INTERSECT_VARIANTS error with run_ancestry #319
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Just for reference, my successful run without ancestry adjustment was as follows: |
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I see you've adjusted Are your target genomes imputed? If not the intersection could fail. I'll double check the intersection process with some plink1 (bed/bim/fam) inputs. |
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Thank you for your reply
The overlap with one of the traits was 23% and the other about 35%. That’s
why adjusted the min-overlap.
My target data is comprised of 2 datasets (one control and one case) which
were imputed separately, and then merged on intersecting snp list. I
suppose this reduces the overlap #snps, and consequently the overlap with
Trait data.
Would you suggest I run the workflow on each dataset separately, to get the
best PGS scores for each dataset?
Hope that helps.
Regards,
Samreen
…On Wed, Jun 19, 2024 at 1:37 AM Benjamin Wingfield ***@***.***> wrote:
I see you've adjusted --min_overlap. Does the standard run complete OK if
you don't adjust it? Adjusting it to get the workflow to complete can be
a problem.
<https://pgsc-calc.readthedocs.io/en/dev/explanation/match.html#adjusting-min-overlap-is-a-bad-idea>
Are your target genomes imputed? If not the intersection could fail. I'll
double check the intersection process with some plink1 (bed/bim/fam) inputs.
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Merged
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Could you try again with the most recent release? There was a problem with plink bfile input to I'm not sure why imputation hasn't helped. How many variants do you have in your target genomes total? https://pgsc-calc.readthedocs.io/en/latest/how-to/change_version.html |
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Hi Benjamin, I am now trying with the latest version, and so far it is stuck at the "INTERSECT_VARIANT" module, do you know how long this module usually takes? |
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just to follow up. |
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Soit did finish with an error in the 2nd to last module of SCORE_REPORT, and looks like it is a permission issue to some directory. How would you suggest I adjust any parameters to not run into this error? |
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I even tried the following and but got the same error. |
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This looks like a problem with the way singularity is configured on your cluster. Perhaps the |
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Hi Benjamin, And this worked for me to run my sample set with ancestry error free. I will now try to see if running PGS on each indivudal sample cohort will give me a better variant overlap, rather than this mergedCohort that I have. |
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Hi
I was successfully able to run 2 PGS traits for my plink format target data (~20K EUR samples).
However when I try to run the same with ancestry adjustment, I am getting an error at the INTERSECT_VARIANTS step. I tried making the hwe, geno and maf thresholds more relaxed but the error persists. I can't identify what the issue maybe.
I'm sorry for the long log, it looks like nextflow made a few re-attempts before actually crashing.
I can't figure out what this error is indicating.
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