I encountered an error while running the XML file

[liamxg]

Dear @tgvaughan ,

I encountered an error while running the XML file:

Running file /Users/liam/Desktop/SCOTTI/xml/KPneu.xml
File: KPneu.xml seed: -4025233910953366980 threads: 1
Loading package BICEPS v1.1.2 SSM v1.2.1 ClaDS v2.1.2 contraband v1.0.1 FastRelaxedClockLogNormal v1.2.0 MGSM v0.4.0 remaster v2.7.2 feast v10.5.0 flc v1.2.0 phylodynamics v1.4.0 BADTRIP v2.0.0 NS v1.2.2 bModelTest v1.3.3 BASTA v4.0.0 CA v2.1.0 LPhyBeastExt v1.0.0 speedemon v1.1.0 starbeast3 v1.1.9 CCD v1.0.3 SpeciesNetwork v1.0.0 timtam v0.4.0 Mascot v3.0.7 PhyDyn v1.4.0 PIQMEE v1.1.0 BDMM-Prime v2.2.2 phylonco v1.2.0 starbeast2 v1.0.0 TreeStat2 v0.2.0 MSBD v2.0.4 Babel v0.4.2 PoMo v1.1.1 SA v2.1.1 BEAST.base v2.7.7 MultiTypeTree v8.2.0 BDMM v2.0.0 GEO_SPHERE v1.4.2 contacTrees v1.2.0 MASTER v7.0.0 DENIM v1.1.1 BEASTLabs v2.0.2 BEAST.app v2.7.7 phylonco.lphybeast v1.2.1 BEAST_CLASSIC v1.6.4 CodonSubstModels v2.0.0 MM v1.2.1 CoupledMCMC v1.2.2 BDSKY v1.5.1 OBAMA v1.1.1 bdtree v0.0.1 snapper v1.1.5 CubeVB v1.0.2 gammaspike v1.0.1 tidetree v1.0.1 SCOTTI v3.0.0 ORC v1.2.0 SNAPP v1.6.1 Recombination v1.0.1 STACEY v1.3.1 BREAK_AWAY v1.2.0 MODEL_SELECTION v1.6.2 lphybeast v1.2.1 CoalRe v1.0.4 bacter v3.0.1 FixedTreeAnalysis v0.0.2 BEASTvntr v0.2.0 EpiInf v8.0.0 BDMM-Prime v2.2.2
beast.base.parser.XMLParserException:
Error 1017 parsing the xml input file

Class could not be found. Did you mean snap.MCMC?
Perhaps a package required for this class is not installed?

Error detected about here:

at beast.base.parser.XMLParser.createObject(Unknown Source)
at beast.base.parser.XMLParser.parseRunElement(Unknown Source)
at beast.base.parser.XMLParser.parse(Unknown Source)
at beast.base.parser.XMLParser.parseFile(Unknown Source)
at beastfx.app.beast.BeastMCMC.parseArgs(Unknown Source)
at beastfx.app.beast.Controller$2.run(Unknown Source)

Could you please advise on how to resolve this?

Best,
Liam

[tgvaughan]

Hi Liam, two things:

1. This tutorial is for a very old version of BEAST 2 (4.7). In particular, there were especially large changes that occurred between version 6.7 and 7.0 which require updates to XMLs in order for them to work. Since this tutorial has not been updated it likely will not work with later versions.

2. I'm not one of the authors of this tutorial, nor of the SCOTTI package itself. Thus I'm not the right person to tag here. Instead I'd encourage you to get in touch with Louis du Plessis or Nicola de Maio.

Cheers,
Tim

[liamxg]

Dear @tgvaughan,

Thank you again for your kind reply.

@laduplessis and @NicolaDM, I’d really appreciate your help with this as well.

Best regards,
Liam

[NicolaDM]

Dear Liam,

Indeed these templates are not compatible with the latest versions of BEAST anymore (but should work fine with BEAST 2.6).
I would recommend instead using the newer SCOTTI templates, available here:
https://bitbucket.org/nicofmay/scotti/src/master/SCOTTI/examples/

Best wishes,
Nicola

[liamxg]

Hi Nicola,

Thanks.

I’ve tested the newer SCOTTI templates, and they’re working well.

Can I use a specific sampling date, such as 2020-09-25, as the date?

Best regards,
Liam

[NicolaDM]

The date needs to be a real value specified in time units (the time unit can be anything, for example days, years or hours), and you have to make sure that the sampling date is between the start and end date of the corresponding host.

[liamxg]

In most cases, researchers do not have access to the exact start and end dates of the corresponding host's infection period.

[NicolaDM]

Hi Liam,

The start and end dates don't need to be exact, the important thing is that they contain the earliest possible time in which the host might have been infected, and latest possible time at which the host might have infected other hosts. Then the transmission history will be inferred within these provided constraints, so the stricter the constraints the less uncertainty there will be in the inference. If the constraints provided are too strict however, SCOTTI might wrongly rule out some true transmission events.