KNOWN ISSUES

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. Jobs on Tresltes usually start within 15 minutes. You can keep the intermediate file page open and refresh from time to time to see when the intermediate fields appear.

If the queue time seems long, there are two possible reasons. First, the queue time might actually be long, and it may take hours for the job to start. Alternatively, the queue may be paused because of scheduled maintenance. A job that requests time thyat extends into a maintenance period will be held in the queue till after mainenance is complete. To check how busy a machine is, you can go here. To check for routine maintenance events, check here.In either situation, it may seem like you are getting no intermediate results, but it really means there aren't 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. 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.

Mr BAYES:
Run Configuration:

  • 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.

Unexplained job termination: Sometimes (rarely) a MrBayes job will terminate without obvious error message. In these cases, the first thing to try is to clone the job, and uncheck the "Use Beagle" option, and resubmit. Often this cures the problem.

A few users have reported receiving this message along with a premature MrBayes termination:

[gcn-2-86.sdsc.edu:33448] *** An error occurred in MPI_Waitall [gcn-2-86.sdsc.edu:33448] *** on communicator MPI_COMM_WORLD [gcn-2-86.sdsc.edu:33448] *** MPI_ERR_TRUNCATE: message truncated [gcn-2-86.sdsc.edu:33448] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort

This is symptomatic of some kind of MPI resource contention issue, and is pretty tough for us to debug. So far, unchecking the box that says "use BEAGLE" in the parameter pane seem to cure the problem. It will make your run go a little slower  (maybe 20%) but the run will complete.

 

RAXML

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

Cloned Jobs Fail: If you try to clone a RAxML job that is pre-V 7.3.0 (early 2012), the job will fail. This is because unlike RAxML 7.2.8, v 7.3.0+ requires the user to specify the parsimony seed for tree inference. The new interface is configured to provide this seed by default. However, if you clone and resubmit an old job, this option will not be set by default.

If you use the RAxML BlackBox interface, if you wish to clone a job created using RAxML 7.2.8, you will need to open the parameter pane, click the reset button on the bottom of the page, reconfigure the job, and resubmit.

If you use the full featured RAxML interface to create a job from RAxML 7.2.8, in order to clone it, you must open the parameter pane and check the -p option, and provide a seed (12345 by default) before submitting. If you don't do this, the job will fail, and there will be an error message in the stdout.txt file citing the failure to provide a parsomony seed. Please contact us if you have an issue with this. 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"

BEAST:Unexplained job termination: Sometimes (rarely) a BEAST job will terminate without obvious error message. In these cases, the first thing to try is to clone the job, and check the "Do Not Use Beagle" option, and resubmit. Often this cures the problem.

Similarly, occasionally a BEAST job will fail with an error message saying the model has a 0 percent probablility. Again, this problem is often alleviated by cloning the job, and checking the "Do Not Use Beagle" option, and resubmitting. If this does not help, the model selected has unsatisfiable conditions, and must be relaxed. The user is referred to the BEAST user group for further advice in this case.

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 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.

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

 


CIPRES – Cyberinfrastructure for Phylogenic Research