Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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A) If the file in gs:// is not too big, you can download it to your local machine and then upload to ukbrap dnax project. B) You could run ttyd app and access public data. I followed the instructio...
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I am observing the same behavior on my end for WGS pVCF. I have informed RAP engineering team.
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"as opposed to just trying to follow the linked instructions exactly (ie just using a papermill cmd string to execute a plain notebook" --> the reason why a snapshot with bcftools --> I think that ...
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I would consider creating a Jupyter snapshot with bcftools and running this spark based JL with snapsnot in non-interactive mode.https://documentation.dnanexus.com/user/jupyter-notebooks/references...
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Thomas, were you able to resolve this issue? I am sharing my thoughts (not tested). It would be interesting to check if the annotation data is stored somewhere else, not on gs. Also whether it woul...
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1) On the worker, what if you list the files via "dx find data"?https://documentation.dnanexus.com/user/objects/searching-data-objects#searching-objects-with-other-criteria Once you have the list w...
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I would do the following steps: Log into AMS account and confirm your application has been approved. If it has and this is persisting, you will need to contact the UK Biobank Access Team (access@...
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Another idea, in your command line: "dx: error: unrecognized arguments: --step 1--lowmem --out pheno_results --bed ukb22418_c1_22_v2_merged --phenoFile pheno_wes_000k.phe --covarFile pheno_wes_000k...
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Perfect! It would be great to hear your experience then!
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And I am really interested to hear more about your use case.
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