Hello everyone, I am looking for someone who has an experience of running CIBERSORTx on biowulf?
I tried doing so with the singularity container but could not succeed. Just to to give a better clarifity, I am also sharing my workflow I used to setup the CIBERSORTx on biowulf ,as given below. Kindly give your valuable comments, if I am missing something here. 1. Setup a cache directory for singularity: export SINGULARITY_CACHEDIR=/data/$USER/.singularity echo "export SINGULARITY_CACHEDIR=/data/$USER/.singularity" >> ~/.bashrc mkdir -p $SINGULARITY_CACHEDIR 2. Start an sinteractive session. For example: sinteractive --mem=8G 3. Load the singularity module module load singularity 4. Create a directory to store the containers. For example: mkdir -p /data/$USER/cibersortx cd /data/$USER/cibersortx 5. Pull the containers from docker singularity pull docker://cibersortx/hires:latest singularity pull docker://cibersortx/gep:latest singularity pull docker://cibersortx/fractions:latest 6. Clean singularity cache: singularity cache clean 7. Checking each command's help message, these are running fine: gep: singularity exec /data/$USER/cibersortx/gep_latest.sif Rscript /src/R_modules/CIBERSORTxGEP.R HiRes: singularity exec /data/$USER/cibersortx/hires_latest.sif /src/CIBERSORTxHiRes Fractions: singularity exec /data/$USER/cibersortx/fractions_latest.sif /src/CIBERSORTxFractions 8. Final Command: singularity exec -B "/data/mehanib2 /input:/src/data" -B "/data/mehanib2/output:/src/outdir" /data/mehanib2/cibersortx/fractions_latest.sif /src/CIBERSORTxFractions --username [email protected] --token my token -single_cell TRUE --refsample refsample.txt --mixture mixture_tpm.txt --sigmatrix signature.txt --sourceGEPs sourceGEP.txt --rmbatchSmode TRUE But getting this error: “”””” terminate called after throwing an instance of 'std::system_error' what(): Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable Aborted “””””” Any suggestion would be highly appreciated. Thanks Bharati From: "Mehani, Bharati (NIH/NCI) [F]" <[email protected]> Date: Thursday, August 4, 2022 at 4:47 PM To: List BIOINFORMATICS-SIG-L <[email protected]> Subject: CIBERSORTx on biowulf Hello everyone, I am looking for someone who has an experience of running CIBERSORTx on biowulf? I tried doing so with the singularity container and got the following error: """"""" >Running CIBERSORTx high-resolution GEP imputation... >[Options] username: [email protected]<mailto:[email protected]> >[Options] token: my token >[Options] refsample: sc_ref.txt >[Options] mixture: mixture.txt >[Options] rmbatchSmode: TRUE terminate called after throwing an instance of 'std::system_error' what(): Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable Aborted “”””””” I am afraid it is because CIBERSORTx is unable setup up a proxy connection while running with singularity container. Can anybody please guide how should I troubleshoot this issue? Or if there is another alternative I can use to install CIBERSORTx on biowulf? Thanks and Regards Bharati
