Hello, I have been trying to run the simple command:
`(zcat "UKBB First Project - Oct 29, 2021:/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - interim 450k release/helper_files/ukb23149_450k_OQFE.annotations.txt.gz" 2>/dev/null ) | head > annotations_head.txt`
but the output is an empty file.
Could you tell what I am doing wrong in this command?
Thank you very much!
Hello, in order to access project files using CLI you should use dxfuse mount system. You can use it by adding /mnt/project before the path to your data.
Following code works for me:
(zcat "/mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - interim 450k release/helper_files/ukb23149_450k_OQFE.annotations.txt.gz" 2>/dev/null ) | head > annotations_head.txt
Important note: code that I posted below will work in the terminal launched from Spark JupyterLab, Other option would be to download files into instance storage using dx download.
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Please send an email to our support at ukbiobank-support@dnanexus.com and they can take a look.
Hello, in order to access project files using CLI you should use dxfuse mount system. You can use it by adding /mnt/project before the path to your data.
Following code works for me:
(zcat "/mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, PLINK format - interim 450k release/helper_files/ukb23149_450k_OQFE.annotations.txt.gz" 2>/dev/null ) | head > annotations_head.txt
Important note: code that I posted below will work in the terminal launched from Spark JupyterLab, Other option would be to download files into instance storage using dx download.
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