Hello everyone!
Has anyone had any success fetching files from dbGap, using fastq-dump through a qsub job? Thing is, I am able to fetch the files easily, when running the fastq-dump command from the workspace directory of dbGap (defined using SRA-Toolkit), which is the requirement for being authorized to fetch files from dbGap. But when doing so from a qsub job, I do not get the authorization to fetch the files, I am being rejected.
I've cd to dbGap's workspace directory, and ran the command using the "-cwd" flag, which means "current working directory", but still no luck.
Does anybody have a clue, or an idea as to how I should approach resolving the matter?
Any ideas would help very much!
Thanks in advance you guys,
Chen
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Is the workspace directory for dbGap available from the nodes when you qsub a job? It is possible that that file system may only be accessible on the head node. If that is the case then you may want to try moving the dbGap directory to a location that is accessible from the worker nodes.
Smart idea! Thank you!