reproduced this now

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Joey Hess 2022-09-22 13:21:10 -04:00
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[[!comment format=mdwn
username="joey"
subject="""comment 8"""
date="2022-09-22T17:02:04Z"
content="""
I've fixed the issue I found with --timestamp combined with -J. Which I do
think could have resulted in the same kind of problem. But you've shown
that is not the cause in your case..
"""]]

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[[!comment format=mdwn
username="joey"
subject="""comment 9"""
date="2022-09-22T17:04:35Z"
content="""
Thanks for the --debug. It shows that git-annex is asking git to refresh the index,
although from this we can't see for sure if it fed the name of the file in on stdin or not:
[2022-09-21 21:30:03.77319] (Utility.Process) process [3968453] feed: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"annex.debug=true\",\"update-index\",\"-z\",\"--index-info\"]
The other thing that seems maybe relevant is that the transfer happens in a `git-annex transferrer` process.
So, I think you have annex.stalldetection set.
[2022-09-21 21:29:59.931525] (Utility.Process) process [3968203] chat: /home/dandi/miniconda3/envs/dandisets/bin/git-annex [\"transferrer\",\"-c\",\"annex.debug=true\"]
And interestingly, that transferrer process fails at the end:
[2022-09-21 21:30:06.373343] (Utility.Process) process [3968203] done ExitFailure 1
Aha! I can reproduce it by setting annex.stalldetection.
"""]]