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files and directories are being deleted from fsaverage and fsaverage5 #1

Closed jbwexler closed 2 years ago

jbwexler commented 2 years ago

This is happened in numerous datasets and I've ruled out that they're being deleted by TACC since I found instances of them being deleted only a few days after being created. I also think I can rule out that it's any recent addition to my script because I found a similar instance in one of the four datasets I ran in august. Now I'm looking into the git history of a particular dataset (ds000003) to see if I can piece together what happened. I found the commit where the files were deleted and have pieced together a little timeline:

2/15: Various initializing commits 2/15: First job submitted (20220215-143852-28f1) 2/18 12:24pm: First job started (20220215-143852-28f1) - this is the earliest time when the freesurfer files could have been created 2/18: First job completed (20220215-143852-28f1) - job cancelled preventing reproman commit upon completion 2/23: Commit 651b09ff - reinstalled tacc-openneuro 2/23 6:26pm: Commit e30420d0 - seems to be the one the commits all the changes from first job. Includes the creation of all the freesurfer files in question. 2/25 5:07pm: Commit 27fa0715 - the culprit, the deletion of the freesurfer files. Also shows the deletion of sub-13 fmriprep output, which I had done intentionally to prepare to rerun this sub. 2/25 5:07pm: Second job submitted (20220225-170719-e028) 2/26: Second job begins (20220225-170719-e028) 2/26: Second job completed (20220225-170719-e028) 2/26: Commit 27fa0715

Thus it seems that the files were deleted sometime between 2/23 at 6:26pm and 2/25 at 5:07pm and did not occur during a job.

jbwexler commented 2 years ago

Update: these files were in fact deleted by TACC!! They were deleted on 2/24, despite the fact that they were created on 2/18, only 6 days earlier. TACC says they don't delete files unless they haven't been accessed for 10 days, and even then they normally wait longer than that. So not sure what happened. Talking to TACC support about this.

jbwexler commented 2 years ago

Here's a list of files that were deleted from ds000003 on 2/24:

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jbwexler commented 2 years ago

This turned out to be a weird issue where the access times of git annex links were taking on the creation times of the files they're linking to, which in the case of fsaverage, is very old. Thus the links would get deleted in TACC purges, and the underlying files would get deleted up on datalad save. TACC was looking into the cause, not sure if they ever figured it out. To avoid the issue, I simply pre-populate with fsaverage and fsaverage5 and alter the creation time to now.