Cipres Science Gateway

GENERAL FUNCTIONALITY:

Intermediate Results: The CIPRES Science Gateway supports delivery of intermediate results. To open the intermediate results page, just click on the "View Status" button. When that page opens, you will see an "Intermediate results" hyperlink. Click it and you will have access to all run files. The link to "intermediate results" will show your submitted input files and scheduling information files as soon as you submit the job.

What if I don't see intermediate results? If you see only input files and scheduling files, but no true intermediate files, it means your job is waiting in the queue. If the job has begun to execute, the first file that appears is start.txt, which notes the beginning of the run time. The other intermediate files will appear shortly after. If you request a short job (0.5 h or so) the job goes into a debug queue, and it would usually start within 15 minutes. For such jobs, you can keep the intermediate file page open and refresh from time to time to see when the intermediate fields appear.

For a long job, the queue time for Abe can be long, and it may take hours for the job to start. In that case, it may seem like you are getting no intermediate results, but it really means there arent any results to see yet. The intermediate results for a given job are only visible while the job is actually executing. Once the job is complete, clicking the intermediate file link will show a blank screen.

Results Delivery: Results delivery is far more robust in the current CIPRES Science Gateway than in its prior incarnations. Sometimes (hopefully rarely) a machine will go offline during a run, and if that happens, you will not be able to see intermediate results.The CIPRES Science Gateway application will detect when the machine comes back on line, and deliver the results within 30 minutes of when they become available. If you should experience a problem with return of results, please contact us, and we will try to recover your results.

Multiple logins: If a user is logged in to the application more than once, submitted jobs will fail. The error message produced (under the View Error button)will look like this:

Tue Jan 19 10:40:34 PST 2010 > INPUTSTAGING : ERROR : NGBW-JOB-yourjobname-somenumbersandletters : Cannot configure FileHandler!

GOOGLE Chrome issue: The GOOGLE Chrome browser has issues with data uploading and job creation. We expect to address this, but it is not a first priority today. Please let us know if you feel use of the Chrome Browser is essential for your work.

GARLI:
 For unknown characters the default is "?", although with Nexus you can define it to be whatever you want.  Thus, a Nexus dataset that uses only X and not ? could be read fine by adding missing=X to the Format line.  If the dataset is in non-Nexus format (usually Phylip), then the only options are ? and -.  In all cases the gap character, by default "-", is treated identically to a missing character.

Managing multiple files produced by GARLI: When running on Lonestar, GARLI will produce one tree file for each bootstrap iteration, but it will not calculate a majority rule consensus tree the way the original GARLI interface did. We plan to address this in the near future, but in the mean time, you can calculate the consensus tree using Consense in the CIPRES Science Gateway, or one of many other available tools, including SumTrees. Currently, the CIPRES Science Gateway interface forces you to download these bootstrap tree files one at a time. HOWEVER, if you login to the NGBW site using your CIPRES Science Gateway credentials, you will see your data (it will be orange instead of blue). The data interface on that site will allow you to download all your result files to your local hard drive as a collection. We hope to introduce this feature into the CIPRES Science Gateway and apologize for the inconvenience.

Mr BAYES:
The interface for MrBayes will overwrite values in the MrBayes block UNLESS the interface is deactivated by checking the box that says "My Nexus file has a MrBayes block." There is no planned fix for this issue, user caution is required.

A "set autoclose = no" statement in the MrBayes block causes an entire disk to fill with a single repeating line from your log file, crashing everyone else’s job in the process.

The command line mcmcp is frequently used for MrBayes on personal computers, but not on the CIPRES Science Gateway. If you use the command

mcmcp ngen= XXXX etc;

in your MrBayes block, the job will not progress.

RAXML

Input Format: RAxML on the CIPRES Science Gateway only accepts input files in relaxed phylip format.

Segmentation Fault: RAxML may throw "segmentation fault" errors. THis has been seen when there is an illegal character, or when there is a duplicate taxon name in the constraint file. Please report any iSegmentation Fault issues to us.

Multiple Outgroups: When specifying more than one outgroup, do not introduce blank spaces. Use outgroup1,outgroup2 not outgroup1, outgroup2. In the latter case you will see the following error message "Error, you must specify a model of substitution with the '-m' option"

If there is a tool or a feature you need, please let us know.