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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Error in creating bmat #82

Closed znavidi closed 4 years ago

znavidi commented 5 years ago

Hi,

Thank you for your tool. I am analyzing some of the 10X scATAC-seq data with SnapATAC and while creating bmat from snap files this error happens for some of the samples in this page (https://support.10xgenomics.com/single-cell-atac/datasets):

Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, : Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter. Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, : Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.

I have never seen this error before and I don't think it related to the size of barcodes, because there are some samples with much higher number of barcodes that work fine while some other samples with different rang of barcode number get this error.

I would really appreciate if have any suggestion for me to solve this problem.

Best,

znavidi commented 5 years ago

Hi, Since I have not been able to solve this problem, any help from you would be appreciated.

Best,

zhongjixing commented 4 years ago

hi, Have you solve this problem? I encountered the same error when running addPmatToSnap.

zhongjixing commented 4 years ago

I updated rhdf5 to 2.30.0 and the problem is gone.

znavidi commented 4 years ago

Hi,

The problem was solved, but I don't remember how since it happened some months ago. Anyway, thanks for letting me know in case it happens again :)