Error using bedtools "intersect" command

Question

[hila]

Hi all,

I'm trying to intersect a vcf file (as file -a) with a bed file (as file -b). I'm getting this error:

ERROR: Received illegal bin number 4294967295 from getBin call.
ERROR: Unable to add record to tree.

After reading some previous similar questions, I made sure that my bed file is tab delimited and sorted.

When using the -sorted flag I got an error on my first position in the bed file:

Error: Sorted input specified, but the file file.bed has the following out of order record
1       2336225 2337283

Would appreciate any suggestions

Thanks
Hila

adding

My command line is:

bedtools intersect -a file_a.gz -b file_b.bed

I don't have headers in both files

[jomo018]

chromosomes on the bed file are: 1, 2, 3 rather than chr1, chr2, chr3?

[hila]

yes, does it matter? should I change it to chr1, chr2...?

[finswimmer]

Yes, this does matter!

All your files in your analyse pipeline should have the same naming schema. Otherwise you are running in problems like this one.

fin swimmer

[jomo018]

In addition to @finswimmer response, your sorting scheme is 1, 2, 3. If the gz file is chr1, chr2, chr3, it is probably sorted lexicographically (chr1, chr10).

[Bastien Hervé]

Hello, can you add your command line and the header of each files in your post please.

[hila]

I've added it to the original post. Thanks!

[Jeffin Rockey]

Do sorting of both the files with sort -V giving appropriate columns (e.g,1-3 in the given file.bed) and then try .

[finswimmer]

Hello hila ,

how did you made the sorting of both files? Also have a look at the line before and after the one bedtools is complaining about. How does they look like?

fin swimmer

[hila]

Hi, the sorting was done by

cat file_name|sort -k1,1n -k2,2n

The line bedtools is complaining about is the first line in the bed file, the line after it is in order Thanks Hila

[finswimmer]

Looks ok. Have you done it for both files?

In your initial post you wrote the filename is file_a.gz. How did you compress it? Using bgzip would be the right way.

fin swimmer

[hila]

I got the gz file from another source, I didn't make it myself. The thing is- this code already worked with the same gz file and another bed file, so I guess the problem is with the new bed file, I just can't find it :(

Answer 1

[Pierre Lindenbaum]

your coordinate system is too large for bedtools. This typically happens when the chromosome is longer than 500mb https://github.com/arq5x/bedtools2/blob/e5ad7e48108681fe93ee4600d07699ab278e3c56/src/utils/BinTree/BinTree.cpp#L118