cat: write error: Disk quota exceeded

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ern...@ebi.ac.uk

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Feb 27, 2019, 7:02:48 AM2/27/19
to Nextflow
Hi,

I was wondering if anyone has experienced some issues with jobs being idle when trying to execute them in a LSF cluster and when I check the .command.log file I see that 
I got the following error:

cat: write error: Disk quota exceeded

I assume that this is because nextflow is trying to write to my home directory and we have a disk quota at my institute that has been surpassed. I was wondering if anyone has had similar issues and
managed to fix them

Thanks,

ernesto

Paolo Di Tommaso

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Feb 27, 2019, 7:45:35 AM2/27/19
to nextflow
Launch your pipeline in a (shared) directory having enough spare or specify it with the `-w` command line option. 

p

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Paolo Di Tommaso

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Feb 28, 2019, 2:11:40 AM2/28/19
to ernesto lowy gallego, nextflow

Yes, the pipeline is run from a shared dir with enough space, so this should not be the issue.

The error message is quite clear..    ¯\_(ツ)_/¯
 

Also, can you please let me know how can i get documentation for this -w command line option, I only get:

Unknown option: -w -- Check the available commands and options and syntax with 'help'


That's an option of the `run` command, checkL 

nextflow run -h 


Hope it helps 

p
 
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