Cipres Web Portal

KNOWN ISSUES

GENERAL FUNCTIONALITY:

Interface Configuration Issue: When jobs are cloned, it is possible that conflicts in logic can occur, making it hard to save the task This is known to occur in the RAxML on Abe interface (but not the Black Box). If you experience difficuly saving a parameter page on a cloned task, just click the Reset button at the bottom of the page. This will restore default settings, and all you to recongifure the task.

Intermediate Results: CIPRES Portal2 V 2.1 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. Intermediate results are visible only when the job is running. Once it is completed, these results disappear, and the hyperlink becomes deactivated.

Results Delivery: The previous issue with results delivery has been resolved in V 2.1. Occasionally, if a TeraGrid resource goes down unexpectedly, users report that results are not returned. If you experience this problem, please contact us, and we will try to recover your results, but this is not always possible. It is best to simply resubmit such a job when the error is noted.

TeraGrid Timeout: After 7 days, the connection between the TeraGrid and CIPRES Portal expires. There is no way to prevent this today. It will throw an error message like this:

Mon Mar 15 08:24:28 PDT 2010 > PROCESSING : ERROR : NGBW-JOB-MRBAYESHYBRID_ABE-4DC0679382E34E12A63988D425B1B460 : Error processing job: 530-globus_xio: Authentication Error 530-OpenSSL Error: s3_srvr.c:2010: in library: SSL routines, function SSL3_GET_CLIENT_CERTIFICATE: no certificate returned 530-globus_gsi_callback_module: Could not verify credential 530-globus_gsi_callback_module: The certificate has expired: Credential with subject: /C=US/O=National Center for Supercomputing Applications/CN=Cipres Community User has expired. 530 End. 

If you get this message, the connection expired. However, your job will complete, and we can recover your data. You just have to notify me, via the bug tracker or at mmiller at sdsc dot edu.
I will get your data to you.

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:
Garli does not accept the ambiguous amino acid characters. These include X, B, and Z. Derrick reports that this will be fixed in a minor bug-fix update that soon. For unknown 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 Portal, or one of many other available tools, including SumTrees. Currently, the CIPRES Portal interface forces you to download these bootstrap tree files one at a time. HOWEVER, if you login to the NGBW site using your CIPRES portal 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 Portal 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.

RAXML

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

Interface Issue: The logic of the interface for RAxML-HPC2 on Abe can cause users to get into a dead end. This can happen if you uncheck "Specify an Explicit Number of Bootstraps" then check and uncheck "Let RAxML halt bootstrapping automatically". As a result, one of the "Select Bootstopping Strategy" boxes will remain checked, making it impossible to save the parameters. Should this happen, just click the Reset button at the bottom of the page, and the interface will reset to its default parameters.

Segmentation Fault: RAxML may throw "segmentation fault" errors when there is an illegal character, or when there is a duplicate taxon name in the constraint file.

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"

RAxML v 7.2.5 is running on Teragrid (ABE). It enables more types of analysis, but some issues have been experienced. We recently eliminated the -m GTRMIX and -m GTRCAT_GAMMA options from the interface, and corrected issues that caused bootstrap requests by the user to be ignored.

REC-I-DCM3

The Rec-I-DCM3 tools all require Nexus files as input, even though RAXML requires Phylip. This is because the REC-I-DCM3 boosting is always run as part of the CORBA software libraries. There is no plan to change the requirement, but file type recognition is planned so improper submission becomes harder.

If there is a tool or a feature you need, you can add it yourself or let us know.