMM_glimmerT_55255-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37737, rend_intergenic: 5563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43058, rend_intergenic: 37923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46447, rend_intergenic: 45872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54913, rend_intergenic: 52286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68177, rend_intergenic: 66302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74389, rend_intergenic: 68191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90241, rend_intergenic: 78931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98612, rend_intergenic: 96253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118951, rend_intergenic: 101232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127361, rend_intergenic: 119138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148887, rend_intergenic: 128556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169560, rend_intergenic: 150180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174588, rend_intergenic: 170679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199115, rend_intergenic: 182912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200450, rend_intergenic: 199977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205060, rend_intergenic: 200728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219768, rend_intergenic: 205294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222718
-exon list size: 508


building trellis

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82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 37737, rend_intergenic: 5563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43058, rend_intergenic: 37923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46447, rend_intergenic: 45872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54913, rend_intergenic: 52286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68177, rend_intergenic: 66302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74389, rend_intergenic: 68191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90241, rend_intergenic: 78931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98612, rend_intergenic: 96253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118951, rend_intergenic: 101232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127361, rend_intergenic: 119138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148887, rend_intergenic: 128556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169560, rend_intergenic: 150180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174588, rend_intergenic: 170679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199115, rend_intergenic: 182912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200450, rend_intergenic: 199977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205060, rend_intergenic: 200728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219768, rend_intergenic: 205294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support