stuck copying files because of cellranger

Discussion in 'Tech Discussion' started by Shiki, Jun 22, 2022.

  1. Shiki

    Shiki Well-Known Member

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    So... I tried to back up my Documents folder. this file named cellranger just halt the copying process. it's from this:https://cran.r-project.org/web/packages/cellranger/index.html since I just installed the R package in my documents previously because I did not give the program admin access.

    The problem right now is that the dialogue box for cancelling is not showing any response. The fan RPM is high (though looking at the task manager, neither disk nor CPU shows overutilization. GPU strangely show some activity though.

    I don't think it's related to GPU. So... it's something strange?

    if it helps, I am trying to copy file from my second SSD to drive.
     
  2. SoulZer0

    SoulZer0 Heaven Refining

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    Give screenshots or something man. Like why it's stopped. Screenshot of the dialogue box.

    It's probably still running in the background and being considered as opened. So that's why it's stopped.

    Try open Task Manager and kill the program related to Cellranger.

    Then try again.
     
  3. Shiki

    Shiki Well-Known Member

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    upload_2022-6-22_15-49-55.png

    Like this. it just goes to zero when it comes to this file.
    Considering it is in my old SSD that has its own OS, why does it have any running program? I reinstalled the OS into my new SSD, and running the OS from my new SSD. So honestly I am doubtful any program other than explorer is accessing it.

    upload_2022-6-22_15-54-32.png
    this is my search. Curiously, cellranger is already deleted.

    To be honest, I don't know where it goes wrong. The file seems to exist in multiple location simultaneously and don't exist at all. When I divide several folders into sets of folders [A-H],[I-R],... the cellranger stop exists in those. upload_2022-6-22_16-2-36.png
    these two are two different, non intersecting sets of folders. They just stop.

    As for reason for this, I suspect it is because the boot loop caused by cancelling samsung SSD data migration. I tried to migrate my OS, and it doesn't have any progress after leaving it overnight, leaving at 0%. Cancelling it causes my second SSD to be unable to boot. I just give up and install my OS on my first SSD right now.
     

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  4. Kemm

    Kemm Custom title

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    From my experience, when something like that happens is because the file is too big or something makes it to slow the copying process to a crawl. Give it enough hours and most likely it will finish.

    Otherwise, cancel the transfer from the Task Manager, copy the rest of the uncopied files (except that program) and reinstall it if you want.
     
  5. Shiki

    Shiki Well-Known Member

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    yep. I try to isolate which file is problematic, because there is no actual cellranger file/folder in my documents.
     
  6. Siebzehn

    Siebzehn 95% Lurker

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    maybe cellranger is in a hidden folder and maybe it is a link to a folder above resulting in a loop
     
  7. Kemm

    Kemm Custom title

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    From what you say, it seems to be a weird direct access that's most likely a hidden system file and which may be acting as some kind of proxy file.
     
  8. Molen

    Molen Well-Known Member

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    Sometimes file name can be a problem, if a file path (folder name + file name) is too long, windows might not be able to copy / move that file. I have this problem when i tried to move a folder into another drive, inside a nested folder. Because the file path is too long the file transfer stuck at 0 and never finished.

    You might also try use robocopy (windows terminal copying library) or fastcopy (software to copy things quickly made by japanese guy).

    You can also try to compress your folder (zip / rar) before copying it.


    Instead of task manager, try to use performance monitor (you can open it from task manager), it shows more information than task manager.

    edit: i just remember that sometimes there are hidden folder/files that cant be seen in windows explorer, even though you enable "show hidden files" option. For example ".git" folder. Sometimes these folder has a specific permission that block the transfer/copy process.