Gabriele Maria Sgarlata
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Latest activity by Gabriele Maria Sgarlata
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Gabriele Maria Sgarlata commented,
Hi,I took a while because I wanted to test your suggestions. I have edited some part of the code you provided since they were not really working (perhaps the code you shared refer to some older ver...
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Gabriele Maria Sgarlata commented,
Thank you a lot Dr. Mc. Ninja!!Yes, this is what I wanted. It is good to know that time is expressed in milliseconds. Also, I would suggest updating the documentation page, specifying that to get t...
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Gabriele Maria Sgarlata commented,
Hi Alexandra, No, I did not encountered this problem. Maybe it is related to how you write the path? ( specifically, how you deal with the space in 'UKB imputation from genotype' ?).I cannot tell. ...
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Gabriele Maria Sgarlata commented,
Yeah, sure! here it is. This is an example of an analysis to which I gave a time limit of 10 minutes.I hope it helps. Thanks you!{ "id": "job-J0g0K08Jy7K0q8K0qQ976KqK", "region": "aws:eu-we...
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Gabriele Maria Sgarlata commented,
Hi Alexandra, I did this in the spark instance with Hail. The analysis itself takes a few seconds (it seems), although you may need to check with your full pipeline. It seems that Hail is “lazy” (f...
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Gabriele Maria Sgarlata created a post,
Efficient GWAS analysis on Imputed data with Hail: expected time and ensuring performance (resources + time)
I am trying to run GWAS with one trait, including about 400K individuals, and the UKB imputation dataset (code 22828) using Hail . I am running my analysis with the dx run app-dxjupyterlab_spark_cl...
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Gabriele Maria Sgarlata commented,
Hi AlexandraI am learning to use the UKB-RAP so I am not sure if what I am suggesting is the best way, but in principle you can do that using the python package Hail, that is:# Create an index file...
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Gabriele Maria Sgarlata commented,
Thank you! This helped solving my problem and now the job stops at the set time limit.However, when I type dx describe <job-id> --json | jq '.timeoutPolicyByExecutable' I do still get null. Note t...
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Gabriele Maria Sgarlata created a post,
Set time limit policy on dx run jobs with 'cmd' input and how to check time limits
Hi!I am trying to run some GWAS analysis on Hail in the UK Biobank RAP. To make things automatised I am using the Spark JupiterLab app through the dx run command. I could not find much information ...
- Gabriele Maria Sgarlata
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