[bedtools][fastaFrombed] could not stat file

[Azazel]

I have a fasta file rn4.fa with the rat genome and also a fai file rn4.fa.fai which I generated with samtools faidx. I want to extract fasta from bed like this (below), but I get an error message "could not stat file".

fastaFromBed -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa
could not stat file../rn4/rn4.fa

I am using fastaFromBed Version: v2.16.1

I am pretty much stuck here - anything I can do to get fastaFromBed working?

Thanks!

[GenoMax]

Are you using the command correctly?

getFastaFromBed OR bedtools getfasta

Manual here: http://bedtools.readthedocs.org/en/l.../getfasta.html

Another thing is to verify that the file in question is actually present at the relative path (../rn4/rn4.fa).

[Azazel]

Are you using the command correctly?

getFastaFromBed OR bedtools getfasta

Manual here: http://bedtools.readthedocs.org/en/l.../getfasta.html

Another thing is to verify that the file in question is actually present at the relative path (../rn4/rn4.fa).

These three commands all give me exactly the same error message (as described above):

fastaFromBed -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa
getFastaFromBed -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa
bedtools getfasta -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa

Yes, the file definitely exists at the relative path:

user@machine-VirtualBox:~/clover$ file ../rn4/rn4.fa
../rn4/rn4.fa: ASCII text

One thing I note is that the error message, as descibed in my original post, is:

could not stat file../rn4/rn4.fa

There is no space between the string "could not stat file" and the path/file - could this mean something?

[GenoMax]

I wonder if the error is related to virtual server (looking at your system prompt). Are those file paths local to the VM? What OS are you running in the VM?

[Azazel]

I wonder if the error is related to virtual server (looking at your system prompt). Are those file paths local to the VM? What OS are you running in the VM?

I am running Xubuntu inside Virtual Box, with Windows 7 as host. Everything is inside VB/Xubuntu, so I don't see how this could affect antyhing.

"file paths local to the VM": sorry, I don not understand what you mean by this at all. The file paths are relative to root (/), inside Xubuntu.

[GenoMax]

I am running Xubuntu inside Virtual Box, with Windows 7 as host. Everything is inside VB/Xubuntu, so I don't see how this could affect antyhing.

"file paths local to the VM": sorry, I don not understand what you mean by this at all. The file paths are relative to root (/), inside Xubuntu.

Since there does not seem to be a logical explanation to what you are seeing I was merely expressing a possibility that this error may be somehow related to the fact that you are running this in a VM.

"file paths" referred to a possibility that your local PC file system may be auto-mounted and visible in your VM.

[Azazel]

Since there does not seem to be a logical explanation to what you are seeing I was merely expressing a possibility that this error may be somehow related to the fact that you are running this in a VM.

"file paths" referred to a possibility that your local PC file system may be auto-mounted and visible in your VM.

Now I understand. No, I don't think this is the reason because I am not mounting anything external, and the file is definitely there when I use the "file" command, open it in an editor etc.

The same error "could not stat" also appears when the rn4.fa and rn4.fa.fai files are in the very same directory from where the command is run, not using relative pathnames.

"there does not seem to be a logical explanation": one logical, obvious explanation is that there could be a bug in bedtools v2.16.1.

Has anyone who uses bedtools v2.16.1 encountered the "could not stat file" error message? Do you know how to fix this? Any help specific to this problem would be much appreciated - thanks!

[GenoMax]

Current version of bedtools is 2.17.0. If that still does not work then consider contacting Aaron Quinlan, the developer of Bedtools.

One more thing. Have you allocated enough RAM to the VM and are you using 64-bit Xubuntu in the VM?