Hello,
I'm trying to run beast in supercomputers that can't connect to the Internet, and installed supported packages manually, but when I run ./beast runa.XML something went wrong, perhaps this 'beast.inference.PathSampler' were not found? this is my std.out:
Random number seed: 1642039851798
File: runa.xml seed: 1642039851798 threads: 1
Loading package SNAPP v1.5.1
Loading package MODEL_SELECTION v1.5.3
Loading package BEASTLabs v1.9.7
Loading package BEAST v2.6.6
Loading package BEAST v2.6.6
Alignment(hemi129)
46 taxa
129 sites
100 patterns
kya: 129 31
coal: 129 13
fas: 129 33
eng: 129 19
Data(snap.hemi129)
4 taxa
129 sites
62 patterns
Seq: seq_kya_GH3_7
Seq: seq_kya_GH3_8
Seq: seq_kya_GH3_9
.
.
.
kya: 129 31
coal: 129 13
fas: 129 33
eng: 129 19
4 taxa
129 sites
71 patterns
java.lang.NullPointerException
at beast.evolution.datatype.DataType$Base.getStatesForCode(Unknown Source)
at beast.evolution.datatype.DataType$Base.isAmbiguousCode(Unknown Source)
at beast.evolution.alignment.distance.Distance$Base.pairwiseDistance(Unknown Source)
at beast.evolution.alignment.distance.JukesCantorDistance.pairwiseDistance(Unknown Source)
at beast.util.ClusterTree.distance(Unknown Source)
at beast.util.ClusterTree.getDistance0(Unknown Source)
at beast.util.ClusterTree.doLinkClustering(Unknown Source)
at beast.util.ClusterTree.buildClusterer(Unknown Source)
at beast.util.ClusterTree.initAndValidate(Unknown Source)
at beast.util.XMLParser.initBEASTObjects(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(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)
Error 110 parsing the xml input file
validate and intialize error: null
Error detected about here:
<beast>
<run spec='beast.inference.PathSampler'>
<mcmc id='mcmc' spec='MCMC'>
<state id='state' spec='State'>
<stateNode id='Tree.hemi129' spec='beast.util.ClusterTree'>
and edited file part:
<run spec='beast.inference.PathSampler'
chainLength="1000"
alpha='0.3'
rootdir='/home/liran/zhangxinmiao/lenok/beast/'
burnInPercentage='0'
preBurnin="10000"
deleteOldLogs='true'
nrOfSteps='24'>
cd $(dir)
java -cp $(java.class.path) beast.app.beastapp.BeastMain $(resume/overwrite) -java -seed $(seed) beast.xml
<mcmc id="mcmc" spec="MCMC" chainLength="10000000" storeEvery="1000">
<state id="state" spec="State" storeEvery="1000">
<stateNode id="Tree.hemi129" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">
<taxa id="snap.hemi129" spec="snap.Data" dataType="integerdata">
Thanks!