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  • cummeRbund errors when "readCufflinks"

    Dear readers,
    When using library cummeRbund, I got errors:
    ----------------------------------------------------------
    > readCufflinks('diff_out')
    Error in sqliteSendQuery(con, statement, bind.data) :
    error in statement: no such table: genes
    ----------------------------------------------------------
    The same computational environment made it when I analyzed the other cuffdiff output "diff_out_1":
    > readCufflinks('diff_out_1')
    CuffSet instance with:
    8 samples
    39170 genes
    94818 isoforms
    88478 TSS
    46842 CDS
    1095696 promoters
    2477384 splicing
    646716 relCDS

    I have tried a lot, however, I can not figure out what is the problem. All packages on my computer and files in 'diff_out' are totally fine. Could you please give me some suggestions? I appreciate your time and reply.

  • #2
    Same problem

    I'm having the same issue. Did you find a solution?

    Comment


    • #3
      Not yet ......

      Comment


      • #4
        I am having the same issue. I also analyzed other dataset and indeed worked. Now i have new cuffdiff dataset I am loading to R and get this:

        Error in sqliteSendQuery(con, statement, bind.data) :
        error in statement: no such table: genes

        does anyone know how to fix this?
        G

        Comment


        • #5
          I found a solution

          After reading a lot yesterday a found a solution.

          1) I deleted the cuffData.db

          2) I ran readCufflinks()

          3) I got this error:
          Creating database path/cuffData.db
          Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
          could not find function "sqliteQuickSQL"


          4) Apparently the latest version of RSQLite doesn't have the function "sqliteQuickSQL". Is issue is described at http://seqanswers.com/forums/showthread.php?p=153446 together with the solution:

          Code:
          library(cummeRbund)
          
          sqliteQuickSQL<-dbGetQuery
          
          dbBeginTransaction<-dbBegin
          
          cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf")
          Although the original solution says to set 'rebuild=T' in readCufflinks, in my case it didn't work. So I had to delete cuffData.db again before executing readCufflinks. It worked perfectly for one dataset but not for the other. So I had to solve this issue too.

          5) I have two different experiments and I'm analyzing them separately. One of them I labeled the groups with letters (S,SR,MR) and the other with numbers (0, 30, 60). I got the following error when I executed readCufflinks() for my 2nd dataset.

          Code:
          Reading /path/gene_exp.diff
          Error in (function (classes, fdef, mtable)  : 
            unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
          In addition: Warning message:
          attributes are not identical across measure variables; they will be dropped

          cummeRbund is picky when comes to labels, and it doesn't handle well labels composed of just numbers. That's why I got the ‘"SQLiteConnection", "integer"’ problem.

          As explained in this thread, cummeRbund doesn't like when you use 'T' and 'F' as labels either. It treats these letters as TRUE and FALSE respectively and throws a logical error:

          Code:
          Error in function (classes, fdef, mtable) :
          unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical
          "

          6) I executed cuffdiff again with new labels: t0, t30, t60. Repeated the step described in 4 and it worked.

          Comment


          • #6
            I think I found a solution

            After reading a lot yesterday a found a solution.

            1) Deleted the cuffData.db

            2) Did readCufflinks()

            3) I got this error:
            Creating database path/cuffData.db
            Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
            could not find function "sqliteQuickSQL"


            4) Apparently the latest version of RSQLite doesn't have the function "sqliteQuickSQL". Is issue is described at http://seqanswers.com/forums/showthread.php?p=153446 together with the solution:

            Code:
            library(cummeRbund)
            
            sqliteQuickSQL<-dbGetQuery
            
            dbBeginTransaction<-dbBegin
            
            cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf")
            Although the original solution says to set 'rebuild=T' in readCufflinks, in my case it didn't work. So I had to delete cuffData.db again before executing readCufflinks. It worked perfectly for one set of data but not for the other. So I had to solve this issue too.

            5) I have two different experiments and I'm analyzing them separately. One of them I labeled the groups with letters (S,SR,MR) and the other with numbers (0, 30, 60). I got the following error when I executed readCufflinks() for my 2nd dataset.

            Code:
            Reading /path/gene_exp.diff
            Error in (function (classes, fdef, mtable)  : 
              unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
            In addition: Warning message:
            attributes are not identical across measure variables; they will be dropped

            cummeRbund is picky when comes to labels, and it doesn't handle well labels composed of just numbers. That's why I got the ‘"SQLiteConnection", "integer"’ problem.

            As explained in this thread, cummeRbund doesn't like when you use 'T' and 'F' as labels either. It treats these letters as TRUE and FALSE respectively and throws a logical error:

            Code:
            Error in function (classes, fdef, mtable) :
            unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical
            "

            6) I executed cuffdiff again with new labels: t0, t30, t60. Repeated the step described in 4 and it worked.

            Comment


            • #7
              I think I found a solution

              After reading a lot yesterday a found a solution.

              1) Deleted the cuffData.db

              2) Did readCufflinks()

              3) I got this error:

              Creating database path/cuffData.db
              Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
              could not find function "sqliteQuickSQL"


              4) Apparently the latest version of RSQLite doesn't have the function "sqliteQuickSQL". Is issue is described at http://seqanswers.com/forums/showthread.php?p=153446 together with the solution:

              Code:
              library(cummeRbund)
              
              sqliteQuickSQL<-dbGetQuery
              
              dbBeginTransaction<-dbBegin
              
              cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf")
              Although the original solution says to set 'rebuild=T' in readCufflinks, in my case it didn't work. So I had to delete cuffData.db again before executing readCufflinks. It worked perfectly for one set of data but not for the other. So I had to solve this issue too.

              5) I have two different experiments and I'm analyzing them separately. One of them I labeled the groups with letters (S,SR,MR) and the other with numbers (0, 30, 60). I got the following error when I executed readCufflinks() for my 2nd dataset.

              Reading /path/gene_exp.diff
              Error in (function (classes, fdef, mtable) :
              unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
              In addition: Warning message:
              attributes are not identical across measure variables; they will be dropped



              cummeRbund is picky when comes to labels, and it doesn't handle well labels composed of just numbers. That's why I got the ‘"SQLiteConnection", "integer"’ problem.

              As explained in this thread, cummeRbund doesn't like when you use 'T' and 'F' as labels either. It treats these letters as TRUE and FALSE respectively and throws a logical error:

              Error in function (classes, fdef, mtable) :
              unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical"


              6) I executed cuffdiff again with new labels: t0, t30, t60. Repeated the step described in 4 and it worked.

              Comment


              • #8
                e1) Deleted the cuffData.db

                2) Did readCufflinks()

                3) I got this error:
                Creating database /home/dxavier/Desktop/Kapler/finalAnalysis/Hiseq/timepoint/cuffdiff/cuffData.db
                Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
                could not find function "sqliteQuickSQL"

                4) Apparently the latest version of RSQLite doesn't have the function "sqliteQuickSQL". Is issue is described at http://seqanswers.com/forums/showthread.php?p=153446 together with the solution:

                library(cummeRbund)

                sqliteQuickSQL<-dbGetQuery

                dbBeginTransaction<-dbBegin

                cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf")

                Although the original solution says to set 'rebuild=T'in readCufflinks, in my case it didn't work. So I had to delete cuffData.db again before executing readCufflinks. It worked perfectly for one set of data but not for the other. So I had to solve this issue too.

                5) I have two different experiments and I'm analysing them separetely. One of them I labeled the groups with letters (S,SR,MR) and the other with numbers (0,30,60). I got the following error when I executed readCufflinks() for my 2nd dataset.

                Reading /path/gene_exp.diff
                Error in (function (classes, fdef, mtable) :
                unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
                In addition: Warning message:
                attributes are not identical across measure variables; they will be dropped


                cummeRbund is picky when comes to labels, and it doesn't handle well labels composed of just numbers. That's why I got the ‘"SQLiteConnection", "integer"’ problem.

                As explained in this thread (https://www.biostars.org/p/42562/), cummeRbund doesn't like when you use T and F as labels either. It treats these letters as TRUE and FALSE respectivetely and throws a logical error:

                Error in function (classes, fdef, mtable) :
                unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical"

                6) So I, executed cuffdiff again with new labels (t0,t30,t60,..), repeated the 4) step and it worked.

                Comment


                • #9
                  With the recent changes in RSQLite, there have been some incompatibility issues between cummerbund and RSQLite. The cummerbund developer(s) have addressed this, so you need to make sure you have the latest version of cummerbund (2.8.2) and RSQLite (1.0.0). If you download through bioconductor, make sure your bioconductor is up-to-date.

                  Once everything is current, make sure you use the "rebuild" option when reading the cuffdiff data. e.g.:

                  data<-readCufflinks("your cuffdiff folder", rebuild = T).

                  Hope that helps.

                  ~YB

                  Comment


                  • #10
                    Thanks Yaz,

                    I still get error messages (through after updating to cummerbund (2.8.2) and RSQLite (1.0.0) they are different errors):

                    > library ("cummeRbund")
                    > cuff<-readCufflinks("05_cuffdiff_ncServ",rebuild=T)
                    Creating database 05_cuffdiff_ncServ/cuffData.db
                    Error in sqliteNewConnection(drv, ...) :
                    RS-DBI driver: (could not connect to dbname:
                    unable to open database file
                    )
                    > cuff
                    Error: object 'cuff' not found
                    >

                    Any idea what could this be?

                    thanks
                    G
                    Last edited by Gonza; 11-09-2014, 01:27 PM.

                    Comment


                    • #11
                      You may be in the wrong directory. When you run:

                      >cuff<-readCufflinks("05_cuffdiff_ncServ",rebuild=T)

                      Make sure you're in the directory where the folder "05_cuffdiff_ncServ" sits. So you should be in "/Users/YOU/someDirectory/" and ""05_cuffdiff_ncServ" is in "/Users/YOU/someDirectory/05_cuffdiff_ncServ".

                      See if that works.

                      ~YB

                      Comment


                      • #12
                        Thanks for your reply. I have the cufdiff folder (05_cuffdiff_ncServ) in desktop. This is what I do to read the output:

                        rm(list=ls())
                        setwd("/Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/")
                        getwd()
                        library ("cummeRbund")
                        cuff<-readCufflinks(rebuild=T)
                        cuff

                        When I try with rebuild=T i get this in red:

                        Creating database /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/cuffData.db
                        Reading Run Info File /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/run.info
                        Writing runInfo Table
                        Reading Read Group Info /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/read_groups.info
                        Writing replicates Table
                        Reading /Users/gonzalovillarino/Desktop/05_cuffdiff_ncServ/genes.fpkm_tracking
                        Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
                        line 1390 did not have 17 elements
                        > cuff
                        Error: object 'cuff' not found
                        >


                        When I try WITHOUT rebuild=T I get this :


                        CuffSet instance with:
                        0 samples
                        0 genes
                        0 isoforms
                        0 TSS
                        0 CDS
                        0 promoters
                        0 splicing
                        0 relCDS



                        Any ideas please.....?

                        Comment


                        • #13
                          Gonza,

                          Have you looked at line 1390 of the genes.fpkm_tracking file?

                          Comment


                          • #14
                            Thanks.
                            I finally solved the problem. The gtf file i was using was corrupted with some '#' symbols. I removed them and now i can import cuffdiff to R without a problem.
                            cheers
                            -G

                            Comment


                            • #15
                              > data<-readCufflinks("diff_out7", rebuild = T)
                              Creating database diff_out7/cuffData.db
                              Reading Run Info File diff_out7/run.info
                              Writing runInfo Table
                              Reading Read Group Info diff_out7/read_groups.info
                              Writing replicates Table
                              Reading Var Model Info diff_out7/var_model.info
                              Writing varModel Table
                              Reading diff_out7/genes.fpkm_tracking
                              Checking samples table...
                              Populating samples table...
                              Error: Column name mismatch.
                              In addition: There were 50 or more warnings (use warnings() to see the first 50)

                              Warning messages:
                              1: In rsqlite_fetch(res@ptr, n = n) :
                              Don't need to call dbFetch() for statements, only for queries
                              2: In rsqlite_fetch(res@ptr, n = n) :
                              Don't need to call dbFetch() for statements, only for queries
                              3: In rsqlite_fetch(res@ptr, n = n) :
                              Don't need to call dbFetch() for statements, only for queries
                              4: In rsqlite_fetch(res@ptr, n = n) :
                              Don't need to call dbFetch() for statements, only for queries

                              How can I solve this problem? Thanks a lot.
                              Last edited by [email protected]; 06-25-2017, 06:07 PM.

                              Comment

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