No output tree file

[Mohammadomer Sawut]

Hello

On the CIPRES website, I uploaded the nexus format converted from phylip format and select tool as a MrBayes on XSEDE(3.2.7a), Data type choose protein, and running the task. Unfortunately, I did not see the evolution tree file in the results. The original gene sequence from gene bank. Could you give me any advise what is the issue for this matter?

Thanks

Mohammdomer

[Mark Miller]

Hi Mohammdomer,

Thanks for reporting that. When you dont get the file you expect it means the job stopped before completing.

There are three possible reasons:

1) the code did not like your dataset format, or there was an instruction in the errors, and the run failed because the command or dataset could not be completed.

2) the job was set for a certain time (default = 30 minutes) and the run was successful, but reached this time before completing.

3) there was a failure at the moment of submission.

How to diagnose:

1) the file stdout.txt for MrBayes is quite verbose, and is very accurate in describing any issues with your data set. Look at the last few lines of this file for an error message. If you read it carefully, you should be able to figure out the issue.

2) A job that "times out" produces an error message in the file scheduler_stderr.txt. Look there to see if there is an error message about reaching the end of the configured time.

3) A failure at the moment of submission "should" produce an error message warning you that there is a problem on our side. There should be an error message at the last line of the job status output page.

The job status out[ut looks like this:

Task Messages

Mon Jun 29 09:53:42 PDT 2020 > QUEUE : SUCCESS : NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2 : Added to run queue.
Mon Jun 29 09:53:52 PDT 2020 > COMMANDRENDERING : SUCCESS : NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2 : Command rendered successfully: mbmpiwrapper_3.2.7a_comet.centos7 paramfile.txt
Mon Jun 29 09:53:52 PDT 2020 > INPUTSTAGING : SUCCESS : NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2 : Staging input files to comet
Mon Jun 29 09:53:52 PDT 2020 > INPUTSTAGING : SUCCESS : NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2 : Input files staged successfully to /projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2/
Mon Jun 29 09:53:53 PDT 2020 > SUBMITTED : SUCCESS : NGBW-JOB-MRBAYES_XSEDE-BFE3EB86CF334D86A1949DA3848C40C2 : Submitted to comet as job '34365641'.

But if it failed because of an issue at cipres, there would be an additional message at the bottom.

Let me know if you have further questions.

Best,

Mark

[Mark Miller]

Sorry I made a mistake.

This line

1) the code did not like your dataset format, or there was an instruction in the errors

should read like this:

1) the code did not like your dataset format, or there was an error in the instructions