[lgoff]

Hi Loyal,
I tried reloading the database and got the same error. If it has anything to do with versioning, I am using R 2.15.1 and cufflinks 2.0.0 with Cummerbund 1.99.

Is there any other way I could try?

> cuff<-readCufflinks()
> myGenes <- getGenes(cuff, myGeneIds)
Getting gene information:
	FPKM
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)

I'm curious as to where the ")" is coming from. Is this somewhere in your 'myGenes'?

-Loyal

[Alex.Manuel]

Hi Loyal,
I'm a newbie in RNAseq and bioinformatics as well. So for me it is a hard way to get into all the "voodoo" .
Currently I have the same issue like vyellapa. I also use the newest software versions...

> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
> diffGenes<-getGenes (cuff,diffGeneIDs)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)


cheers
Alex

[tankman]

RS-DBI driver errors in cummerbund 2.0

Hi Loyal,

Same type of issue (I'm getting driver errors), not sure what to do!

thanks!

tm

> cuff
CuffSet instance with:
3 samples
81928 genes
276141 isoforms
167337 TSS
0 CDS
245784 promoters
502011 splicing
0 relCDS
> gene.repFpkm<-repFpkm(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
>
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] cummeRbund_2.0.0 Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.1 IRanges_1.16.2
[6] fastcluster_1.1.7 reshape2_1.2.1 ggplot2_0.9.2.1 RSQLite_0.11.2 DBI_0.2-5
[11] BiocGenerics_0.4.0 BiocInstaller_1.8.1

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.0 Biobase_2.18.0 biomaRt_2.14.0 Biostrings_2.26.1 biovizBase_1.6.0
[6] bitops_1.0-4.1 BSgenome_1.26.0 cluster_1.14.2 colorspace_1.1-1 dichromat_1.2-4
[11] digest_0.5.2 GenomicFeatures_1.10.0 gtable_0.1.1 Hmisc_3.9-3 labeling_0.1
[16] lattice_0.20-10 MASS_7.3-22 memoise_0.1 munsell_0.4 parallel_2.15.1
[21] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.95-0.1.2 Rsamtools_1.10.1
[26] scales_0.2.2 stats4_2.15.1 stringr_0.6.1 tools_2.15.1 XML_3.95-0.1
[31] zlibbioc_1.4.0
>

I'm curious as to where the ")" is coming from. Is this somewhere in your 'myGenes'?

-Loyal

[lgoff]

tankman,
Can you send me your cuffData.db file? I will try to see if I can pinpoint the problem.

Thanks

-Loyal

[tankman]

Hello Loyal,

It's a bit big --~ 5 Gb.

can you create a dummy account for me and i can scp it over?

[bparr]

Hi,

I am having trouble with the 'features' method in version 2.0.0. Going through the manual everything seems to behave nicely, except I keep hitting errors when I try to look at gene feature plots. This appears to be a result of a null data frame being returned from the features() method when called on a CuffGene instance. Has anyone else run into this before, or have any recommendations on what to do differently (relative to the online manual)? I did create the cuffData database with the genome build and transcript gtf set.

>
> myGene
CuffGene instance for gene XLOC_000301
Short name: PINK1
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 5
TSS CuffFeature instance of size 3
CDS CuffFeature instance of size 1
> features(myGene)
[1] seqnames start end width
[5] strand source type score
[9] phase exon_number gene_biotype gene_id
[13] gene_name protein_id isoform_id transcript_name
<0 rows> (or 0-length row.names)
>

Thanks,
bparr

[Frithjof]

Hi,

I can confirm the problem of bparr above. Seems the CuffGene features are not created/interpreted correctly.
Subsequently the gene feature plots are giving an error, when calling the function "makeGeneRegionTrack"

Any ideas how to fix this ?

Thanks
Frithjof



> cuff
CuffSet instance with:
2 samples
119511 genes
406612 isoforms
201547 TSS
77479 CDS
119511 promoters
201547 splicing
18611 relCDS

> myGene
CuffGene instance for gene XLOC_000020
Short name: RP11-206L10.6,RP11-206L10.7,RP11-206L10.9
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 8
TSS CuffFeature instance of size 6
CDS CuffFeature instance of size 0

head(fpkm(myGene))
gene_id sample_name fpkm conf_hi conf_lo quant_status
1 XLOC_000020 cond1 0.747664 3.16391 0 OK
2 XLOC_000020 cond2 0.380987 1.71967 0 OK

> head(features(myGene))
[1] feature_id gene_id isoform_id seqnames source type start end
[9] score strand frame
<0 rows> (or 0-length row.names)

> genetrack<-makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
undefined columns selected


> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 GenomicRanges_1.10.5
[5] IRanges_1.16.4 fastcluster_1.1.7 reshape2_1.2.2 ggplot2_0.9.3
[9] RSQLite_0.11.2 DBI_0.2-5 BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0
[4] Biostrings_2.26.2 biovizBase_1.6.2 bitops_1.0-5
[7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0
[10] dichromat_1.2-4 digest_0.6.0 GenomicFeatures_1.10.1
[13] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1
[16] lattice_0.20-13 MASS_7.3-23 munsell_0.4
[19] parallel_2.15.2 plyr_1.8 proto_0.3-10
[22] RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2
[25] scales_0.2.3 stats4_2.15.2 stringr_0.6.2
[28] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0

[lgoff]

Hi guys,
Please make sure that when you are building your cuffData.db file (with readCufflinks()) that you are providing values to both the 'gtfFile' and 'genome' arguments. Also, the .gtf file MUST be the same .gtf file that you used for cuffdiff as this will guarantee that the gene_id and other feature IDs will map appropriately.

cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9')

If you did not do this from the get-go, you can do the following:

cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9',rebuild=T)

to rebuild the database and add these elements to the cuffData.db database. These are not populated by default when you run readCufflinks. I make this a bit more seamless in later versions of cummeRbund.

Cheers,
Loyal

[Frithjof]

Dear Loyal,

thank you for the quick response. Indeed I used the merged.gtf file from cuffmerge for the initial DB construction. Using the gtf from the cufflinks input yet produces a new error also resulting from an empty features set.

Obviously the features are not imported properly. Any suggestions where this might originate from and how to fix this ?

Thanks
Frithjof

>cuff<-readCufflinks(gtfFile="./Homo_sapiens.GRCh37.68.clean.gtf",
genome="hg19",rebuild=T)

> myGene
CuffGene instance for gene XLOC_000020
Short name: RP11-206L10.6,RP11-206L10.7,RP11-206L10.9
Slots:
annotation
features
fpkm
repFpkm
diff
count
isoforms CuffFeature instance of size 8
TSS CuffFeature instance of size 6
CDS CuffFeature instance of size 0

> head(features(myGene))
[1] seqnames start end width strand
[6] source type score phase gene_id
[11] isoform_id exon_number gene_name gene_biotype transcript_name
[16] protein_id
<0 rows> (or 0-length row.names)

> genetrack<-makeGeneRegionTrack(myGene)
Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") :
Rle of type 'list' is not supported

[lgoff]

Can you post the lines of the .gtf file that correspond to the gene_id 'XLOC_000020'

grep "XLOC_000020" ./Homo_sapiens.GRCh37.68.clean.gtf

I'd like to see what the structure of your .gtf file looks like. If there I can't find anything in this, perhaps you can send me your .gtf file and cuffData.db so I can take a peek and see what happened in the import.

Thanks,
Loyal

[Frithjof]

Ok, problem solved ...
As mentioned above I first tried the merged.gtf from cuffmerge and also the original .gtf provided to cufflinks. Both giving me errors.
I now re-run the analysis, deleting the old .db first and then recreating the DB with the merged.gtf file from cuffmerge.

Now everything seems to work fine.

Thank you again Loyal for the immediate help

Cheers
Frithjof

[g781]

Hi Loyal,

I have the same problem when ran makeGeneRegionTrack().
I've done with previously solutions but it doesn't seem to work for me.
I am also confused the genome argument. Should I have to tell makeGeneRegionTrack() the exactly name indicating which genome builds to the .gtf annotation?

What information I have are shown below:
diff_out: is a output directory from cuffdiff
merged.gtf: is a gtf file from cuffmerge (I post in the bottom and it has a gene_id in the merged.gtf)

cuff<-readCufflinks('diff_out',gtfFile='diff_out/merged.gtf',rebuild=T,genome='tb427')

> myGene
CuffGene instance for gene XLOC_000166 
Short name:	 Tb427.01.710 
Slots:
	 annotation
	 features
	 fpkm
	 repFpkm
	 diff
	 count
	 isoforms	 CuffFeature instance of size 1 
	 TSS		 CuffFeature instance of size 1 
	 CDS		 CuffFeature instance of size 1

> head(features(myGene))
 [1] seqnames   start      end        width      strand     source    
 [7] type       score      phase      isoform_id gene_id    gene_name 
<0 rows> (or 0-length row.names)

> genetack<-makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) : 
  undefined columns selected

Tb427_01_v4 Cufflinks exon  228118  229962  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000307"; exon_number "1"; gene_name "Tb427.01.670"; oId "rna_Tb427.01.670-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.670-1"; class_code "="; tss_id "TSS296"; p_id "P256";
Tb427_01_v4 Cufflinks exon  230768  231499  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000308"; exon_number "1"; gene_name "Tb427.01.690"; oId "rna_Tb427.01.690-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.690-1"; class_code "="; tss_id "TSS297"; p_id "P257";
Tb427_01_v4 Cufflinks exon  232575  233897  . - . gene_id "XLOC_000165"; transcript_id "TCONS_00000309"; exon_number "1"; gene_name "Tb427.01.700"; oId "rna_Tb427.01.700-1"; contained_in "TCONS_00000296"; nearest_ref "rna_Tb427.01.700-1"; class_code "="; tss_id "TSS285"; p_id "P258";
Tb427_01_v4 Cufflinks exon  234247  235509  . - . gene_id "XLOC_000166"; transcript_id "TCONS_00000310"; exon_number "1"; gene_name "Tb427.01.710"; oId "rna_Tb427.01.710-1"; nearest_ref "rna_Tb427.01.710-1"; class_code "="; tss_id "TSS298"; p_id "P260";
Tb427_01_v4 Cufflinks exon  235715  237370  . - . gene_id "XLOC_000167"; transcript_id "TCONS_00000311"; exon_number "1"; gene_name "Tb427.01.720"; oId "rna_Tb427.01.720-1"; nearest_ref "rna_Tb427.01.720-1"; class_code "="; tss_id "TSS299"; p_id "P261";
Tb427_01_v4 Cufflinks exon  240449  241756  . - . gene_id "XLOC_000169"; transcript_id "TCONS_00000313"; exon_number "1"; gene_name "Tb427.01.740"; oId "rna_Tb427.01.740-1"; nearest_ref "rna_Tb427.01.740-1"; class_code "="; tss_id "TSS301"; p_id "P263";

Many thanks in advance.

[biokari]

I have the same problem!


> sig_gene_unic<-getGenes(cuff,gene_uniq)
Erreur dans sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

Help please

[Steph35]

getGenes error

Hi,

I am getting an error when I create gene sets with the last version of cufflinks (2.0.2).When I rebuild the cuffData.db (rebuild=T) as suggested by Loyal, I always get the error «*RS-DBI driver: (error in statement: near ")": syntax error)*»

Any help much appreciated, commands below,
Steph

> cuff_data <- readCufflinks('Diff_out',rebuild=T)
> cuff_data
CuffSet instance with: 3 samples
43025 genes
43025 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
> data(sampleData)
> myGeneIds<-sampleIDs
> myGeneIds
[1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132" "XLOC_001265"
[6] "XLOC_000151" "XLOC_001359" "XLOC_000069" "XLOC_000170" "XLOC_000105"
[11] "XLOC_001262" "XLOC_001348" "XLOC_001411" "XLOC_001369" "XLOC_000158"
[16] "XLOC_001370" "XLOC_001263" "XLOC_000115" "XLOC_000089" "XLOC_001240"

> myGenes<-getGenes(cuff_data,myGeneIds)
Getting gene information:
FPKM
Erreur dans sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2
[4] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.9
[7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.2
[10] DBI_0.2-5 BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 Biobase_2.18.0 biomaRt_2.14.0
[4] Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5
[7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1
[10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.10.2
[13] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1
[16] lattice_0.20-14 MASS_7.3-23 munsell_0.4
[19] parallel_2.15.3 plyr_1.8 proto_0.3-10
[22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.10.2
[25] scales_0.2.3 stats4_2.15.3 stringr_0.6.2
[28] tools_2.15.3 XML_3.96-0.2 zlibbioc_1.4.0

[Charitra]

Dear All
I got problem with cummeRbund.... my RNA-seq data has fusion gene HLA-DQB1. When I conducted diff analysis (cufflinks), cummeRbund can not show this gene. I tried HLA-DQB1, HLADQB1, HLADQB, HLA, DQB1, DQB etc... it says:
> mygene<- getGene(cuff_data,'HLA-DQB1')
No gene set returned (Gene might not be in database?)
Error in validObject(.Object) : invalid class “CuffGene” object: FALS

However, I can find other genes with no problem with same commands...

Is anybody out there has somthing to help me ?
Thanks in advance.