HDF5 error: Object 'GeneScoreMatrix/chrX/x' does not exist in this HDF5 file.

[bj-chen]

Hi ArchR team,

I was trying to subset 5k cells from the original ArchR object which contains ~260K cells. However, I run into problems with the function getMarkerFeatures which gives the following error:

Error in .safelapply(seq_along(matchObj[[1]]), function(x) { :
Error Found Iteration 3 :
[1] "Error in h5read(ArrowFile, paste0(useMatrix, "/", seqnamex, "/x")) : \n Object 'GeneScoreMatrix/chrX/x' does not exist in this HDF5 file.\n"
<simpleError in h5read(ArrowFile, paste0(useMatrix, "/", seqnamex, "/x")): Object 'GeneScoreMatrix/chrX/x' does not exist in this HDF5 file.>
Error Found Iteration 4 :
[1] "Error in h5read(ArrowFile, paste0(useMatrix, "/", seqnamex, "/x")) : \n Object 'GeneScoreMatrix/chrX/x' does not exist in this HDF5 file.\n"
<simpleError in h5read(ArrowFile, paste0(useMatrix, "/", seqnamex, "/x")): Object 'GeneScoreMatrix/chrX/x' does not exist in this HDF5 file.>
Calls: ... getMarkerFeatures -> do.call -> -> .safelapply
Execution halted

I attached the logfile and would really appreciate any help.

Thank you!

ArchR-getMarkerFeatures-5f6e43f99ed2-Date-2022-02-10_Time-12-15-00.log

[rcorces]

Since this is an error report, it should go to Issues.