Run LD clumping, returned non-zero exit status 255.

Shengcun Li

Dear UK Biobank Computational Team,


 

I am currently working on a project that involves Run LD clumping, as outlined in the notebook titled "end_to_end_gwas_phewas/run_ld_clumping.ipynb". Up to this point, all the preliminary steps including file downloads, decompression, and setup have been executed successfully. Specifically, I am working with GWAS files named "concat.ischemia_cc.REGENIE_WGR_PLOT_CONCAT_additive.lmm.tsv.gz", which seem to be correctly named and formatted. Additionally, I have successfully imported .bgen and .big files into the directory "imputed" that is located within the notebook's directory. Furthermore, I have managed to import samples and keepsnps from my own DX platform, with files following the naming convention "ukb21008_c21_b0_v1_qc_pass.id". The code snippets for importing the data are as follows:

# Create symlink for imputed data 

#DIR='/mnt/project/Bulk/Imputation/Imputation*from*genotype*(GEL)' 

#ln -sf $DIR /opt/notebooks/imputed 

#DIR2='/mnt/project/Bulk/Imputation/Imputation*from*genotype*(GEL)' 

#ln -sf $DIR2 /opt/notebooks/samples 

#DIR3=/mnt/project/cardiac/ 

#ln -sf $DIR3 /opt/notebooks/keepsnps 

However, I encountered an issue with the .big files in the directory /mnt/project/Bulk/Imputation/Imputation*from*genotype*(GEL), which appear to be incorrect. I have generated a new .bgen.big located in DIR4=/mnt/project/DATA2/.

The problem I am facing is understanding how to address this issue. Despite my efforts over the past day, I continually encounter the following error in my code:

 

“-> 31 subprocess.check_call(['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', f'imputed/ukb21008_c{chromosome}_b0_v1.bgen', 32 '-incl-rsids', 'rs_batch.txt'], stdout=new_bgen, stderr=subprocess.PIPE) 33 print(f'Make PLINK files') 34 subprocess.check_call(['./plink2', '--bgen', new_bgen_name, 'ref-first', '--sample', 35 f'samples/ukb21008_c{chromosome}_b0_v1.sample', '--rm-dup', 'force-first', '--out', plink_output_prefix, 36 '--keep-fam', 'eids_to_keep.txt', '--make-bed']) File /opt/conda/lib/python3.9/subprocess.py:373, in check_call(*popenargs, **kwargs) 371 if cmd is None: 372 cmd = popenargs[0] --> 373 raise CalledProcessError(retcode, cmd) 374 return 0 CalledProcessError: Command '['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', 'imputed/ukb21008_c1_b0_v1.bgen', '-incl-rsids', 'rs_batch.txt']' returned non-zero exit status 255.” 

 

Could you please provide me with guidance on how to resolve this issue? Your expertise and assistance would be greatly appreciated.


 

Thank you for your time and support.


 

Best regards,

sl

 

 

 


 

 

 

 

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