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 #001: 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 #002: 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 #003: 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 #004: 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

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[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