Table exporter job fail
Hi, I am trying to use the table exporter to export fields from my dataset. I am using the cohort browser to manually select my fields of interest, then save it as a dashboard view, then input it into the table exporter. I tried a test run and the job failed after 5 min, there is no clear reason provided under “cause of failure”, and when I tried to look at the log it simply would not load.
Can anyone advise what the reason could be here, or what I can do resolve the issue? Thank you very much.
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2 comments
Hello Jeffrey,
When the failure reason is not apparent from the error message or job log, please feel free to use the ‘Send Failure Report to UK Biobank Support’ button to notify the DNAnexus UKB-RAP support team. More information about available support can be found in the UKB-RAP documentation:
https://dnanexus.gitbook.io/uk-biobank-rap/administrator/technical-support
In this case, the issue is likely caused by unescaped whitespace characters in the ‘Output Prefix’ input string. Since UKB-RAP apps usually run in Linux containers, we recommend to follow UNIX naming conventions for any input fields that modify potential output file names, so either modify the input to not contain any whitespace characters, or escape them with the backslash \ symbol, e.g:
More information on escaping special characters is available in DNAnexus core documentation:
https://documentation.dnanexus.com/user/projects/path-resolution#special-characters
Best regards,
Alois Kozubik | Bioinformatics Scientist | Care
DNAnexus
Hello, may I ask if you've solved the problem? I also tried to manually select the fields I'm interested in using the queue browser, then saved them and imported them into the table exporter. It failed after running for 5 minutes, and no clear reason was provided. My operation was almost exactly the same as yours. I'd like to ask if you've solved it now.
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