-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_13126478-13318619

-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.g10878.t1
Valid prediction for GeneMark_model.26947_t
Valid prediction for Augustus_model.g10868.t1
Valid prediction for GlimmerHMM_glimmerT_16133-T1
Valid prediction for GlimmerHMM_glimmerT_16128-T1
Valid prediction for HiQ_model.g10865.t1
Valid prediction for GlimmerHMM_glimmerT_16136-T1
Valid prediction for HiQ_model.g10862.t1
Valid prediction for CodingQuarry_transcript_55147-T1
Valid prediction for snap_scaffold_6-snap.2756-T1
Valid prediction for HiQ_model.g10873.t1
Valid prediction for GlimmerHMM_glimmerT_16126-T1
Valid prediction for pasa_asmbl_47441.p1
Valid prediction for GlimmerHMM_glimmerT_16141-T1
Valid prediction for snap_scaffold_6-snap.2773-T1
Couldn't classify 101247, 101247
Sorry, prediction CodingQuarry_transcript_55145-T1 fails validation.
(AGT)	 CC	101247-101247	GT	CAG
(TGC)	 AG	101496-101605	GT	AGG
(ATC)	 AG	101865-101994	GT	CGG
(GGA)	 AG	102494-102616	GT	TGG
(GCC)	 AG	102907-103021	GT	ACG
(GGA)	 AG	103146-103246	GT	AGG
(GAG)	 AG	103627-103762	GT	AGG
(GGG)	 AG	103911-103950	TC	GAT
-recovered CodingQuarry_transcript_55145-T1, terminal, 103911, 103950
-recovered CodingQuarry_transcript_55145-T1, internal, 101496, 101605
-recovered CodingQuarry_transcript_55145-T1, internal, 101865, 101994
-recovered CodingQuarry_transcript_55145-T1, internal, 102494, 102616
-recovered CodingQuarry_transcript_55145-T1, internal, 102907, 103021
-recovered CodingQuarry_transcript_55145-T1, internal, 103146, 103246
-recovered CodingQuarry_transcript_55145-T1, internal, 103627, 103762
Valid prediction for GeneMark_model.26939_t
Valid prediction for CodingQuarry_transcript_55140-T1
Valid prediction for GeneMark_model.26931_t
Valid prediction for Augustus_model.g10877.t1
Valid prediction for snap_scaffold_6-snap.2759-T1
Valid prediction for GeneMark_model.26949_t
Couldn't classify 69752, 70118
Sorry, prediction pasa_asmbl_47428.p1 fails validation.
(CGT)	 CA	69752-70118	GT	GCG
(ATT)	 AG	70240-70314	GT	ATG
(TCA)	 AG	70636-70814	GT	AGG
(ACA)	 AG	73332-73385	GT	CGG
(ATC)	 AG	73606-73770	GT	TGG
(TCC)	 AG	74613-74702	GT	AGG
(ATA)	 AG	74915-75055	GT	AGG
(GAG)	 AG	75243-75336	GT	CAG
(GTT)	 AG	75672-75822	GT	AGG
(CCA)	 AG	77684-77838	GT	AGG
(TGG)	 AG	78190-78254	TA	GAT
-recovered pasa_asmbl_47428.p1, terminal, 78190, 78254
-recovered pasa_asmbl_47428.p1, internal, 70240, 70314
-recovered pasa_asmbl_47428.p1, internal, 70636, 70814
-recovered pasa_asmbl_47428.p1, internal, 73332, 73385
-recovered pasa_asmbl_47428.p1, internal, 73606, 73770
-recovered pasa_asmbl_47428.p1, internal, 74613, 74702
-recovered pasa_asmbl_47428.p1, internal, 74915, 75055
-recovered pasa_asmbl_47428.p1, internal, 75243, 75336
-recovered pasa_asmbl_47428.p1, internal, 75672, 75822
-recovered pasa_asmbl_47428.p1, internal, 77684, 77838
Valid prediction for Augustus_model.g10851.t1
Valid prediction for snap_scaffold_6-snap.2753-T1
Valid prediction for GeneMark_model.26933_t
Valid prediction for snap_scaffold_6-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_16124-T1
Valid prediction for snap_scaffold_6-snap.2768-T1
Valid prediction for snap_scaffold_6-snap.2775-T1
Couldn't classify 64030, 64148
Sorry, prediction pasa_asmbl_47425.p1 fails validation.
(AAG)	 CC	64030-64148	GT	AGG
(CGT)	 AG	64396-64465	GT	AGG
(AAA)	 AG	64895-64966	GT	AGG
(GAA)	 AG	65218-65361	GT	AGG
(GAG)	 AG	66326-66415	GT	AGG
(ATG)	 AG	66613-66750	GT	AGG
(CCT)	 AG	67170-67928	CA	GAC
-recovered pasa_asmbl_47425.p1, initial, 66613, 66750
-recovered pasa_asmbl_47425.p1, terminal, 67170, 67928
-recovered pasa_asmbl_47425.p1, internal, 64396, 64465
-recovered pasa_asmbl_47425.p1, internal, 64895, 64966
-recovered pasa_asmbl_47425.p1, internal, 65218, 65361
-recovered pasa_asmbl_47425.p1, internal, 66326, 66415
-recovered pasa_asmbl_47425.p1, internal, 66613, 66750
Valid prediction for CodingQuarry_transcript_55141-T1
Valid prediction for GeneMark_model.26934_t
Valid prediction for HiQ_model.g10872.t1
Couldn't classify 66613, 66659
Couldn't classify 67174, 67180
Sorry, prediction CodingQuarry_transcript_55138-T1 fails validation.
(ATG)	 AG	61926-61942	GT	GAG
(CGT)	 AG	62454-62525	GT	GGG
(GGG)	 AG	63552-63648	GT	AGG
(AAA)	 AG	64895-64966	GT	AGG
(GAA)	 AG	65218-65361	GT	AGG
(GAG)	 AG	66326-66415	GT	AGG
(ATG)	 AG	66613-66659	AT	GAA
(ATA)	 TC	67174-67180	CG	GAC
-recovered CodingQuarry_transcript_55138-T1, initial, 61926, 61942
-recovered CodingQuarry_transcript_55138-T1, internal, 61926, 61942
-recovered CodingQuarry_transcript_55138-T1, internal, 62454, 62525
-recovered CodingQuarry_transcript_55138-T1, internal, 63552, 63648
-recovered CodingQuarry_transcript_55138-T1, internal, 64895, 64966
-recovered CodingQuarry_transcript_55138-T1, internal, 65218, 65361
-recovered CodingQuarry_transcript_55138-T1, internal, 66326, 66415
Valid prediction for pasa_asmbl_47451.p1
Valid prediction for GeneMark_model.26942_t
Valid prediction for GeneMark_model.26928_t
Valid prediction for Augustus_model.g10846.t1
Valid prediction for Augustus_model.g10863.t1
Valid prediction for snap_scaffold_6-snap.2758-T1
Valid prediction for Augustus_model.g10856.t1
Valid prediction for snap_scaffold_6-snap.2767-T1
Valid prediction for snap_scaffold_6-snap.2738-T1
Valid prediction for GeneMark_model.26948_t
Valid prediction for GlimmerHMM_glimmerT_16135-T1
Couldn't classify 163437, 163485
Sorry, prediction pasa_asmbl_47909.p1 fails validation.
(GTA)	 AT	163437-163485	GT	TGG
(GTA)	 AG	163639-163762	GT	ACG
(ATA)	 AG	163891-164015	GT	GGG
(TGG)	 AG	164246-164370	GT	AGG
(ATG)	 AG	164515-164664	AA	GAA
-recovered pasa_asmbl_47909.p1, terminal, 164515, 164664
-recovered pasa_asmbl_47909.p1, internal, 163639, 163762
-recovered pasa_asmbl_47909.p1, internal, 163891, 164015
-recovered pasa_asmbl_47909.p1, internal, 164246, 164370
Valid prediction for snap_scaffold_6-snap.2741-T1
Valid prediction for GlimmerHMM_glimmerT_16115-T1
Valid prediction for CodingQuarry_transcript_55137-T1
Valid prediction for GeneMark_model.26936_t
Valid prediction for snap_scaffold_6-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_16112-T1
Valid prediction for GeneMark_model.26951_t
Valid prediction for Augustus_model.g10875.t1
Valid prediction for snap_scaffold_6-snap.2735-T1
Valid prediction for CodingQuarry_transcript_55142-T1
Valid prediction for snap_scaffold_6-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_16132-T1
Valid prediction for HiQ_model.g10867.t1
Valid prediction for snap_scaffold_6-snap.2762-T1
Valid prediction for GlimmerHMM_glimmerT_16119-T1
Couldn't classify 90929, 91166
Sorry, prediction pasa_asmbl_47435.p1 fails validation.
(ATG)	 AC	88920-88932	GT	TGG
(ATT)	 AG	89668-89692	GT	GGG
(GTA)	 AG	89780-89940	GT	TGG
(GAG)	 AG	90139-90307	GT	AAG
(CTA)	 AG	90929-91166	AA	GTA
-recovered pasa_asmbl_47435.p1, initial, 88920, 88932
-recovered pasa_asmbl_47435.p1, internal, 89668, 89692
-recovered pasa_asmbl_47435.p1, internal, 89780, 89940
-recovered pasa_asmbl_47435.p1, internal, 90139, 90307
Valid prediction for CodingQuarry_transcript_55144-T1
Valid prediction for HiQ_model.g10874.t1
Valid prediction for Augustus_model.g10854.t1
Valid prediction for GlimmerHMM_glimmerT_16121-T1
Valid prediction for Augustus_model.g10864.t1
Valid prediction for GlimmerHMM_glimmerT_16125-T1
Valid prediction for Augustus_model.g10857.t1
Valid prediction for GlimmerHMM_glimmerT_16117-T1
Valid prediction for GlimmerHMM_glimmerT_16137-T1
Valid prediction for snap_scaffold_6-snap.2736-T1
Valid prediction for CodingQuarry_transcript_55143-T1
Valid prediction for Augustus_model.g10880.t1
Valid prediction for snap_scaffold_6-snap.2754-T1
Valid prediction for CodingQuarry_transcript_55148-T1
Valid prediction for GeneMark_model.26943_t
Valid prediction for snap_scaffold_6-snap.2743-T1
Valid prediction for snap_scaffold_6-snap.2769-T1
Valid prediction for GlimmerHMM_glimmerT_16139-T1
Valid prediction for HiQ_model.g10861.t1
Valid prediction for pasa_asmbl_47452.p1
Valid prediction for snap_scaffold_6-snap.2746-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2752-T1
Valid prediction for snap_scaffold_6-snap.2771-T1
Valid prediction for snap_scaffold_6-snap.2761-T1
Valid prediction for snap_scaffold_6-snap.2757-T1
Valid prediction for snap_scaffold_6-snap.2739-T1
Valid prediction for snap_scaffold_6-snap.2751-T1
Valid prediction for snap_scaffold_6-snap.2760-T1
Valid prediction for snap_scaffold_6-snap.2750-T1
Valid prediction for Augustus_model.g10879.t1
Valid prediction for GlimmerHMM_glimmerT_16138-T1
Valid prediction for GeneMark_model.26953_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 pasa_asmbl_48832.p2
Valid prediction for GlimmerHMM_glimmerT_16118-T1
Valid prediction for GlimmerHMM_glimmerT_16114-T1
Valid prediction for GeneMark_model.26941_t
Valid prediction for CodingQuarry_transcript_55136-T1
Valid prediction for GlimmerHMM_glimmerT_16134-T1
Valid prediction for HiQ_model.g10870.t1
Valid prediction for HiQ_model.g10849.t1
Valid prediction for GeneMark_model.26929_t
Valid prediction for GeneMark_model.26930_t
Valid prediction for pasa_asmbl_48821.p1
Valid prediction for snap_scaffold_6-snap.2774-T1
Valid prediction for Augustus_model.g10858.t1
Valid prediction for GeneMark_model.26937_t
Valid prediction for snap_scaffold_6-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_16130-T1
Valid prediction for Augustus_model.g10852.t1
Valid prediction for pasa_asmbl_48842.p1
Valid prediction for GlimmerHMM_glimmerT_16140-T1
Valid prediction for GeneMark_model.26938_t
Valid prediction for GlimmerHMM_glimmerT_16127-T1
Valid prediction for GlimmerHMM_glimmerT_16116-T1
Valid prediction for snap_scaffold_6-snap.2770-T1
Valid prediction for HiQ_model.g10869.t1
Valid prediction for GeneMark_model.26935_t
Valid prediction for snap_scaffold_6-snap.2740-T1
Valid prediction for pasa_asmbl_48840.p1
Valid prediction for Augustus_model.g10859.t1
Valid prediction for Augustus_model.g10871.t1
Valid prediction for snap_scaffold_6-snap.2772-T1
Couldn't classify 148422, 148589
Sorry, prediction pasa_asmbl_48824.p1 fails validation.
(AAT)	 TG	148422-148589	GT	AGG
(GTG)	 AG	149546-149617	GT	AGG
(GCA)	 AG	149755-149964	GT	TGG
(AGT)	 AG	150479-150642	GT	TCG
(GTC)	 AG	150769-150790	CC	AGC
-recovered pasa_asmbl_48824.p1, terminal, 150769, 150790
-recovered pasa_asmbl_48824.p1, internal, 149546, 149617
-recovered pasa_asmbl_48824.p1, internal, 149755, 149964
-recovered pasa_asmbl_48824.p1, internal, 150479, 150642
Valid prediction for Augustus_model.g10866.t1
Valid prediction for GlimmerHMM_glimmerT_16113-T1
Valid prediction for snap_scaffold_6-snap.2747-T1
Valid prediction for snap_scaffold_6-snap.2744-T1
Valid prediction for CodingQuarry_transcript_55134-T1
Valid prediction for GeneMark_model.26932_t
Valid prediction for snap_scaffold_6-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_16131-T1
Valid prediction for GlimmerHMM_glimmerT_16129-T1
Valid prediction for Augustus_model.g10853.t1
Valid prediction for CodingQuarry_transcript_55133-T1
Valid prediction for HiQ_model.g10860.t1
Couldn't classify 135052, 135174
Sorry, prediction pasa_asmbl_48833.p1 fails validation.
(ATG)	 GG	134059-134205	GT	AGG
(GAC)	 AG	134299-134361	GT	AGG
(AGG)	 AG	134530-134584	GT	TTG
(GGG)	 AG	134666-134730	GT	TGG
(AAC)	 AG	134911-134973	GT	GGG
(ATA)	 AG	135052-135174	CC	CCC
-recovered pasa_asmbl_48833.p1, initial, 134059, 134205
-recovered pasa_asmbl_48833.p1, internal, 134299, 134361
-recovered pasa_asmbl_48833.p1, internal, 134530, 134584
-recovered pasa_asmbl_48833.p1, internal, 134666, 134730
-recovered pasa_asmbl_48833.p1, internal, 134911, 134973
Valid prediction for snap_scaffold_6-snap.2764-T1
Valid prediction for CodingQuarry_transcript_55146-T1
Valid prediction for snap_scaffold_6-snap.2765-T1
Valid prediction for snap_scaffold_6-snap.2745-T1
Valid prediction for Augustus_model.g10876.t1
Valid prediction for Augustus_model.g10850.t1
Valid prediction for GeneMark_model.26946_t
Valid prediction for GlimmerHMM_glimmerT_16122-T1
Valid prediction for snap_scaffold_6-snap.2742-T1
Valid prediction for GlimmerHMM_glimmerT_16123-T1
Valid prediction for GeneMark_model.26954_t
Valid prediction for GlimmerHMM_glimmerT_16120-T1
Valid prediction for snap_scaffold_6-snap.2748-T1
Valid prediction for HiQ_model.g10855.t1
Valid prediction for GeneMark_model.26950_t
Valid prediction for GeneMark_model.26945_t
Valid prediction for Augustus_model.g10848.t1
Valid prediction for Augustus_model.g10847.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 9922, rend_intergenic: 9919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145274, rend_intergenic: 142565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192142
-exon list size: 514


building trellis

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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    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 9922, rend_intergenic: 9919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145274, rend_intergenic: 142565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 43 predictions persist after filtering for low support