SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem with cummeRbund and RSQLite noplacetoh1de Bioinformatics 9 11-03-2014 01:33 PM
gene tracking with cummerBund - persistent problem stephenhart Bioinformatics 2 11-03-2014 01:03 PM
Segfault in tophat_reports miseiler Bioinformatics 22 03-28-2014 05:41 AM
Problem with cummeRbund and RSQLite :( dadada4ever Bioinformatics 3 07-31-2013 09:13 AM
bwa 0.6.1-r104 segfault problem rwhet052 Bioinformatics 4 10-30-2012 05:23 AM

Reply
 
Thread Tools
Old 05-04-2013, 05:11 AM   #1
vd4mindia
Member
 
Location: Milan

Join Date: May 2013
Posts: 40
Unhappy CummeRbund problem in R with segfault

Hello guys, I am new to R an using it in Mac OSx which I started handling 4 months back. I am using cummeRbund to visualize my data outputs of the cuffdiff analysis and get an idea of the DE genes through different plots. I am unable to create the database after I load the library cummeRbund. When am executing the command cufflinks , it runs for a while and then stops with a segfault error and memory not mapped message. I tried to clear all the cache memory as well but still I am unable to fix it. I have to work on some data urgently and am stuck. It would be nice if you could suggest me something. I am not an expert in R so directly dealing with the diff_exp gene outputs of cuffdiff for creating the matrix and plots is being a bit cumbersome for me. Below are the errors am receiving. Please assist me.

And then when I am calling the library of cummeRbund its is called but as I create the database with the output with readCuffLinks() the below error occurs. Please assist.

Creating database ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/cuffData.db Reading Run Info File ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/run.info Writing runInfo Table Reading Read Group Info ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/read_groups.info Writing replicates Table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading ~/Documents/RNA-Seq_Smaples_Udine_08032013/cuffdiff_UD_allvsall3/gene_exp.diff

* caught segfault * address 0x51a41311b, cause 'memory not mapped'

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection:

It would be appreciable if you can give me some idea and help me out.

Thanks,
vd4mindia is offline   Reply With Quote
Old 05-30-2013, 06:03 PM   #2
lgoff
Member
 
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Can you post the first few lines of your gene_exp.diff file? It may be something in there. I'll be happy to take a look...


Loyal
lgoff is offline   Reply With Quote
Reply

Tags
bioinformatic analaysis, cummerbund, r programming, segfault

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO