Question: multiIntersectBed Error: The requested bed file could not be opened. Exiting!
0
gravatar for yren0429
2.5 years ago by
yren04290
yren04290 wrote:

Hi fellow bioinformaticians,

I am trying to use multiIntersectBed to find intersections of genomic regions (copy number variations) in ~1400 samples. For each sample, I have a sorted bed file.

When I used multiIntersectBed on 5 bed files as a test, it worked perfectly. But when I used it on all ~1400 samples, I received the following error: "Error: The requested bed file (file1.bed) could not be opened. Exiting!"

However, this bed file runs fine if I only input a few bed files instead of 1400 . Therefore it seems to me like a problem regarding the number of files I can open at a time.

Does anyone know if there is a limit in the number of bed files that multiIntersectBed accepts? If so, is there a way to work around it?

Thank you very much for your help!

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by yren04290
1

I guess this more a limitation by the OS.

On many linux distribution the maximum number of open files is 1024. You can find it out on your system with

$ ulimit -n

There seems to be many ways to increase the number if necessary, e.g. like here

fin swimmer

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by finswimmer14k

Do you mean the multiIntersectBed in bedtools 2.14.1? Can you give us the exact command you're using as well the bedtools version please?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Ram32k
0
gravatar for yren0429
2.5 years ago by
yren04290
yren04290 wrote:

Great thanks to Ram and finswimmer for offering your help! Turns out it was indeed a problem with the max number of open files. The soft limit on my linux system is 1024, but the hard limit is 4096. I was able to increase my soft limit to up to 4096, and multiIntersectBed ran perfectly.

Below are codes to increase the soft limit for people who need it:

## view original soft limit
ulimit -Sn

## increase soft limit to 4096
ulimit -n 4096

##check soft limit again, now it should be 4096
ulimit -Sn

Many thanks again!

ADD COMMENTlink modified 2.5 years ago by Ram32k • written 2.5 years ago by yren04290
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