FileNotFoundError: [Errno 2] No such file or directory: 'result_merge_confound_metadata.pklz' #1819
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Here is the output from fmriprep-docker.
Error 1: Error 2: |
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Hi @ppdac, although you are right this is somewhat related to #1807, you are experiencing the worst case of these problems. We are still investigating the conditions that lead to the problem you've seen - could you send us the full output log from fmriprep? Is the problem solidly replicable (i.e., if you remove the work directory and rerun it will happen the same)? |
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Okay, I will do that as soon as I can. But I just wanted to let you know that I pulled the image with the unstable tag and that ran successfully.
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Hi @oesteban, Thanks for looking at this. Here is the full output of the run: I will remove the work directory, rerun and post the output of that when it's finished. |
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Second run: Error 1 Error 2 |
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If it helps, I ran into a similar issue (referenced here) with this crash log: @ppdac is it also true for you that the 'missing' files actually do exist in the working dir? Original comment: #1697 (comment)_ |
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Hi @jarodroland, would these be the working directories in the container or host machine? If it's on the container, can you help me understand how to take a look at that? The containers seem to remove themselves after running. |
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Hi @oesteban, the unstable tag wound up producing semi-inconsistent errors too. 1.5.1rc1 was successful on the initial run. I'll let you know how future runs look. |
@ppdac, Did you @ the wrong person? |
Yes, sorry. That was meant for @jeroenvanbaar. |
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Hi @oesteban, an update on 1.5.1rc1: no inconsistent errors so far with jobs completing successfully. File: 1.5.1rc1.run1.log.txt File: 1.5.1rc1.run2.log.txt Please let me know if there's anything I can test further. |
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@ppdac I can find these files in the working dir on my host machine. In my case, I manually set the working dir to a designated scratch directory on the computing cluster using the -w flag in the fmriprep command. All intermediate files will remain there after running fmriprep it seems |
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@jeroenvanbaar, thank you for the suggestion. I will try it if 1.5.1rc1 starts to give my users problems. But I may be misunderstanding you, I don't think I have the correct files. -- There are many |
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So does the current release candidate solve this issue? I'm trying to run a large amount of subjects through fmriprep on our HPC. So far a few hundred succeeded, but a few hundred others had errors along the lines of any of the following: |
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We've just seen this problem with fMRIPrep 1.5.1rc1 on our HPC: |
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Ugh. I was really hoping this was resolved. Does the file actually exist? Since we at least have a full path now, perhaps it is just a FS synchronization issue? |
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I guess in the worst case, we could do |
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pinging @satra for him to check on the latest 3 posts.
It is shaping us as such.
We could call @mangstad as you can see in my traceback, I am getting one of those FileNotFoundError but the node that actually breaks is not that corresponding to the missing file, it is a different one (called |
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Ran that find on my output directory, then a few sed's to trim off everything but the node name. Looks like in my case it's not usually update_metadata. This is over everyone in my output folder, not just those with the No such file or directory: 'result_...pklz' errors, so it's definitely possible there are some other unrelated crashes in there as well. $ find ./ -name "crash-*" | sed 's/./.mangstad//' | sed 's/^-//' | sed 's/-.//' | sort | uniq -c |
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What is the status on that bug? Is it solved with rc1 or rc2? |
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We are pushing to cut a new full-release ASAP. |
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About Errors Thank you all for the hard work! To other users, sorry, I don't know which patch resolved this issue. |
Hello we've been getting file not found errors with fmriprep-docker.
I've tried running without the wrapper:
sudo docker run -v /louis/raw_bids:/data -v /louis/derivatives:/out -v /louis/tmp:/scratch -v /usr/local/freesurfer:/freesurfer poldracklab/fmriprep:1.5.0 --fs-license-file=/freesurfer/license.txt --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345 -w /scratch /data /out participantRather late in processing the following error occurs:
A second error #1807 also occurs.
I will post the log of fmriprep-docker when that finishes.
I understand an update is slated for #1807, is this related?
Many thanks,
Louis
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