Error Using Intersect Tool: "Problem: 536870912 Is Larger Than The Size Of This Bitset (536870912)."

Question: Error Using Intersect Tool: "Problem: 536870912 Is Larger Than The Size Of This Bitset (536870912)."

3.9 years ago by

sjosa • 10

European Union

sjosa • 10 wrote:

Hello,

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 https://usegalaxy.org/u/sjosa/h/cns-regions

I do not know how to overcome this problem.

Thanks

Santiago

--------

Santiago Josa De Ramos
Centro Nacional de Biotecnología (CNB-CSIC)
Lab. 111
Campus de Cantoblanco
C/ Darwin, 3
28049 Madrid (Spain)
e-mail: sjosa@cnb.csic.es
WEB: http://www.cnb.csic.es/~montoliu/

galaxy intersect • 1.0k views

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modified 3.7 years ago by olivernozzycat • 0 • written 3.9 years ago by sjosa • 10

3.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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:
https://trello.com/c/Hgye7i1n

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 COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

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:

https://usegalaxy.org/u/dkolbe/h/unnamed-history

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 REPLY • link written 3.7 years ago by diana-kolbe • 0

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

https://trello.com/c/Hgye7i1n

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

3.7 years ago by

olivernozzycat • 0

United States

olivernozzycat • 0 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.
Jennifer

ADD COMMENT • link written 3.7 years ago by olivernozzycat • 0

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