no space left on device [errno28]
cyber-ux opened this issue · comments
Hi, I tried to convert multi fast5_pass into sigle fast5 with the following command : multi_to_single_fast5 -i fast5_pass -s fast5_single --overwrite
but at the end of this command some reads seem to have not been placed in the 'fast5_single' folder. How can I solve these problem?
Best Regards
Hi @LUCIO-CYBER -- are you saying that you did not have enough disk space to write out all the single-read files?
Yes, at the end of the process, the shell says me “no space left on device” with the reads that are missing.
But it is strange because I am on the server not on my pc, could it be that having created a space, this same space is too small? Or does it concern anything else?
I would check the space left on your server, and specifically in the output folder (try df -h fast5_single to see how much space is available) -- the error you're seeing is not from ont-fast5-api, but from your filesystem.
Okay, he says to me:
Filesystem Size Used Avail Use%
Tank ______ 27T 27T ___0 100%
That'll do it -- 100% used means you have no space left on your device. You'll need to free some up.
Sorry if I answer now, I did a couple of tests but when I start the following command: “multi_to_single_fast5 -fast5_pass -s fast5_single - - recursive -t 80” it always hangs at the same point, why ?
I made some space always stopping at the same point "\ 3184 of 3585 |################ | 88% ETA: 0:44:26".
What can depend on the size of my fast5_pass file?
In addition, it also locks my account on the server, makes me enter the password but does not allow me to access the account, makes me wait ... maybe I should start considering the fast5 subset command?
Ok I checked, it's definitely a question of space ... I had also clogged the server. Some advice ?
There's not a whole lot to say here, unfortunately -- fundamentally you need to find more space. You could try and work on a smaller number of files in the meantime.
Ok ok, thanks so much for your support!
Best regards