-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_8021779-8176732

-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: +)Couldn't classify 82774, 83101
Sorry, prediction pasa_asmbl_5735.p1 fails validation.
(TCT)	 CC	82774-83101	GT	GGG
(ACC)	 AG	83238-83346	GT	AGG
(GAA)	 AG	83632-83744	GT	TGG
(GTG)	 AG	84007-84106	GT	TGG
(GAA)	 AG	84266-84335	AA	AGA
-recovered pasa_asmbl_5735.p1, terminal, 84266, 84335
-recovered pasa_asmbl_5735.p1, internal, 83238, 83346
-recovered pasa_asmbl_5735.p1, internal, 83632, 83744
-recovered pasa_asmbl_5735.p1, internal, 84007, 84106
Valid prediction for HiQ_model.g18179.t1
Valid prediction for GlimmerHMM_glimmerT_27462-T1
Valid prediction for pasa_asmbl_5713.p1
Valid prediction for snap_scaffold_11-snap.1837-T1
Valid prediction for Augustus_model.g18186.t1
Valid prediction for CodingQuarry_transcript_8149-T1
Valid prediction for snap_scaffold_11-snap.1847-T1
Valid prediction for pasa_asmbl_5721.p1
Valid prediction for Augustus_model.g18183.t1
Valid prediction for GlimmerHMM_glimmerT_27487-T1
Valid prediction for snap_scaffold_11-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_27475-T1
Valid prediction for GlimmerHMM_glimmerT_27476-T1
Valid prediction for snap_scaffold_11-snap.1855-T1
Couldn't classify 71073, 71546
Couldn't classify 71652, 71860
Sorry, prediction CodingQuarry_transcript_8150-T1 fails validation.
(ATG)	 AA	66135-69770	GT	AGG
(CTC)	 AG	70003-70160	GT	GGG
(GTA)	 AG	70537-70712	GT	AGG
(GAA)	 AG	70830-70928	GT	CGG
(ATG)	 AG	71073-71546	AC	TTA
(ACC)	 GC	71652-71860	GT	TGG
(GAT)	 AG	72070-72495	GC	AGG
-recovered CodingQuarry_transcript_8150-T1, initial, 66135, 69770
-recovered CodingQuarry_transcript_8150-T1, terminal, 72070, 72495
-recovered CodingQuarry_transcript_8150-T1, internal, 70003, 70160
-recovered CodingQuarry_transcript_8150-T1, internal, 70537, 70712
-recovered CodingQuarry_transcript_8150-T1, internal, 70830, 70928
-recovered CodingQuarry_transcript_8150-T1, internal, 72070, 72495
Valid prediction for snap_scaffold_11-snap.1840-T1
Valid prediction for snap_scaffold_11-snap.1843-T1
Couldn't classify 24944, 24985
Sorry, prediction pasa_asmbl_5709.p1 fails validation.
(CAA)	 TA	24944-24985	GT	AAG
(ACT)	 AG	25299-25437	GT	CGG
(GGG)	 AG	25611-25882	GT	AGG
(AAG)	 AG	26169-26331	GT	AGG
(ACA)	 AG	26473-26582	TC	AAT
-recovered pasa_asmbl_5709.p1, terminal, 26473, 26582
-recovered pasa_asmbl_5709.p1, internal, 25299, 25437
-recovered pasa_asmbl_5709.p1, internal, 25611, 25882
-recovered pasa_asmbl_5709.p1, internal, 26169, 26331
Valid prediction for snap_scaffold_11-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_27468-T1
Valid prediction for HiQ_model.g18182.t1
Valid prediction for snap_scaffold_11-snap.1839-T1
Valid prediction for HiQ_model.g18180.t1
Valid prediction for snap_scaffold_11-snap.1856-T1
Valid prediction for CodingQuarry_transcript_8152-T1
Valid prediction for CodingQuarry_transcript_8151-T1
Valid prediction for GlimmerHMM_glimmerT_27467-T1
Valid prediction for Augustus_model.g18173.t1
Valid prediction for Augustus_model.g18176.t1
Couldn't classify 29441, 29609
Sorry, prediction pasa_asmbl_5712.p1 fails validation.
(AGT)	 CC	29441-29609	GT	AGG
(GTA)	 AG	29752-29948	GT	AGG
(TAT)	 AG	30213-30284	GG	AAG
-recovered pasa_asmbl_5712.p1, terminal, 30213, 30284
-recovered pasa_asmbl_5712.p1, internal, 29752, 29948
Valid prediction for HiQ_model.g18181.t1
Valid prediction for snap_scaffold_11-snap.1842-T1
Valid prediction for GlimmerHMM_glimmerT_27461-T1
Valid prediction for pasa_asmbl_5706.p1
Valid prediction for CodingQuarry_transcript_8142-T1
Valid prediction for GlimmerHMM_glimmerT_27478-T1
Valid prediction for snap_scaffold_11-snap.1862-T1
Valid prediction for snap_scaffold_11-snap.1833-T1
Valid prediction for snap_scaffold_11-snap.1849-T1
Valid prediction for snap_scaffold_11-snap.1841-T1
Valid prediction for HiQ_model.g18172.t1
Valid prediction for snap_scaffold_11-snap.1851-T1
Valid prediction for GlimmerHMM_glimmerT_27477-T1
Valid prediction for snap_scaffold_11-snap.1861-T1
Valid prediction for HiQ_model.g18169.t1
Valid prediction for pasa_asmbl_5734.p1
Valid prediction for GlimmerHMM_glimmerT_27460-T1
Valid prediction for Augustus_model.g18175.t1
Valid prediction for CodingQuarry_transcript_8148-T1
Valid prediction for snap_scaffold_11-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_27474-T1
Valid prediction for Augustus_model.g18174.t1
Valid prediction for GlimmerHMM_glimmerT_27470-T1
Valid prediction for snap_scaffold_11-snap.1844-T1
Valid prediction for pasa_asmbl_5717.p1
Valid prediction for GlimmerHMM_glimmerT_27466-T1
Valid prediction for snap_scaffold_11-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_27463-T1
Valid prediction for CodingQuarry_transcript_8141-T1
Valid prediction for snap_scaffold_11-snap.1852-T1
Valid prediction for CodingQuarry_transcript_8143-T1
Valid prediction for GlimmerHMM_glimmerT_27479-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_11-snap.1854-T1
Valid prediction for Augustus_model.g18190.t1
Valid prediction for GlimmerHMM_glimmerT_27486-T1
Valid prediction for GlimmerHMM_glimmerT_27480-T1
Valid prediction for snap_scaffold_11-snap.1836-T1
Valid prediction for GlimmerHMM_glimmerT_27471-T1
Valid prediction for pasa_asmbl_6818.p1
Valid prediction for GlimmerHMM_glimmerT_27481-T1
Valid prediction for CodingQuarry_transcript_8144-T1
Valid prediction for GlimmerHMM_glimmerT_27488-T1
Valid prediction for GlimmerHMM_glimmerT_27483-T1
Couldn't classify 55658, 55722
Sorry, prediction pasa_asmbl_6839.p1 fails validation.
(ATC)	 TT	55658-55722	GT	CTG
(GCT)	 AG	56007-56121	GT	AGG
(GTG)	 AG	56244-56372	AG	AAA
-recovered pasa_asmbl_6839.p1, terminal, 56244, 56372
-recovered pasa_asmbl_6839.p1, internal, 56007, 56121
Valid prediction for snap_scaffold_11-snap.1835-T1
Valid prediction for Augustus_model.g18171.t1
Valid prediction for CodingQuarry_transcript_8145-T1
Valid prediction for snap_scaffold_11-snap.1853-T1
Valid prediction for HiQ_model.g18185.t1
Valid prediction for snap_scaffold_11-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_27482-T1
Couldn't classify 31453, 31596
Sorry, prediction pasa_asmbl_6846.p1 fails validation.
(CAG)	 CC	31453-31596	GT	ACG
(GTG)	 AG	31734-31824	GT	GAG
(ATA)	 AG	32879-32958	GT	AGG
(GGA)	 AG	33308-33384	GT	AGG
(TGA)	 AG	33732-33918	GT	GGG
(CCA)	 AG	34212-34307	GC	GAG
-recovered pasa_asmbl_6846.p1, terminal, 34212, 34307
-recovered pasa_asmbl_6846.p1, internal, 31734, 31824
-recovered pasa_asmbl_6846.p1, internal, 32879, 32958
-recovered pasa_asmbl_6846.p1, internal, 33308, 33384
-recovered pasa_asmbl_6846.p1, internal, 33732, 33918
-recovered pasa_asmbl_6846.p1, internal, 34212, 34307
Valid prediction for GlimmerHMM_glimmerT_27484-T1
Valid prediction for CodingQuarry_transcript_8147-T1
Valid prediction for GlimmerHMM_glimmerT_27490-T1
Valid prediction for GlimmerHMM_glimmerT_27469-T1
Valid prediction for HiQ_model.g18184.t1
Valid prediction for snap_scaffold_11-snap.1859-T1
Valid prediction for GlimmerHMM_glimmerT_27473-T1
Valid prediction for snap_scaffold_11-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_27465-T1
Valid prediction for snap_scaffold_11-snap.1834-T1
Valid prediction for CodingQuarry_transcript_8153-T1
Valid prediction for pasa_asmbl_6830.p1
Valid prediction for GlimmerHMM_glimmerT_27472-T1
Valid prediction for snap_scaffold_11-snap.1845-T1
Couldn't classify 38139, 38301
Sorry, prediction pasa_asmbl_7291.p1 fails validation.
(GGC)	 AC	38139-38301	GT	CGG
(AGA)	 AG	38440-38577	GT	TGG
(GTC)	 AG	38933-39024	GT	AGG
(ACA)	 AG	39363-39653	AG	GAA
-recovered pasa_asmbl_7291.p1, terminal, 39363, 39653
-recovered pasa_asmbl_7291.p1, internal, 38440, 38577
-recovered pasa_asmbl_7291.p1, internal, 38933, 39024
Valid prediction for HiQ_model.g18178.t1
Valid prediction for GlimmerHMM_glimmerT_27485-T1
Valid prediction for CodingQuarry_transcript_8146-T1
Valid prediction for snap_scaffold_11-snap.1857-T1
Couldn't classify 131925, 132110
Couldn't classify 134804, 134890
Sorry, prediction pasa_asmbl_6820.p1 fails validation.
(CCT)	 TG	131925-132110	GT	AGG
(TAT)	 AG	132268-132333	GT	TGG
(GTT)	 AG	132487-132538	GT	TGG
(TTA)	 AG	132634-132701	GT	TGG
(GGT)	 AG	132837-132991	GT	GAG
(CCT)	 AG	133273-133413	GT	ATG
(GTC)	 AG	133504-133633	GT	CGG
(ATG)	 AG	134093-134181	GT	AGG
(TTC)	 AG	134446-134558	GT	GGG
(CCT)	 AG	134651-134721	GT	AGG
(GTG)	 AG	134804-134890	GT	GTG
-recovered pasa_asmbl_6820.p1, initial, 134093, 134181
-recovered pasa_asmbl_6820.p1, internal, 132268, 132333
-recovered pasa_asmbl_6820.p1, internal, 132487, 132538
-recovered pasa_asmbl_6820.p1, internal, 132634, 132701
-recovered pasa_asmbl_6820.p1, internal, 132837, 132991
-recovered pasa_asmbl_6820.p1, internal, 133273, 133413
-recovered pasa_asmbl_6820.p1, internal, 133504, 133633
-recovered pasa_asmbl_6820.p1, internal, 134093, 134181
-recovered pasa_asmbl_6820.p1, internal, 134446, 134558
-recovered pasa_asmbl_6820.p1, internal, 134651, 134721
-recovered pasa_asmbl_6820.p1, internal, 134804, 134890
Valid prediction for GlimmerHMM_glimmerT_27464-T1
Valid prediction for Augustus_model.g18187.t1
Valid prediction for snap_scaffold_11-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_27489-T1
Valid prediction for pasa_asmbl_6838.p1
Valid prediction for snap_scaffold_11-snap.1846-T1
Valid prediction for HiQ_model.g18188.t1
Valid prediction for HiQ_model.g18177.t1
Valid prediction for Augustus_model.g18189.t1
Valid prediction for Augustus_model.g18170.t1
Couldn't classify 37990, 38141
Sorry, prediction pasa_asmbl_6842.p1 fails validation.
(ATG)	 AT	34711-34818	GT	AGG
(GAC)	 AG	35358-35423	GT	AGG
(AAT)	 AG	35523-35591	GT	TGG
(GGG)	 AG	37610-37784	GT	AGG
(AGA)	 AG	37990-38141	AG	GCA
-recovered pasa_asmbl_6842.p1, initial, 34711, 34818
-recovered pasa_asmbl_6842.p1, internal, 35358, 35423
-recovered pasa_asmbl_6842.p1, internal, 35523, 35591
-recovered pasa_asmbl_6842.p1, internal, 37610, 37784
Valid prediction for pasa_asmbl_6834.p2

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23192, rend_intergenic: 19493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116991, rend_intergenic: 115302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131084, rend_intergenic: 123105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154954
-exon list size: 353


building trellis

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27.3    
27.6    
27.9    
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30.1    
30.4    
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31.3    
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33.0    
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34.4    
34.6    
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35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
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38.0    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
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40.6    
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41.1    
41.4    
41.7    
42.0    
42.3    
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44.2    
44.5    
44.8    
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45.6    
45.9    
46.2    
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46.8    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
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50.1    
50.4    
50.7    
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52.4    
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81.1    
81.4    
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87.0    
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97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23192, rend_intergenic: 19493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116991, rend_intergenic: 115302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131084, rend_intergenic: 123105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support