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Question: cummeRbund problem in creating database
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gravatar for majeedaasim
28 days ago by
majeedaasim0 wrote:

I ran cummRbund on cuffdiff output directory. Following error is depicted.

 

library(cummeRbund)

getwd()
setwd("E:/AASIM/tx_win_cummeRbund/tx_win_cuffdiff_output/")
list.files()

 [1] "bias_params.info"               "cds.count_tracking"             "cds.diff"                      
 [4] "cds.fpkm_tracking"              "cds.read_group_tracking"        "cds_exp.diff"                  
 [7] "cuffData.db"                    "gene_exp.diff"                  "genes.count_tracking"          
[10] "genes.fpkm_tracking"            "genes.read_group_tracking"      "isoform_exp.diff"              
[13] "isoforms.count_tracking"        "isoforms.fpkm_tracking"         "isoforms.read_group_tracking"  
[16] "promoters.diff"                 "read_groups.info"               "run.info"                      
[19] "splicing.diff"                  "SuperDuper.fasta.fasta"         "transcripts.gtf"               
[22] "tss_group_exp.diff"             "tss_groups.count_tracking"      "tss_groups.fpkm_tracking"      
[25] "tss_groups.read_group_tracking" "var_model.info"  

cuff= readCufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output/", gtfFile = "transcripts.gtf",

+                     genome = "SuperDuper.fasta.fasta", rebuild = T)

Creating database tx_win_cuffdiff_output//cuffData.db

Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) : 

  Could not connect to database:

unable to open database file

> cuff

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

Where did I err?

ADD COMMENTlink written 28 days ago by majeedaasim0

Since the update of some of the SQL R pacakages cummeRbund have had quite a few problems. Try updating to the latest version from the devel branch (by typing "useDevel()" before installing). 

If it still does not work remember to repport the output from sessionInfo().

ADD REPLYlink written 28 days ago by k.vitting.seerup10
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