Bus Error When Using Bedtools Coverage

Question

[R]

Hi,

I am new to bioinformatics, and this forum, so apologies if I have done anything incorrectly, or if this is a stupid question. But I have attempted to search for the answer and not gotten anything relevant to what I'm doing. Currently I am trying to use bedtools coverage with my windows (.bed file) and data (.bam file), however, each time I try to run it, I get 'bus error,' and the job will not complete. Does anyone know what this means, and how I can fix it? All help is appreciated!

[Alex Reynolds]

Here's an alternative that performs the same calculation: A: Use bedtools intersect to see how much coverage you had of a specific coordinate

[R]

Thank you for your help! But I even get the 'bus error' as I'm trying to sort the .bed file.

[Alex Reynolds]

Perhaps post your files somewhere (Google Drive etc.) and copy/paste your command. That would help troubleshoot the exact error message.

Answer 1

[tim.triche]

a bus error in this context means that

1) your machine doesn't have enough memory for the task, and 2) the processor doesn't even have enough memory to ask for the memory it can't have

buy more RAM