Hello, I have downloaded the gnomAD files to my cloud bucket and go the following tree: https://console.cloud.google.com/storage/browser/gnomad-public/release-170228 I would like to work with data at the format of VDS, as described on Hail.is : https://hail.is/hail/overview.html#variant-dataset-vd…

The VDS format is folder! We often refer to it as a file for simplicity. Take a look at this post for how to get started on Google cloud: Using Hail on the Google Cloud Platform

Thank you for the quick response. I have followed the guidelines and running the sample python script and received an error about decorator module. Is there any additional pre-requisite that I have missed? Many thanks!!! gcloud dataproc jobs submit pyspark --cluster=hail-start --files=gs://hail-…

thank you. the --initialization-actions is done. I am getting the below permission issue when executing the python script. I am the owner of the project and I am not sure why am I getting this error. luster-1-m:~$ gcloud dataproc jobs submit pyspark --cluster=cluster-1 --files=gs://hail-common/ha…

I think this will solve your authentication issue: http://stackoverflow.com/questions/35928534/403-request-had-insufficient-authentication-scopes-during-gcloud-container-clu If not, searching the error message turns up a bunch of other possibilities too. Regarding BigQuery: I don’t see any reason …

[image] eilalan: spark.driver.extraClassPath=./hail-hail-is-master-all-spark2.0.2-e4880e9.jar,s park.executor.extraClassPath=./hail-hail-is-master-all-spark2.0.2-e4880e9.ja thank you. I was able to figure this and running into file not found from hail-common. see below. I would like the use…

I am all set. running with iphyton on spark machine Thanks!!!

is there a way to keep the machines setup and keeping the cost low. should i save the image or any other idea?

not that I know of. If you’ve got your data in a google bucket, then the best way to save your ‘state’ is to save the Hail code you ran! Run it again the next time you’re doing analysis! Alternatively, you can write a VDS to a new file (really a folder, as you’ve discovered ;)) if you want a perman…

thank. I guess that I will have to finish the export data soon :slight_smile: I was running the command to convert VDS to CSV (from this thread).An error is being fired when I am defining the columns that I want to export to CSV. I think that I need some king of definition import for the keyTable (…

New hail and gnomAD, setup help is needed badly :-)

Help [0.1]

jbloom May 11, 2017, 3:36pm 4

See here: Python error: ImportError: No module named decorator

Topic		Replies	Views
Using Hail on the Google Cloud Platform Help [0.1]	17	14216	September 14, 2017
Extracting gnomad counts into a vcf file Hail Query & hailctl	7	1273	March 12, 2021
Help for finding rare variants for 100 patients Hail Query & hailctl	10	523	March 20, 2023
Reading VDS from google bucket fires error Help [0.1]	9	3993	May 13, 2017
UKBiobank Research Analysis Platform (RAP) MatrixTable Write Issues Hail Query & hailctl	21	2787	February 22, 2023

New hail and gnomAD, setup help is needed badly :-)

Related topics