Error when converting h5Seurat to h5ad

[zoan128]

Convert("I:/result/csph-skuh/csph-skuh/csph.h5Seurat",overwrite = T,dest = "h5ad")

Validating h5Seurat file
Adding data from RNA as X
Error in assay.group$obj_copy_to(dst_loc = dfile, dst_name = "X", src_name = x.data) :
HDF5-API Errors:
error #000: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Ocopy.c in H5Ocopy(): line 259: source object not found
class: HDF5
major: Symbol table
minor: Object not found
error #1: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Gloc.c in H5G_loc_find(): line 430: can't find object
class: HDF5
major: Symbol table
minor: Object not found
error #2: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Gtraverse.c in H5G_traverse(): line 861: internal path traversal failed
class: HDF5
major: Symbol table
minor: Object not found
error #3: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Gtraverse.c in H5G_traverse_real(): line 641: traversal operator failed
class: HDF5
major: Symbol table
minor: Callback failed
error #4: D:/a/rtools-packages/

[jayypaul]

I also have this issue. I'm thinking it's v5 related?

[CeciPR]

I have the same error!

[LeaLe88]

Same here!

[zoan128]

I haven't reslove the problem, but the files can be converted by another tool named SCP.
https://link.zhihu.com/?target=https%3A//github.com/zhanghao-njmu/SCP

[CeciPR]

Thanks for the tip! I'll try that!

…

On Tue, Jan 16, 2024 at 1:34 PM zoan128 ***@***.***> wrote: I haven't reslove the problem, but the files can be converted by another tool named SCP. https://link.zhihu.com/?target=https%3A//github.com/zhanghao-njmu/SCP — Reply to this email directly, view it on GitHub <#162 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BEZNLDJA7K24SXU4QGB35VDYOZXVXAVCNFSM6AAAAAA4F2HF4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJTGY2TINJWGY> . You are receiving this because you commented.Message ID: ***@***.***>

-- *Cecilia Pessoa Rodrigues PhD*

[LeaLe88]

Thank you

[LorenzoMerotto]

Same issue here, even though I don't have Seurat v5

[thoalaubodah]

I also have this issue with a Seurat v5 object.

[zyzy-98]

Not using Seurat V5, but I do have this issue as well.

[matejasoretic]

same issue here, on Seurat v4

[Nicomakii]

Hey all, I found the solution here, you have to convert Seurat V5 back to V3 first