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CalledProcessError: Command '['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', 'imputed/ukb21008_c1_b0_v1.bgen', '-incl-rsids', 'rs74045046']' returned non-zero exit status 255.
Hi,
I was trying to perform phewas for my data in ukb rap. I was following: https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb
I am getting the above-mentioned error in the last cell (attached notebook).
Any help? What am I doing wrong here?
Comments
3 comments
I think the file paths (directory names) might have changed. Does file ukb21008_c1_b0_v1.bgen exist in folder imputed in your folder structure?
Hi Rachael,
Thank you. You might be right. I investigated further.
!ls '/mnt/project/Bulk/Imputation/Imputation from genotype (GEL)'
It contains the bgen files. But failing to create the symbolic link.
%%bash
# Create symlink for imputed data
DIR='/mnt/project/Bulk/Imputation/Imputation from genotype (GEL)'
ln -sf "${DIR}" /opt/notebooks/imputed
DIR2=/mnt/project/Bulk-DRL/GEL_imputed_sample_files_fixed/
ln -sf "${DIR2}" /opt/notebooks/samples
It show: ln: failed to create symbolic link '/opt/notebooks/imputed/Imputation from genotype (GEL)': Read-only file system
Any help on this?
Hi Mohammad,
Please note that I am only guessing here: I have not yet attempted to run these notebooks. That said:
Should there be quote marks ( ' ' ) in the DIR2 statement?
Do you have write access to the data in the project you are using?
The Administrator of a project can set different levels of access for different collaborators. I think you will need to be Admin or Contributor.
See this post. https://community.dnanexus.com/s/question/0D582000004dDcaCAE/when-i-create-a-notebook-in-jupyterlab-from-the-dnanexus-tab-project-storage-i-cant-open-it-message-says-its-a-protected-project-any-suggestions-do-i-have-too-always-use-dx-download-then
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