Warning and Error in tensorQTL trans mode

[hnaeem]

Warning and Error in tensorQTL trans mode

[hnaeem]

there has been no response regarding the error

[francois-a]

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?

[hnaeem]

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

[hnaeem]

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?

[francois-a]

In principle yes. Please update tensorQTL to the latest version, the torch.qr warning was resolved a while ago.

[hnaeem]

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.

[hnaeem]

Is this the updated version : v1.0.9?

[lintingyi2014]

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.

[lintingyi2014]

Also, try --partition=gpu to allocate gpu