BedTools intersect - Segmentation fault
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6.5 years ago
Maria333 ▴ 20

Hi,

Has anyone experienced the "segmentation fault" error while trying to use bedtools intersect option? I am trying to see overlap exons between 2 bed files but I'm getting this error all the time. Any help will be much appreciated.

Thank you

bedtools human exons • 4.2k views
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Output of three commands: `ẁhich bedtools`, `bedtools --version` and `uname -a` could be helpful to know about your setup

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6.5 years ago

If you are working with very large files, sort the bed files based on Chr and then Pos.  sort -k1,1 -k2,2n and then use -sorted option.

From manual

-sorted    For very large B files, invoke a “sweeping” algorithm that requires position-sorted (e.g., sort -k1,1 -k2,2n for BED files) input. When using -sorted, memory usage remains low even for very large files

If you still face the problem, split the files by Chr and then try to run the program at chromosome level. Otherwise provide more details about your data and post the exact error

 

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Thank you very much for that, it helped a lot. I sorted the bed file and then used  sort -k1,1V to reverse the order so it is in ascending order.. Now I get the error: Error: The genome file sorted.bed.ascending has no valid entries. Exiting. 

Do you know why is this? The files seem fine now.. 

Thank you once again!

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can you post few lines from your files ?

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6.5 years ago

Another option:

$ sort-bed exons1.bed > sorted_exons1.bed
$ sort-bed exons2.bed > sorted_exons2.bed
$ bedops --element-of 1 sorted_exons1.bed sorted_exons2.bed > exons1_that_overlap_exons2.bed
$ bedops --element-of 1 sorted_exons2.bed sorted_exons1.bed > exons2_that_overlap_exons1.bed
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