Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally:
docker run \ -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data \ -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir \ cibersortx/fractions \ --username <my_user_name> \ --token <my_token> \ --single_cell TRUE \ --refsample reference.txt \ --mixture rsem_mixture_TPM.tsv \ --fraction 0 \ --rmbatchSmode TRUE
I get the following output to the terminal:
>Running CIBERSORTxFractions... >[Options] username: <my_user_name> >[Options] token: <my_token> >[Options] single_cell: TRUE >[Options] refsample: reference.txt >[Options] mixture: rsem_mixture_TPM.tsv >[Options] fraction: 0 >[Options] rmbatchSmode: TRUE Killed ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv ERROR: Could not read /src/outdir//temp.Fractions.adj_save.tsv
I did not kill it, it terminated with this error. The files:
are indeed are not in the outdir. It was however able to write the following files to the outdir:
CIBERSORTx_cell_type_sourceGEP.txt CIBERSORTx_reference_inferred_phenoclasses.CIBERSORTx_reference_inferred_refsample.bm.K999.pdf CIBERSORTx_reference_inferred_phenoclasses.CIBERSORTx_reference_inferred_refsample.bm.K999.txt CIBERSORTx_reference_inferred_phenoclasses.txt CIBERSORTx_reference_inferred_refsample.txt
But based on a sample run I performed using Fig2ab-NSCLC_PBMCs (from the downloaded examples which ran normally), failure was before the following files were to be written:
CIBERSORTx_Adjusted.txt CIBERSORTx_Mixtures_Adjusted.txt CIBERSORTx_sigmatrix_Adjusted.txt
My reference file and mixture file have the same layout as the examples.
I have over 1tb free space on the drive /media/mark/seagate2.