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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error in gzfile(file, mode) : cannot open the connection #333

Open caoligang-git opened 2 years ago

caoligang-git commented 2 years ago

When I run run'runSCENIC_2_createRegulonss', 'error in gzfile (file, mode): cannot open the connection.' causes me not to proceed to the next step

tfguinan commented 2 years ago

Hi there, I've run into a similar error at earlier steps in the analysis.

To resolve, I first checked my session was running in the correct directory. There should be ./int present (normally created by SCENIC), as this is where the tool will store some RDS files.

Secondly, make sure the path that is trying to be written does not point to a pre-existing file (i.e from an old run) - this may cause the issue also.