bedtools intersect: ERROR: Received illegal bin number -1 from getBin call.

[phil-grayson]

Hi!

I recently ran into a new error with bedtools v2.29.2. I started using a new system for an analysis pipeline I had built on a different system under bedtools v2.25.0 and I am getting the error below when I try to intersect the two files that I have attached down2.txt down1.txt bedtools intersect -wo -a down1.txt -b down2.txt > down_both.txt

ERROR: Received illegal bin number -1 from getBin call.
Maximum values is: 2396745
This typically means that your coordinates are
negative or too large to represent in the data
structure bedtools uses to find intersections.ERROR: Unable to add record to tree.

I took the files back to my v2.25.0 system and they work fine there. I also tried on a different machine with v2.29.2 installed and the identical error as on my v2.29.2 system.

ERROR: Received illegal bin number -1 from getBin call.
Maximum values is: 2396745
This typically means that your coordinates are
negative or too large to represent in the data
structure bedtools uses to find intersections.ERROR: Unable to add record to tree.

I had installed my v2.29.2 via brew install bedtools. The other v2.29.2 system I tried it on is a Compute Canada SLURM system with that version as one of the available modules.

Thanks!

[arq5x]

@38 would you mind looking into this please?

[38]

Hi,

I think the issue is the input file down2.txt contains invalid record:

NW_021821572.1  0       0

And this causes the bin tree failed to lookup the bin.

[tshtatland]

Hi,

I think the issue is the input file down2.txt contains invalid record:

NW_021821572.1  0       0

And this causes the bin tree failed to lookup the bin.

I am having the same error.

I do not think that chr1 0 0 should be considered an illegal record. This is the position 5' of the first base of the chromosome. It is the end of the chromosome.

I am using bedtools v2.30.0, installed by conda on M1 Max MacBook Pro.