Question: Error Using Intersect Tool: "Problem: 536870912 Is Larger Than The Size Of This Bitset (536870912)."
gravatar for sjosa
3.9 years ago by
European Union
sjosa10 wrote:


I am using the intersect tool of galaxy to overlap two intervals and I am having the next error "Skipped 1 invalid lines of 1st dataset, 1st line #45: "chrX 152661391 152661717 exon ", problem: 536870912 is larger than the size of this BitSet (536870912)."

I do not know if it is affecting my results or is only a warning error

The history is

I do not know how to overcome this problem.




Santiago Josa De Ramos
Centro Nacional de Biotecnología (CNB-CSIC)
Lab. 111
Campus de Cantoblanco
C/ Darwin, 3
28049 Madrid (Spain)

galaxy intersect • 1.0k views
ADD COMMENTlink modified 3.7 years ago by olivernozzycat0 • written 3.9 years ago by sjosa10
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You have come across a very (very) rare bug that we have not been able to track down and resolve fully. A ticket exists for this issue here, if curious:

Sometimes adjusting the inputs slightly can avoid the issue. Change the sort order or something similar that does not impact the content in any meaningful way. This has worked in some cases, and not in others. If it doesn't, then try running the data through in batches by breaking up one or both of the datasets into two or more sub-files, then merge the results. This will almost certainly avoid the issue but is a more tedious route. Tools in Text Manipulation can subset datasets by line and "Concatenate" results back together, then use the "Sort" tools if you wish.

Very sorry for the inconvenience, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k

I don't think this error is as rare as you think it is; I encounter it fairly often.  I've put up a public minimal example:

This history uses the intersect tool on 2 single-line bed files, and gives the error.  I note that, at least in this case, the correct output is still generated, but I don't know if that's generally the case when encountering this bug.

ADD REPLYlink written 3.7 years ago by diana-kolbe0

Thank you for sending this in. I ran several more tests with a simple set of inputs grouped in various ways and perhaps this will help to uncover the issue (I wasn't able to pinpoint one specific issue except for some connection to the "order" of the inputs on the tool form). I linked my test cases to the existing Trello ticket. You can follow this ticket for updates about any corrections. Best, Jen, Galaxy team

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Jennifer Hillman Jackson25k
gravatar for olivernozzycat
3.7 years ago by
United States
olivernozzycat0 wrote:

I just came across this error intersecting my gene list bed files with a CpG island file for the rat genome. I created that file on Wed Feb 18 21:07:27 2015 (UTC) . When I created a new rat genome CpG file ,Tue Mar 3 17:18:54 2015 (UTC), the error didn't occur.

ADD COMMENTlink written 3.7 years ago by olivernozzycat0
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