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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 createSnap() #31

Closed IMJoeyZhu closed 5 years ago

IMJoeyZhu commented 5 years ago

When I running the createSnap() I got these following error information:

> x.sp = createSnap(file="atac_v1_adult_brain_fresh_5k_2.snap",sample="atac_v1_adult_brain_fresh_5k",num.cores=1)
Epoch: reading the barcode session ...
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  HDF5. Dataset. Read failed.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
  HDF5. Dataset. Read failed.
Error in data.frame(barcode, TN, UM, PP, UQ, CM) : 
  arguments imply differing number of rows: 0, 8033

I check my R version: 3.5.1 and upgrade the rhdf5 package to version: 2.26.2. But still get these information, how can I fix it?

Best,

r3fang commented 5 years ago

This is likely because the dependencies Rhdf5 and Rhdf5lib are not successfully installed. Can you install these two R packages separately?

https://bioconductor.org/packages/3.7/bioc/html/rhdf5.html

Let me know if this still does not solve the problem

Are you running this on windows?

IMJoeyZhu commented 5 years ago

I run this on linux, and you advices are pretty helpful. I upgraded these two R packages and found out it works. Thanks a lot!

Best