CummeRbund error with SQLite.

[ramma]

I'm having an issue with the database permissions it seems. When running readCufflinks and pointing it to my cuffdiff output folder it starts just fine, then gives the error below.

Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (RS_SQLite_exec: could not execute1: database is locked)

Running Cufflinks 2.0.1
CummeRbund 1.2.0
Rstudio 0.96

[billstevens]

Hi guys, I'm working with the CummeRbund package. I have used the package before and have found it to be very useful. I just upgraded to the new cufflinks package (2.0.1), but when I run use CummeRbund to analyze my cuffdiff output, I receive the following error:


> cuffy <- readCufflinks('diff_out')
Creating database diff_out/cuffData.db
Error in sqliteNewConnection(drv, ...) :
RS-DBI driver: (could not connect to dbname:
unable to open database file
)

I re-ran this on a 'diff_out' folder that I've used previously with success (version 1.3), and I received the same error. I noticed someone else in a different forum had the same issue. Do you guys have any idea what's going on? Its the first step, I just run "library(cummeRbund)" and then this command, but somehow, it won't work. I'm using cummeRbund 1.2 and R 2.15.

[billstevens]

Sorry, this is actually a really silly mistake. My working directory was diff_out, not the folder that points to diff_out.

[Charitra]

I have the same problem, what is the solution ???

cuff_data <- readCufflinks('diff_out')
Creating database diff_out/cuffData.db
Error in sqliteNewConnection(drv, ...) :
RS-DBI driver: (could not connect to dbname:
unable to open database file


> csDensity(genes(cuff_data))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)

[shabhonam]

Hello Charita,

I had the similar problem, try to remove all the # from gene names from the genes.fpkmtracking or any other file which shows error. Always remove the cuffData.db from your working directory before rerunning the commands:
library(cummeRbund)
cuff <- readCufflinks()

Cheers
Shab

[Charitra]

Thank you so much for your kind help.
Now its going smooth.
O\One more thing, can you tell me something about how to do pathway analysis after differential expression (cuffdiff).

Charitra

[Charitra]

Hello Charita,

I had the similar problem, try to remove all the # from gene names from the genes.fpkmtracking or any other file which shows error. Always remove the cuffData.db from your working directory before rerunning the commands:
library(cummeRbund)
cuff <- readCufflinks()

Cheers
Shab

Dear shabhonam
I got another problem with cuffdiff or cummeRbund.
in R cummeRbund, it can not find gene but gene is there in my cuffdiff output when I checked manually ... is this errog in cuffdiff or cummeRbund ??

[wacguy]

Hi all,

Quite some errors in CummeRbund; here is the list including the sessionInfo() at the end. I've been trying to solve these isuues for the last 2-3 weeks with little success. Some features worked on our server, quite some more when I ran it on my computer (mac 10.6.8), but still a lot of errors which are very cryptic to me: not a programmer/R master; just learn all Bowtie/tophat/cuff*...

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


> genes.MDS<-MDSplot(genes(cuff))#sthash.hkJEYpTT.dpuf
Error in cmdscale(d, eig = TRUE, k = 2) :
'k' must be in {1, 2, .. n - 1}

ic<-csCluster(myGenes,k=4)
Error in csCluster(myGenes, k = 4) :
error in evaluating the argument 'object' in selecting a method for function 'csCluster': Error: object 'myGenes' not found

mySimilar<-findSimilar(cuff,"PINK1",n=20)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

mySimilar2<-findSimilar(cuff,myProfile,n=10)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
In addition: There were 50 or more warnings (use warnings() to see the first 50)



> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (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 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] cummeRbund_2.2.0 Gviz_1.4.4 rtracklayer_1.20.4
[4] GenomicRanges_1.12.4 IRanges_1.18.2 fastcluster_1.1.11
[7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.4
[10] DBI_0.2-7 BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.22.6 Biobase_2.20.1 biomaRt_2.16.0
[4] Biostrings_2.28.0 biovizBase_1.8.1 bitops_1.0-5
[7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2
[10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.12.3
[13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2
[16] lattice_0.20-15 MASS_7.3-28 munsell_0.4.2
[19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5
[22] RCurl_1.95-4.1 rpart_4.1-1 Rsamtools_1.12.3
[25] scales_0.2.3 stats4_3.0.1 stringr_0.6.2
[28] tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0

Help would be highly appreciate; Thanks a lot,
Guy

[IBseq]

hi,
can anyone help me out with this?
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> cuff <- readCufflinks()
> cuff
CuffSet instance with:
2 samples
24300 genes
42209 isoforms
28820 TSS
25042 CDS
24300 promoters
28820 splicing
0 relCDS


why us relCDS 0?

Also, when I try to use many function of cummerbund such as cs Boxplot, cs Dendro and many others I have a error message and thus I cannot build up the pic or graph, its like I do not have that function..

any suggestion will be much appreciated!

ibseq

[wacguy]

can you give us a bit more info

which organism, how many samples and replicas, the commands and errors messages. Are you familiar with R?

Guy

[IBseq]

Hi,
I have human cervical samples. No replicates. this one i posted is one of the samples I have compared with the negative sample...

i'm struggling writing down commands...! I need to create a gene set I have to work with out of all those that came from the sequencing. How can I do that??

Any help much appreciated!
ibseq

[IBseq]

im new to r btwa
abd unix/linux as well...

gosh!helpppp!

[IBseq]

dear all,
any suggestion more than wellcome!

<environment: namespace:cummeRbund>
> cuff<-readCufflinks(rebuild=T)
Creating database /home/bsib/Cuffdiff/caski/cuffData.db
Reading /home/bsib/Cuffdiff/caski/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /home/bsib/Cuffdiff/caski/gene_exp.diff
Writing geneExpDiffData table
Reading /home/bsib/Cuffdiff/caski/promoters.diff
Writing promoterDiffData table
Reading /home/bsib/Cuffdiff/caski/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /home/bsib/Cuffdiff/caski/isoform_exp.diff
Writing isoformExpDiffData table
Reading /home/bsib/Cuffdiff/caski/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /home/bsib/Cuffdiff/caski/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /home/bsib/Cuffdiff/caski/splicing.diff
Writing splicingDiffData table
Reading /home/bsib/Cuffdiff/caski/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /home/bsib/Cuffdiff/caski/cds_exp.diff
Writing CDSExpDiffData table
Indexing Tables...
> d<-dispersionPLot(genes(cuff))
Error: could not find function "dispersionPLot"
>


thanks a lot!

[gwilymh]

I have had the same error and not been able to resolve it:

Input:
geneList<-as.vector(read.table("genesofInterest.txt",sep = "\t",header= FALSE),mode="list")
geneList
geneExp<-getGenes(cuff,geneList)
Output:
Getting gene information:
FPKM
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)

I am working with CummeRbund version 2.0, and (I think) the CuffDiff data was generated with Cufflinks 2.0.2.

I have tried clearing the workspace and reconnecting with CummeRbund; re-downloading all the CuffDiff output files and rebuilding the cuffData.db database; but I still get the same error.

CummeRbund was working fine a few weeks ago with these commands, then abruptly started producing this error message.

Has anyone found away around this problem?

Hi all,

Quite some errors in CummeRbund; here is the list including the sessionInfo() at the end. I've been trying to solve these isuues for the last 2-3 weeks with little success. Some features worked on our server, quite some more when I ran it on my computer (mac 10.6.8), but still a lot of errors which are very cryptic to me: not a programmer/R master; just learn all Bowtie/tophat/cuff*...

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


> genes.MDS<-MDSplot(genes(cuff))#sthash.hkJEYpTT.dpuf
Error in cmdscale(d, eig = TRUE, k = 2) :
'k' must be in {1, 2, .. n - 1}

ic<-csCluster(myGenes,k=4)
Error in csCluster(myGenes, k = 4) :
error in evaluating the argument 'object' in selecting a method for function 'csCluster': Error: object 'myGenes' not found

mySimilar<-findSimilar(cuff,"PINK1",n=20)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

mySimilar2<-findSimilar(cuff,myProfile,n=10)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
In addition: There were 50 or more warnings (use warnings() to see the first 50)



> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (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 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] cummeRbund_2.2.0 Gviz_1.4.4 rtracklayer_1.20.4
[4] GenomicRanges_1.12.4 IRanges_1.18.2 fastcluster_1.1.11
[7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.4
[10] DBI_0.2-7 BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.22.6 Biobase_2.20.1 biomaRt_2.16.0
[4] Biostrings_2.28.0 biovizBase_1.8.1 bitops_1.0-5
[7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2
[10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.12.3
[13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2
[16] lattice_0.20-15 MASS_7.3-28 munsell_0.4.2
[19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5
[22] RCurl_1.95-4.1 rpart_4.1-1 Rsamtools_1.12.3
[25] scales_0.2.3 stats4_3.0.1 stringr_0.6.2
[28] tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0

Help would be highly appreciate; Thanks a lot,
Guy

[Ntobe]

Hi

I have been trying to use my CummeRbund and it keep giving me the same error. I removed the cuffData.db from my working directory but it didn't help.

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

Can anyone please help, I'm stuck.

Nonto