BioHPC Site Logo

Computational Biology Service Unit
BioHPC Web Computing Resources
(compute nodes status)
User: guest: | Only registered users can use the resource below. | Login | Apps Home | FAQ |

APPLICATIONS
(click on a category below
to access programs)

   


MISCELLANEOUS
Subscribe
Apps Home
Clusters Status
Applications Statistics
BioHPC Home
CBSU Home
CBSU ftp server
CBSU SeqDB
CTC Windows Bioinformatics Applications
DISTRUCT
T-REX (T-RFLP manager)
Next-Gen@BioHPC
CBSU Survey
Read Survey (adm)
Reset Password
F A Q
Contact Us

Version 1 Rev 454
(2011/12/21 10:37:26)

Frequently Asked Questions


General
What is BioHPC?
How do I run my analysis?
How do I register with CBSU?
How do I log in to the CBSU web page?
How do I unpack a "gzipped tarball" on Windows?
My job finished prematurely. Why? Is there a way to run it longer?
What is "cluster maintenance" and how does it affect my jobs?
I want to submit to Athena, but my jobs get re-routed to other clusters. Why?
Your server says there something wrong with my e-mail address, but I'm sure it is correct
While submiting a job, I get a message that I have other active jobs in the system
Which e-mail addresses can I use to submit a job?
What happens to the data I upload to your server once the job finishes?

Next Generation Sequencing data analysis
How to run Next-Gen applications offered by BioHPC?

BEAST
Can I extend the timeout of my BEAST run?

IM / IMa
Can I extend the timeout of my IMa run?
My IMa run hangs or crashes immediately after starting
My IMa run hangs or crashes after running for some time
My IMa run exits earlier than expexted
My IM run ends half-way, long before timeout
My IM run crashes when restarted from checkpoint file
I can't get my IM job to stop by changing the IMrun file
How do I represent indels in my input file?
I can't seem to find information I'm looking for in the manual.

InStruct
My InStruct job crashes
My InStruct job times out
What, after all, are the memory requirements of InStruct?
I downloaded Windows executable of InStruct from your site, I click on it and... nothing happens.

MDIV
How do I represent gaps in input to MDIV?
I'm getting an error message "Allowed characters are 'a' 'c' 't' 'g','.' or blank".
I'm getting ERROR 83. What does it mean?

MrBayes
I have my nex file, but how do I specify MrBayes commands?
I'm getting a message "number of chains could not be determined"
My MrBayes job timed out, but I could use intermediate result files. Where are they?
I would like to run MrBayes in interactive mode
I'm getting an error "The number of chains must be at least as great as the number of processors".
My MrBayes run completed the MCMC part and then crashed before summarizing results
In the output file I see a message "lastError = 6". What is wrong?

MSVAR
Why are outputs from all my replicate runs identical?
Why is the submission page complaining about missing input files? They are all in my input zip file!

STRUCTURE
How to run STRUCTURE for different values of K?
What deos it mean "maximum number of processors" and "repeat the run"?

STRUCTURAMA
Why is STRUCTURAMA setting K=2 even though I explicitly specify "model numpops=rv"?
Why is STRUCTURAMA not summarizing results"?


Messages:
Cluster Athena under maintenance:
Cluster biosim operating normally
Cluster biosim2K8 operating normally
Cluster cbsum2k8 operating normally
Cluster cbsusrv05 operating normally
Cluster cbsulm01 under maintenance:
Cluster CAC_v4_lease under maintenance:
Cluster biosim_linux operating normally
Cluster cbsuss04 operating normally
Cluster cbsum1c1b001 operating normally
Cluster cbsum2 operating normally

Application P-IPRSCAN under maintenance: