XSEDE Symptoms/Warnings/Error Messages

This page is created to help disseminate information about warning messages/failure messages you might see in your output. If the suggested fixes do not work, please do let us know.  
Rapid failure of BEAST or MrBayes with no useful error message  

Occasionally a MrBayes or BEAST job will terminate almost immediately. It begins, but suddenly halts and produces no useful error message. The first thing to try in the situation is to clone the job, and use the parameter pane to make sure the run does not use BEAGLE. It seems there are some data sets that just don't like to run on BEAGLE. We have not identified the specific issue yet, but it seems to be at the interface between BEAST and BEAGLE. Disabling BEAGLE usually cures this issue. Although it is not an obvious error message, this kind of failure with MrBayes seems to produce an error message like this: [gcn-19-65.sdsc.edu:75624] *** An error occurred in MPI_Waitall

Cannot configure FileHandler!  

Wed Jun 16 07:36:09 PDT 2010 > INPUTSTAGING : ERROR : NGBW-JOB-MRBAYESHYBRID_ABE-E20EC65DC8CC4AC18553CD91447C09C8 : Cannot configure FileHandler!

This issue arises when a user is logged in to the application twice. The first login prevents the second login from configuring the file handler. The simplest thing is to log out from the first application. If you have closed that window already, just wait for the login to time out from inactivity. Any login will terminate after 20 min of inactivity, and then the error will go away.

Error in command "Execute"  

Could not open file "infile.nex.run1.t"
AddTreeSamples error on at least one processor
Error in command "Mcmc"
There was an error on at least one processor
Error in command "Execute"

This error arises as the result of a file system read/write problem, and it is strictly due to an issue at SDSC as opposed to user error. Please report these issues to us via the bug tracker.

Parsing error - poorly formed BEAST file, infile.xml:  

Parsing error - poorly formed BEAST file, infile.xml:
The '' element with id, 'txt.tn93', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of name frequencies REQUIRED containing
Exactly one ELEMENT of type FrequencyModel REQUIRED

The CIPRES Science Gateway runs BEAST on BEAGLE by default. However, there are some kinds of BEAST files that, while perfectly legal, throw a parsing error message when run on BEAGLE. To fix this issue, just check the box that says "Do not use BEAGLE". The job will run slower, but it should run.


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

CIPRES – Cyberinfrastructure for Phylogenic Research