Cuff Error In File
0 4.3 years ago by Hardcastle, Justin • 20 Hardcastle, Justin • 20 wrote: Hi, I'm having an issue running cummeRbund on my cuffdiff output. CummeRbund is giving me a DB error and not r error in .local(drv, ...) : could not connect to database: unable to open database file creating the DB. The code and error are below. library("cummeRbund") dir = "~/Test" outdir = error: cuffdiff requires at least 2 sam files "output/cuffdiff" cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE) The error given is > cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = cuffdiff bam files TRUE) Creating database ~/Test/output/cuffdiff/cuffData.db Error in sqliteNewConnection(drv, ...) : RS-DBI driver: (could not connect to dbname: unable to open database file ) I am running cummeRbund 1.2.0, and Cufflinks 2.0.1. Thanks for any help. cummerbund ADD COMMENT cummerbund manual • link • Not following Follow via messages Follow via email Do not follow modified 4.3 years ago by Loyal Goff • 130 • written 4.3 years ago by Hardcastle, Justin • 20 0 4.3 years ago by Loyal Goff • 130 Loyal Goff • 130 wrote: Hi Justin, Can you confirm that "~/Test/output/cuffdiff" is a valid path? I cannot seem to re-create this issue using a similar approach to yours. Alternatively, can you just provide the directory path directly to readCufflinks instead of going through file.path()? -Loyal On Jun 26, 2012, at 2:03 PM, Hardcastle, Justin wrote: > Hi, > I'm having an issue running cummeRbund on my cuffdiff output. CummeRbund is giving me a DB error and not creating the DB. The code and error are below. > > library("cummeRbund") > > dir = "~/Test" > outdir = "output/cuffdiff" > cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE) > > The error given is > >> cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE) > Creating database ~/Test/output/cuffdiff/cuffData.db > Error in sqliteNewConnection(drv, ...) : > RS-DBI driver: (could not connect to dbname: > unable to open database file > ) > > I am running cummeRbund 1.2.0, and Cufflinks 2.0.1. > > Thanks for any help. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ADD COMMENT • link written 4.3 years ago by Loyal Goff • 130 I've managed to make it run using the absolute path. I thought I was using the absolute path, but it turns out I could have been more explicit which made it start at least. I'm getting a new error now though. The error is below. Reading /Volumes/home/Justin/Projects/Test/output/cuffdiff/cds.diff Writing CDSDiffData table Indexing Tables... Error in s
limits your access. Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... Similar Threads Thread Thread Starter Forum Replies Last Post could not find function "readCufflinks" cummeRbund jhsandgren RNA Sequencing 5 12-19-2015 01:00 PM MiSeq gDNA reads still fail "Kmer content" and "per base seq content" after trimming" ysnapus Illumina/Solexa 4 11-12-2014 07:25 https://support.bioconductor.org/p/46507/ AM avoid cummeRbund "getGenes" automatically sorting geneIDs GuiFF Bioinformatics 1 07-07-2014 10:05 AM DEXSeq error in estimateDispersions: match.arg(start.method, c("log(y)", "mean")) fpadilla Bioinformatics 14 07-03-2013 02:11 PM CummeRbund csDendro error: "need finite ylim values" when replicates=TRUE mebbert Bioinformatics 4 07-18-2012 08:22 AM Thread Tools 11-03-2014, 08:20 AM #1 wendy liu Junior Member http://seqanswers.com/forums/showthread.php?t=47982 Location: Germany Join Date: Feb 2013 Posts: 2 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. wendy liu View Public Profile Send a private message to wendy liu Find More Posts by wendy liu 11-03-2014, 08:49 AM #2 ddias Junior Member Location: USA Join Date: Aug 2014 Posts: 1 Same problem I'm having
file, cummeRbund error. Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] I've managed to make it run using the absolute path. I thought I was https://stat.ethz.ch/pipermail/bioconductor/2012-June/046585.html using the absolute path, but it turns out I could have been more https://github.com/cole-trapnell-lab/cufflinks/issues/55 explicit which made it start at least. I'm getting a new error now though. The error is below. Reading /Volumes/home/Justin/Projects/Test/output/cuffdiff/cds.diff Writing CDSDiffData table Indexing Tables... Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: database is locked) cds.diff exists and has data, and the permissions on the DB file look fine for error in my user. Thanks for any help. -Justin ----- Original Message ----- From: "Loyal Goff"
Support Search GitHub This repository Watch 37 Star 96 Fork 62 cole-trapnell-lab/cufflinks Code Issues 43 Pull requests 6 Projects 0 Pulse Graphs New issue cuffnorm says "Error: cuffdiff requires at least 2 SAM files" #55 Open yuifu opened this Issue Mar 3, 2016 · 0 comments Projects None yet Labels None yet Milestone No milestone Assignees No one assigned 1 participant yuifu commented Mar 3, 2016 When I run cuffnorm (v2.2.1 (4237)) on single CXB file, I received a error massage "Error: cuffdiff requires at least 2 SAM files". I found the corresponding code in cuffnorm.cpp. cuffnorm.cpp Can't I apply cuffnorm on single CXB file? yuifu changed the title from cuff norm says "Error: cuffdiff requires at least 2 SAM files" to cuffnorm says "Error: cuffdiff requires at least 2 SAM files" Mar 3, 2016 Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Contact GitHub API Training Shop Blog About © 2016 GitHub, Inc. Terms Privacy Security Status Help You can't perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.