FAQ

Section: CCB FAQ (7)
Updated:
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OVERVIEW

Answers to common questions about the cluster and your account.  

YOUR CCB ACCOUNT

What can I do with my account? Please see welcome(7) for a comprehensive introduction to your CCB account and our systems.

Why am I getting e-mails about my memory usage on the head node? Please see memwatch(7).

Why is my login session really unresponsive? Please see cpuwatch(7) for a possible explanation. Alternatively, if you're using X2Go from home it may be your internet connection - try using SSH instead.

How do I reset my password if I've forgotten it? Please contact us via genmail@molbiol.ox.ac.uk from the same address that you registered as your contact e-mail.

How do I reopen my account if it's expired? Please submit a request for a new account via our website and we'll match your request up with your old account based on your name and e-mail address. Remember not to click the option to renew, as this only works if you hold a valid account.  

USING BIOINFORMATICS SOFTWARE

How do I load applications to use in my account? Please see modules(7).

How do I use bioinformatics software in Python and R? Please see python-cbrg(7) and R-cbrg(7).  

ANALYSING YOUR NEXT-GEN DATA

How do I access my recently uploaded Miseq data? Please see miseq(7).

How do I find out what my quota is and how much I have used? Please see getquota(1).

How do I share data with other people on the cluster? Please see project(7).

How do I share data files externally? Please see datashare(7).

How do I transfer files to/from the server? Please see "Transferring files to and from the server" in welcome(7).

How do I backup my data and my results? Please see backup(7).

How do I get files from my Basespace account to my CCB account? Please see https://help.basespace.illumina.com/articles/descriptive/introduction-to-basemount/#Mounting. Basemount is installed on the login nodes.

How do I download Fastq format data from GEO? Please see https://www.imm.ox.ac.uk/files/ccb/downloading_fastq_geo for instructions on downloading your data.

How do I access reference sequences & annotation files for commonly analyzed organisms? Please see igenomes(7).  

RUNNING SLURM JOBS

How do I run jobs in the queue? Please see slurm-basics(7).

How do I optimise my cluster jobs to speed up my research? Please see profiling(7).  

USING UNIX/LINUX

If you're unsure about using Unix/Linux systems, please contact us via courses@molbiol.ox.ac.uk for details of our introductory course.  

GETTING HELP

You can email the CCB team using the email address genmail@molbiol.ox.ac.uk. Using this address ensures your email is logged and assigned a tracking number, and will go to all the core team, which means the appropriate person or people will be able to pick it up.  

COPYRIGHT

This text is copyright University of Oxford and MRC and may not be reproduced or redistributed without permission.  

AUTHOR

Duncan Tooke <duncan.tooke@imm.ox.ac.uk>


 

Index

OVERVIEW
YOUR CCB ACCOUNT
USING BIOINFORMATICS SOFTWARE
ANALYSING YOUR NEXT-GEN DATA
RUNNING SLURM JOBS
USING UNIX/LINUX
GETTING HELP
COPYRIGHT
AUTHOR