Question: Ballgown Error in file(file, "rt") : invalid 'description' argument
0
gravatar for vinayjrao
19 months ago by
vinayjrao110
JNCASR, India
vinayjrao110 wrote:

Hi, I am trying out the new tuxedo protocol (hisat, stringtie and ballgown). While calling the ballgown function with bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data), I get Error in file(file, "rt") : invalid 'description' argument

Any help in this regard would be appreciated.

Thanks in advance :)

rna-seq ballgown • 2.0k views
ADD COMMENTlink written 19 months ago by vinayjrao110

I can't find an explicit reference to a description argument in the ballgown constructor function so it must be an error from a function called within the ballgown constructor function. When you run R what is your working directory? The ballgown constructor function will look for data files in a subfolder of that directory called "ballgown" and then will look for files with the "ERR" pattern in the filename. Instead try explicitly giving the samples argument a vector of file paths to folders containing sample-specific ballgown data.

ADD REPLYlink written 19 months ago by James Ashmore2.6k

Firstly, thanks for the reply. My working directory is the parent directory of ballgown, and as mentioned in the paper "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown", the ballgown directory has a folder for each sample, within which my sample file with the ERR pattern is contained.

ADD REPLYlink written 19 months ago by vinayjrao110

Are you using a GFF file anywhere? If yes, how do mRNA or transcript lines look like, especially in the 9th field?

ADD REPLYlink written 19 months ago by Macspider2.8k

I am using gtf files, whose field 9 contains gene_id ; transcript_id ; cov ; FPKM ; TPM

ADD REPLYlink written 19 months ago by vinayjrao110

I think the problem might be dataDir = "ballgown". What happens if you use the fullpath?

ADD REPLYlink written 19 months ago by Macspider2.8k

I used the absolute path. It's still the same :(

ADD REPLYlink written 19 months ago by vinayjrao110

I have no idea how to solve it but googling a bit I found that Error in file(file, "rt") : invalid 'description' argument happens when a file is, for some reason, not accessible or not existing when trying to open it from R (and in other situations that are not R-related).

How is the permissions situation of the file? -rwxr--r-- ?

ADD REPLYlink written 19 months ago by Macspider2.8k

The permissions to the gtf file is -rw-rw-r--

ADD REPLYlink written 19 months ago by vinayjrao110

It probably won't work, but try chmodding it to 777!

ADD REPLYlink written 19 months ago by Macspider2.8k

You were right. That doesn't work either.

ADD REPLYlink written 19 months ago by vinayjrao110

Ok, then my job ends here, I can't help further ^^ However:

Let doctor Google help me, please!

ADD REPLYlink modified 18 months ago • written 18 months ago by Macspider2.8k

Hello Mr. Vinayrao, This error occurs when your files are not accessible

Just make sure you have set your path correctly using command setwd() and also mention the path while accessing your stringtie results:

bg_chrX = ballgown(dataDir = "path/to/folder/where/your/StrinTie/results/are/stored", samplePattern = "ERR", pData=pheno_data)

Another possibility could be the different and sophisticated name Keep the name of folders simple, and same as .gtf files have for eg., SRRXXX.gtf must be present in SRRXXX folder.

ADD REPLYlink written 4 months ago by swarajgaikwad150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1848 users visited in the last hour