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dnanexus / UKB_RAP

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.
MIT License
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Query exceeded timeout [120] #29

Closed M-xiao815 closed 9 months ago

M-xiao815 commented 1 year ago

command: cohort_template <- "dx extract_dataset {dataset} --fields {field_list} -o cohort_data.csv" cmd <- glue::glue(cohort_template) system(cmd)

bug: {'type': 'QueryTimeOut', 'message': 'Query exceeded timeout [120]. Cancelled', 'details': {}, 'time': '05/30/2023, 08:08:18'}

Arkarachai commented 9 months ago

Thanks for reporting. This is a known issue. By design, the large number of field extraction should be done in spark.

anastazie-dnanexus commented 9 months ago

Check documentationdx extract_dataset to generate SQL query.