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!
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written
by
R •
1 answer
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
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Here's an alternative that performs the same calculation: A: Use bedtools intersect to see how much coverage you had of a specific coordinate
Thank you for your help! But I even get the 'bus error' as I'm trying to sort the .bed file.
Perhaps post your files somewhere (Google Drive etc.) and copy/paste your command. That would help troubleshoot the exact error message.