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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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no space left on device [errno28] #42

Closed cyber-ux closed 4 years ago

cyber-ux commented 4 years ago

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

fbrennen commented 4 years ago

Hi @lucio-cyber -- are you saying that you did not have enough disk space to write out all the single-read files?

cyber-ux commented 4 years ago

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?

fbrennen commented 4 years ago

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.

cyber-ux commented 4 years ago

Okay, he says to me: Filesystem Size Used Avail Use% Tank __ 27T 27T ___0 100%

fbrennen commented 4 years ago

That'll do it -- 100% used means you have no space left on your device. You'll need to free some up.

cyber-ux commented 4 years ago

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?

cyber-ux commented 4 years ago

Ok I checked, it's definitely a question of space ... I had also clogged the server. Some advice ?

fbrennen commented 4 years ago

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.

cyber-ux commented 4 years ago

Ok ok, thanks so much for your support! Best regards