Errors finding likelihood.log and beast.xml.state files

[Jane]

Dear All, 

I'm new to beast, and am having some trouble getting SNAPP to run with my data. I've been working through the BFD* tutorial with my data, and I'm repeatedly running into two errors, which I've pasted below. When I run beast using the gecko SNP data that goes with the tutorial, it runs fine, so I don't think its anything to do with the beast command itself - is someone able to tell me whats going on here? I've attached my xml files below - run3.xml gives the first error, and trial.xml gives the second. In both cases, the files that its having problems finding are indeed missing, but are being produced when I use the tutorial data. Any ideas why? I'm also not clear why I don't get the same error every time?

I have java 8 installed and have checked that the path to beast.jar in the run.sh files is correct. 

Any help would be appreciated.

Thanks,

Jane

Error given with run3.xml:

Starting step 0

Starting step 1

Starting step 3

Starting step 2

Finished step 2

Finished step 1

Finished step 3

Finished step 0

Loading /fastdata/bo4jeh/beast_firstruns/April/run3//step0/likelihood.logFile error: /fastdata/bo4jeh/beast_firstruns/April/run3/step0/likelihood.log (No such file or directory)

java.lang.RuntimeException: An error was encounted. Terminating BEAST

        at beast.app.util.ErrorLogHandler.publish(Unknown Source)

        at java.util.logging.Logger.log(Logger.java:738)

        at java.util.logging.Logger.doLog(Logger.java:765)

        at java.util.logging.Logger.log(Logger.java:788)

        at java.util.logging.Logger.severe(Logger.java:1464)

        at beast.app.beastapp.BeastMain.<init>(Unknown Source)

        at beast.app.beastapp.BeastMain.main(Unknown Source)

        at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Error given with trial.xml:

Starting step 0

Starting step 1

Starting step 3

Starting step 2

Finished step 0

Finished step 1

Finished step 2

Finished step 3

File error: /fastdata/bo4jeh/beast_firstruns/April/trial/step3/beast.xml.state (No such file or directory)

java.lang.RuntimeException: An error was encounted. Terminating BEAST

        at beast.app.util.ErrorLogHandler.publish(Unknown Source)

        at java.util.logging.Logger.log(Logger.java:738)

        at java.util.logging.Logger.doLog(Logger.java:765)

        at java.util.logging.Logger.log(Logger.java:788)

        at java.util.logging.Logger.severe(Logger.java:1464)

        at beast.app.beastapp.BeastMain.<init>(Unknown Source)

        at beast.app.beastapp.BeastMain.main(Unknown Source)

        at beast.app.beastapp.BeastLauncher.main(Unknown Source)

[Remco Bouckaert]

Hi Jane,

In both XML files there is a parameter u set to Infinity:

<parameter id="u" estimate="false" lower="0.0" name="mutationRateU">Infinity</parameter>

which results in undefined likelihoods and the MCMC fails. Setting u to a more reasonable value should fix the problem.

Cheers,

Remco

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.
<run3.xml><trial.xml>

[Jane]

Thank you very much for the quick response. 

I've just corrected the xml files and set them running again - the likelihood.log files have been generated. Thanks!

Jane

[Catalina Ramirez-Portilla]

To unsubscribe from this group and stop receiving emails from it, send an email to beast...@googlegroups.com.

To unsubscribe from this group and stop receiving emails from it, send an email to beast...@googlegroups.com.

To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.
<run3.xml><trial.xml>

Dear all,

I ran into the same issue, but I checked my xml file (see attached) and the configuration of the parameter u is not set to infinity, so I am not sure what is generating the problemm (see STDERR(1)). I am new to BEAST and SNAPP analyses so I would really appreciate any help you could give me in that regard.

Cheers,

Catalina R-P

 

[Mukta Joshi]

Hi Catalina,

Did you manage to solve this issue? Because I'm also facing this problem since months.

Regards,

Mukta 

[Alex Krohn]

Hi there,

Adding to this chain (get it?). I'm facing the same problem and am not sure why.

-Alex

Error message:

....

Loading /home/tangled/tbc/compute/alex_compute/ast/trees/snapp/yes-admix-standard-priors//step0/likelihood.log, burnin 50%, skipping 500 log lines

|---------|---------|---------|---------|---------|---------|---------|---------|

********************************************************************************

Calculating statistics

|---------|---------|---------|---------|---------|---------|---------|---------|

********************************************************************************

marginalLs[0 ] = -49494.232917120884

Loading /home/tangled/tbc/compute/alex_compute/ast/trees/snapp/yes-admix-standard-priors//step1/likelihood.log, burnin 50%, skipping 500 log lines

|---------|---------|---------|---------|---------|---------|---------|---------|

********************************************************************************

Calculating statistics

|---------|---------|---------|---------|---------|---------|---------|---------|

********************************************************************************

marginalLs[1 ] = -49718.47388197573

Loading /home/tangled/tbc/compute/alex_compute/ast/trees/snapp/yes-admix-standard-priors//step2/likelihood.logFile error: /home/tangled/tbc/compute/alex_compute/ast/trees/snapp/yes-admix-standard-priors/step2/likelihood.log (No such file or directory)

java.lang.RuntimeException: An error was encounted. Terminating BEAST

        at beast.app.util.ErrorLogHandler.publish(Unknown Source)

        at java.util.logging.Logger.log(Logger.java:738)

        at java.util.logging.Logger.doLog(Logger.java:765)

        at java.util.logging.Logger.log(Logger.java:788)

        at java.util.logging.Logger.severe(Logger.java:1464)

        at beast.app.beastapp.BeastMain.<init>(Unknown Source)

        at beast.app.beastapp.BeastMain.main(Unknown Source)

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

        at java.lang.reflect.Method.invoke(Method.java:498)

        at beast.app.beastapp.BeastLauncher.run(Unknown Source)

        at beast.app.beastapp.BeastLauncher.main(Unknown Source)

[Alex Krohn]

Sorry, I should note that in my XML file u is set to 1.0 (not infinity), and is not estimated. Estimations worked for Step 0 and Step 1, so I'm not sure what happened with Step 2.

On Monday, February 1, 2021 at 12:31:11 PM UTC-5 mukta...@gmail.com wrote:

[Ales Bucek]

I noticed that the error with missing *.xml.state file occurs also when attempting to resume a BEAST run (with the "-resume" argument) while not having the .xml.state file in the run directory.