FOR HELP- RUN LD Clumping
I am facing significant difficulties during the LD Clumping step “subprocess.check_call(['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', f'imputed/ukb21008_c{chromosome}_b0_v1.bgen', '-incl-rsids', 'rs_batch.txt'], stdout=new_bgen, stderr=subprocess.PIPE)”
and keep encountering an error on this line of code. The error message is:
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.
I have tried dozens of times, and bgenix does exist in this directory, as well as the bgen file and batch.txt file.
By the way, I am currently performing preliminary calculations on chromosome 1, and I have also uploaded a picture of the problem.
Would you like to help me resolve this issue? Thank you!"
Chen
Comments
8 comments
As show in these pictures， bgenix does exist in this directory, as well as the bgen file and batch.txt file.
Hope assistance from a professional， thanks.
Is there any more information in the logs?
Thank your. The all logs ：
Welcome to bgenix
(version: 1.1.7, revision )
(C) 2009-2017 University of Oxford
Building query : (0/?,0.0s,0.0/s)
Building query : (1/?,2.0s,0.5/s)
Building query : (284/?,10.3s,27.5/s)
Building query : (305/?,10.7s,28.4/s)
!! Size of file "imputed/ukb21008_c2_b0_v1.bgen" (109771949597 bytes) differs from that recorded in the index file (109776344051 bytes).
Do you need to recreate the index?
Thank you for using bgenix.
Extract significant rsIDs for chromosome 2
The file “tmp/{chromosome}_{i}.bgen(2_0.bgen)” is empty
It is possible that one of the files was not dispensed correctly, either the bgen or the index.
I am not a geneticist, but I suggest you try dispensing to a new RAP project. and running the same process there.
If you know how to create a new index file, you could try that instead.
If this doesn't fix it, please post again.
Hi Rufu,
I've talked to Rachael about this and we think the issue is the same as that described here How to resolve REGENIE errors with GEL and TOPmed BGEN indices – UK Biobank, where GEL bgi files are incorrect. If you follow the instructions in that post to recreate the bgi files, hopefully the problem will resolve - let us know if it doesn't
HI Rachael and Daisy, thank you for these help, I have resolved this problem which confused me about a week because of the wrong “Bgen bgi” file. I am a new learner, thank you very much again.
Hello Rofu, Thank you for this conversation. I am also facing significant difficulties with this part, starting with accessing the BGEN files through the notebook.
I was able to download into the notebook the regenie output file and also the phenotypic and snplist files using dx download commands, but when trying to run the cell block with the PLINK commands faced the same error with the symbolic links to the bgen and sample file.
Please sign in to leave a comment.