Comments (9)
there has been no response regarding the error
from tensorqtl.
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?
from tensorqtl.
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
done
from tensorqtl.
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?
from tensorqtl.
In principle yes. Please update tensorQTL to the latest version, the torch.qr warning was resolved a while ago.
from tensorqtl.
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.
from tensorqtl.
Is this the updated version : v1.0.9?
from tensorqtl.
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.
from tensorqtl.
Also, try --partition=gpu to allocate gpu
from tensorqtl.
Related Issues (20)
- Issues with TensorQTL in Trans Mode HOT 1
- AttributeError: 'dict' object has no attribute 'T' tensorqtl HOT 2
- broken link HOT 1
- Tensorqtl installation HOT 3
- No credible sets output from susie.map because pval_nominal=0 HOT 3
- ValueError: array must not contain infs or NaNs HOT 1
- interaction HOT 1
- [Susie] ValueError: prior variance must be non-negative HOT 4
- [trans] trans.map_permutations(): KeyError: 'r2' HOT 2
- [map_trans] R2 not returned in interaction analysis HOT 2
- [pval post-processing] Interaction output for cis/trans HOT 1
- Which beta coresponds to which allele in the outputs? HOT 3
- cis-mapping with interaction HOT 1
- Errors in the BackgroundGenerator cause main thread to get stuck HOT 1
- Questions about the `map_permutations` and `apply_permutations` functions
- cis_independent requires covariate_df HOT 1
- Phenotype file format HOT 3
- Any way i can go around this error? HOT 2
- Categorical covariates HOT 1
- Corections for multiple tests for trans-eQTL HOT 1
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from tensorqtl.