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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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gem-indexer and tmp file #20

Closed descostesn closed 3 years ago

descostesn commented 3 years ago

Hi,

When using the gem-indexer, I get the error Could not write to file 'chr1.sa.tmp'.

This is because this file is written to my home folder that has only 800 mb of space on our hpc.

Is it possible to redirect the location of this temporary file?

Thanks for you help.

Nicolas

smarco commented 3 years ago

Yes. The easiest option is to change the working directory from which you call the gem-indexer.

cd /tmp /usr/local/bin/gem-mapper [...]

descostesn commented 3 years ago

I am not calling it from my home directory, however it is putting this file in the home directory by default. If you mean something different, I do not get it.

smarco commented 3 years ago

By default, it puts all the temporal files where the command specifies. That is:

cd /tmp
/usr/local/bin/gem-mapper -i /data/chr1.fa -o /tmp/chr1

Will save everything on the temporal folder '/tmp' However, you can always use the option '--tmp-folder=/tmp/' I hope this helps.

descostesn commented 3 years ago

Thank you. At the end I redirected my home folder to a share drive on the hpc and it worked.