Error with BEDTools

[fanwei]

Dear all,
I want your help!
I want to use bedtools to calculate the overlap between two bed format files.It recorded chromosome，startposition and endposition informations.
When i run bedtools, there was no error indicated and no results displayed. But i'm sure overlaps exist!
Maybe bedtools restricted the file size?
I feel confused. Can you kindly help me?

[Jetse]

What is the command you used?
How do the files look like?

[fanwei]

What is the command you used?
How do the files look like?

I used bedtools intersect -a A.bed -b.B.bed
The first few lines are as follows,

[Jetse]

What is your output when you use the command:

bedtools intersect -a A.bed -b B.bed -wao | less

Do you see a lot of output, all with a zero at the end? (this means they don't have overlaps)

[fanwei]

What is your output when you use the command:

bedtools intersect -a A.bed -b B.bed -wao | less

Do you see a lot of output, all with a zero at the end? (this means they don't have overlaps)

There was nothing even zero.
But it works when i write some data in new files to test that.
Is it necessary to sort my data?

[Jetse]

It could be your computer ran out of memory, then sorting would solve your problem.

From the manual:

Note
If you are trying to intersect very large files and are having trouble with excessive memory usage, please presort your data by chromosome and then by start position (e.g., sort k1,1 -k2,2n in.bed > in.sorted.bed for BED files) and then use the -sorted option. This invokes a memory-efficient algorithm designed for large files.

[fanwei]

It could be your computer ran out of memory, then sorting would solve your problem.

From the manual:

I have tried it,but it doesn't work.
Any other suggestions?

[fanwei]

It could be your computer ran out of memory, then sorting would solve your problem.

From the manual:

It has been resolved.Thank you!

[Jetse]

How did you solve it?
So other people who find this thread with the same problem can try your solution too...

[fanwei]

How did you solve it?
So other people who find this thread with the same problem can try your solution too...

It is due to file format error caused by newline character.
And your suggestions are also really important!