Closed hnaeem closed 2 months ago
there has been no response regarding the error
It's not clear what the error is — you can ignore the rfunc and torch.qr warnings. Are the expected output files generated? Can you please provide more details about how you're running this? Are R and rpy2 installed in the same environment that tensorqtl is run in?
Dear @francois-a, Thank you for your message. All the TensorQTL, R, and rpy2 packages are available on the HPC where I am running the script. Here is the command for running TensorQTL in trans mode. I am getting the expected outcome (a log file and a txt.gz file containing trans-QTL results).
Submitting the jobs per chromosome on LSF
for chr in {1..22}; do echo "tensorqtl ${plink_prefix_path}chr${chr} ${bed} ${prefix}_${chr} --mode trans --covariates ${cov} --maf_threshold 0.01 --output_text --output_dir $path/output/tensorqtl --return_r2" |bsub -q bionanoNFS -n 32 -P tensorqtl -J tensorqtl -e $path/log/tensorqtl.${chr}.e -o $path/log/tensorqtl.${chr}.o done
Dear @francois-a, I am receiving the anticipated outcome (a log file and a txt.gz file containing trans-QTL results). Can I rely on the output despite the error message mentioned above?
In principle yes. Please update tensorQTL to the latest version, the torch.qr warning was resolved a while ago.
Dear @francois-a, Thank you for your message. I will install the latest version of the tool and let you know if there are any issues. Thank you.
Hey hnaeem, I used to have this error too, the hpc we use installs tensorqtls as singularities on the hpc but the dependencies are needed separately. The singularities does not access the hpc's packages (rpy2). I suggest that you contact your institution's IT office.
Also, try --partition=gpu to allocate gpu
Dear,
TensorQTL in trans mode (tran-eQTL) displays the following error message at the Terminal window. It also shows the warning: " 'rfunc' cannot be imported. R and the 'rpy2' Python package are needed", despite both the R and rpy2 packages being available on the HPC. Any advice will be appreciated Thank you.
Warning: 'rfunc' cannot be imported. R and the 'rpy2' Python package are needed. [Feb 26 15:32:26] Running TensorQTL: trans-QTL mapping