Is there an existing issue for this?
Have you loaded the SQANTI3.env conda environment?
Are you running SQANTI3 on its latest release?
Problem description
The following error pops up when running Sqanti3 filter
`ERROR:
Details: Command '/opt/conda/bin/Rscript /opt/conda/share/sqanti3-6.0.1-0/src/utilities/report_filter/SQANTI3_filter_report.R -d ./sqanti3_results -o test_cohort -u /opt/conda/share/sqanti3-6.0.1-0/src/utilities -f rules' returned non-zero exit status 1.
INFO:
ERROR:
-------------------------------------------------
SQANTI3 Rules filter report
--------------------------------------------------
Loading required package: magrittr
Warning message:
package ‘magrittr’ was built under R version 4.5.3
Reading Rules result classification table...
Warning message:
One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
dat <- vroom(...)
problems(dat)
Loading required package: ggplot2
Warning message:
package ‘ggplot2’ was built under R version 4.5.3
Warning in install.packages("RColorConesa") :
'lib = "/opt/conda/lib/R/library"' is not writable
Error in install.packages("RColorConesa") : unable to install packages
Calls: suppressMessages -> withCallingHandlers -> install.packages
Execution halted
`
I used seqera containers to build a singularity image for sqanti using the bioconda sqanti package (v6.0.1). The recipe needs an update to write R files on a writtable path and not in read-only conda directories.
Would like to know your thoughs. Thanks :)
Code sample
No response
Error
No response
Anything else?
No response
Is there an existing issue for this?
Have you loaded the SQANTI3.env conda environment?
Are you running SQANTI3 on its latest release?
Problem description
The following error pops up when running Sqanti3 filter
I used seqera containers to build a singularity image for sqanti using the bioconda sqanti package (v6.0.1). The recipe needs an update to write R files on a writtable path and not in read-only conda directories.
Would like to know your thoughs. Thanks :)
Code sample
No response
Error
No response
Anything else?
No response