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  • CummeRbund error with SQLite.

    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.

    Code:
    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
    Last edited by ramma; 06-25-2012, 11:30 AM.

  • #2
    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.

    Comment


    • #3
      Sorry, this is actually a really silly mistake. My working directory was diff_out, not the folder that points to diff_out.

      Comment


      • #4
        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)

        Comment


        • #5
          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

          Comment


          • #6
            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

            Comment


            • #7
              Originally posted by shabhonam View Post
              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 ??

              Comment


              • #8
                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

                Comment


                • #9
                  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

                  Comment


                  • #10
                    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

                    Comment


                    • #11
                      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

                      Comment


                      • #12
                        im new to r btwa
                        abd unix/linux as well...

                        gosh!helpppp!

                        Comment


                        • #13
                          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!

                          Comment


                          • #14
                            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?


                            Originally posted by wacguy View Post
                            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

                            Comment


                            • #15
                              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

                              Comment

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