Question: Error in CummeRbund
gravatar for majeedaasim
2.7 years ago by
United States
majeedaasim40 wrote:

I try to run CummeRbund on output generated by cuffdiff i.e. tx_win_cuffdiff_output. I just put it in a directory and the made this a working directory. How I am not able to generate SQLite database. I used the following commands: My machine details are

R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

library(cummeRbund)                                                              getwd() 



`[1] "" "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" "" ""
[19] "splicing.diff" "SuperDuper.fasta" "transcripts.gtf"
[22] "tss_group_exp.diff" "tss_groups.count_tracking" "tss_groups.fpk _tracking"
[25] "tss_groups.read_group_tracking" ""cuff= read

 cuff= read Cufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output/", gtfFile = "transcripts.gtf" genome = "SuperDuper.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

Why is not SQLite database produced in my case? What I have to do?

cummerbund R • 1.0k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by majeedaasim40

Is it an issue with just the current working directory?

When it is "Creating database tx_win_cuffdiff_output//cuffData.db", I think that the file that it's aiming to create is: E:/AASIM/tx_win_cummeRbund/tx_win_cuffdiff_output/tx_win_cuffdiff_output//cuffData.db, i.e., tx_win_cuffdiff_output, is there twice.

Change the working directory to E:/AASIM/tx_win_cummeRbund/ and then execute:

cuff= read Cufflinks(dbFile = "cuffData.db",dir = "tx_win_cuffdiff_output", gtfFile = "tx_win_cuffdiff_output/transcripts.gtf" genome = "tx_win_cuffdiff_output/SuperDuper.fasta", rebuild = T)
ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Kevin Blighe61k
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