Generic error on Cipres

[aparna...@gmail.com]

Hi all,

I am using BEAST 2.7.6 and generating the xml for more than 400 taxa. I seem to be getting this generic error when I run it on CIPRES which doesn't get resolved even after changing the seed. Would appreciate suggestions on how to resolve this. 

Inactive Modules:
  1) subversion/1.14.0

The following have been reloaded with a version change:
  1) cpu/0.17.3b => cpu/0.15.4

File: infile.xml seed: 12345 threads: 1
Loading package ORC v1.2.0 FastRelaxedClockLogNormal v1.2.0 Recombination v1.0.1 LPhyBeastExt v0.3.0 TreeStat2 v0.1.1 timtam v0.4.0 PIQMEE v1.1.0 bacter v3.0.1 GEO_SPHERE v1.4.1 FixedTreeAnalysis v0.0.2 bModelTest v1.3.3 feast v10.3.0 contacTrees v1.2.0 DENIM v1.1.1 SpeciesNetwork v1.0.0 ClaDS v2.0.3 Mascot v3.0.7 BREAK_AWAY v1.2.0 BEAST_CLASSIC v1.6.3 MGSM v0.4.0 BASTA v4.0.0 OBAMA v1.1.1 CoalRe v1.0.4 contraband v1.0.1 PhyDyn v1.4.0 starbeast2 v1.0.0 SA v2.1.1 MSBD v2.0.2 BEAST.app v2.7.6 SSM v1.2.0 NS v1.2.1 bdtree v0.0.1 CA v2.1.0 MultiTypeTree v8.1.0 MODEL_SELECTION v1.6.2 speedemon v1.1.0 BEASTvntr v0.2.0 EpiInf v8.0.0 MM v1.2.1 PoMo v1.1.1 CodonSubstModels v2.0.0 snapper v1.1.4 BDSKY v1.5.0 SNAPP v1.6.1 STACEY v1.3.1 BEASTLabs v2.0.2 MASTER v7.0.0 SCOTTI v3.0.0 starbeast3 v1.1.8 phylonco v1.0.1 BICEPS v1.1.2 lphybeast v1.1.0 remaster v2.6.2 BEAST.base v2.7.6 phylodynamics v1.4.0 Babel v0.4.2 BDMM v2.0.0 CoupledMCMC v1.2.1 BADTRIP v2.0.0    
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 322 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 279 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 380 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 264 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 258 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 307 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 343 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 770 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 412 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 506 unique site patterns.
  Using rescaling scheme : dynamic
  Ignoring ambiguities in tree likelihood.
  Ignoring character uncertainty in tree likelihood.
  With 676 unique site patterns.
  Using rescaling scheme : dynamic
java.io.FileNotFoundException: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-BEAST2_XSEDE-04794F4FC8D04B8EA0372B74DC68E24D/infile.xml.state (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(Unknown Source)
at java.base/java.io.FileInputStream.<init>(Unknown Source)
at java.base/java.io.FileInputStream.<init>(Unknown Source)
at java.base/sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
at java.base/sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
at java.xml/com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at java.xml/javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
at beast.base.inference.State.restoreFromFile(Unknown Source)
at beast.base.inference.MCMC.run(Unknown Source)
at beastfx.app.beast.BeastMCMC.run(Unknown Source)
at beastfx.app.beast.BeastMain.main(Unknown Source)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source)
at beast.pkgmgmt.launcher.BeastLauncher.main(Unknown Source)

[Pfeiffer, Wayne]

Hi,

I help maintain the CIPRES gateway, and this error is not associated with the gateway. Rather, there is something in your input xml file that prevents BEAST2 from generating an initial state.

The error message from your first run (before you changed the seed) was

java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed.

See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

Perhaps one of the suggestions at the listed url will help.

Wayne

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[Aparna Lajmi]

Thank you Wayne for your reply. 

I did go over this url, but most of the suggestions don't seem relevant. I am yet to try out giving a starting tree. I hope that helps.

Best,

Aparna

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--

Aparna Lajmi,

Assistant Professor,

GITAM University,

Visakhapatnam.

aparnalajmi.weebly.com

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