Problem with datalad on HPC: Index file smaller than expected - git-annex: fd:23: hPutBuf: resource vanished (Broken pipe)`

Dear Community,

I try to process structural data with smriprep. My workflow follows a datalad handbook tutorial (3.3. Walkthrough: Parallel ENKI preprocessing with fMRIprep — The DataLad Handbook).

I have an issue with datalad / git-annex when trying to push freesurfer results (in a subdataset freesurfer/) from a remote branch in an ephemeral clone to the main dataset. As far as I understand the error, the index file in freesurfer/.git/annex/ gets somehow corrupted resulting in the following error:

“0: fatal: DATASET_ROOT/data/smriprep/.git/annex/index: index file smaller than expected
0: git-annex: fd:23: hPutBuf: resource vanished (Broken pipe)”

As I have a deadline incoming for that particular project in two weeks your help would be highly appreciated :slightly_smiling_face: