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immunogenomics / symphony

Efficient and precise single-cell reference atlas mapping with Symphony
GNU General Public License v3.0
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error: Mat::init(): requested size is too large #22

Closed plantformatics closed 2 years ago

plantformatics commented 2 years ago

The error arises when running mapQuery. I successfully built the reference object and can process the integrated reference using my preferred analytical framework. I should mention that I am working with scATAC-seq data (the reference is ~100,000 nuclei) and the query contains multiple libraries encompassing ~400,000 cells. The feature size is around 66K and are matched between the reference and query data sets. Any suggestions for a work around would be welcome. Thank you for producing this tool, it is a big advance for the field.

plantformatics commented 2 years ago

Seems the issue was the large number of query cells to be placed on the reference. I solved the problem by mapping each query library in parallel and merging the output.