Gabriele Maria Sgarlata

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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• 04 June 2025 17:03
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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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• 22 May 2025 23:12
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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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• 22 May 2025 22:57
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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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• 21 May 2025 17:12
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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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• 21 May 2025 16:54
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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...

• Gabriele Maria Sgarlata
• 21 May 2025 04:06
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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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• 21 May 2025 02:02
• 2 votes

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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• 21 May 2025 01:27
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