Fetching dbGap files using SRA-Toolkit's fastq-dump and qsub jobs

0

Entering edit mode

8.0 years ago

Chen Mor • 0

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

dbGap RNA-Seq rna-seq qsub sra-toolkit • 2.1k views

ADD COMMENT • link 8.0 years ago by Chen Mor • 0

1

Entering edit mode

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.