snapper error (but not with snapp)

[atigano]

Hi,
I've prepared the input files in the same identical way for both snapp and snapper using the script snapp_prep.rb by Matschiner.

ruby $ANNA/sw/snapp_prep.rb -a SNAPP -v kokanee_batch123p_filtered_nomiss_maf05_0miss_maxd20_hwe_1sample.vcf -s tree_tremix_m0.txt -c constraint.txt -t ind2pop.txt -m 1000
ruby $ANNA/sw/snapp_prep.rb -a SNAPPER -v kokanee_batch123p_filtered_nomiss_maf05_0miss_maxd20_hwe_1sample.vcf -s tree_tremix_m0.txt -c constraint.txt -t ind2pop.txt -m 1000

The analysis is running fine using snapp but I get this error when I use snapper.
Any idea about what could be wrong?
Thanks,
Anna

File: snapper.xml seed: 1657818823876 threads: 1
Loading package BEAST v2.6.3
Loading package snapper v1.0.2
Loading package SNAPP v1.5.2
Loading package BEAST v2.6.3
java.lang.RuntimeException: Programmer error in class snapper.Data: multiple inputs with name rawdata found (perhaps in sub and super classes)
Classes should have unique input names
at beast.core.BEASTInterface.listInputs(Unknown Source)
at beast.core.parameter.Map.setInputValue(Unknown Source)
at beast.util.XMLParser.setInput(Unknown Source)
at beast.util.XMLParser.createBeastObject(Unknown Source)
at beast.util.XMLParser.createObject(Unknown Source)
at beast.util.XMLParser.parseInputs(Unknown Source)
at beast.util.XMLParser.createObject(Unknown Source)
at beast.util.XMLParser.parseInputs(Unknown Source)
at beast.util.XMLParser.createObject(Unknown Source)
at beast.util.XMLParser.parseInputs(Unknown Source)
at beast.util.XMLParser.createObject(Unknown Source)
at beast.util.XMLParser.parseRunElement(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 java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at beast.app.beastapp.BeastLauncher.run(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Error 124 parsing the xml input file

Programmer error in class snapper.Data: multiple inputs with name rawdata found (perhaps in sub and super classes)
Classes should have unique input names

Error detected about here:

[mmatschiner]

Hi Anna,
I haven't seen this issue before, thanks for reporting it! The script prepares the SNAPP and SNAPPER XMLs in almost exactly the same way, the only difference being:
<taxa id="data" spec="snap.Data" dataType="integerdata">
vs.
<taxa id="data" spec="snapper.Data" dataType="integerdata">
,
<distribution spec="snap.likelihood.SnAPTreeLikelihood" id="SnAPTreeLikelihood" data="@data" non-polymorphic="false" pattern="coalescenceRate" tree="@tree">
vs.
<distribution spec="snapper.SnapperTreeLikelihood" id="SnapperTreeLikelihood" data="@data" initFromTree="false" pattern="theta" useBetaRootPrior="true" tree="@tree">
, and the exact point in the XML where <coalescentRate idref="coalescenceRate"/> is defined. None of this has to do with the definition of any input with name "rawdata". But perhaps SNAPPER is just a bit scricter about the format and in principle SNAPP should also throw an error, but doesn't.
"rawdata" occurs twice in the XML (both SNAPP and SNAPPER), namely before the sequences are defined in <data id="snps" dataType="integer" name="rawdata"> and later as part of the taxa definitions:
<taxa id="data" spec="snapper.Data" dataType="integerdata"> <rawdata idref="snps"/>
Curiously, when I remove the second line with "rawdata" on it from the XML, the error message remains the same. So I think it lies not with my script but with the implementation of SNAPPER.

[atigano]

Hi Michael, thank you for your quick reply. So you tested it and got the same error? Is it possible that snapper expects more than one individual per species?

…

On Fri, Jul 15, 2022 at 5:47 AM Michael Matschiner ***@***.***> wrote: Hi Anna, I haven't seen this issue before, thanks for reporting it! The script prepares the SNAPP and SNAPPER XMLs in almost exactly the same way, the only difference being: <taxa id="data" spec="snap.Data" dataType="integerdata"> vs. <taxa id="data" spec="snapper.Data" dataType="integerdata"> , <distribution spec="snap.likelihood.SnAPTreeLikelihood" id="SnAPTreeLikelihood" ***@***.***" non-polymorphic="false" pattern="coalescenceRate" ***@***.***"> vs. <distribution spec="snapper.SnapperTreeLikelihood" id="SnapperTreeLikelihood" ***@***.***" initFromTree="false" pattern="theta" useBetaRootPrior="true" ***@***.***"> , and the exact point in the XML where <coalescentRate idref="coalescenceRate"/> is defined. None of this has to do with the definition of any input with name "rawdata". But perhaps SNAPPER is just a bit scricter about the format and in principle SNAPP should also throw an error, but doesn't. "rawdata" occurs twice in the XML (both SNAPP and SNAPPER), namely before the sequences are defined in <data id="snps" dataType="integer" name="rawdata"> and later as part of the taxa definitions: <taxa id="data" spec="snapper.Data" dataType="integerdata"> <rawdata idref="snps"/> Curiously, when I remove the second line with "rawdata" on it from the XML, the error message remains the same. So I think it lies not with my script but with the implementation of SNAPPER. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJ6ZI4TU6I3RDHL5PEKOFDVUFMUXANCNFSM53S672RQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Anna Tigano, Ph.D. Postdoctoral Associate The Ecological and Conservation Genomics Lab University of British Columbia - Okanagan annatigano.weebly.com

[mmatschiner]

Yes I got the same error, and also with a dataset that included two individuals per population.

…

On Jul 15, 2022, at 10:41 PM, atigano ***@***.***> wrote: Hi Michael, thank you for your quick reply. So you tested it and got the same error? Is it possible that snapper expects more than one individual per species? On Fri, Jul 15, 2022 at 5:47 AM Michael Matschiner ***@***.***> wrote: > Hi Anna, > I haven't seen this issue before, thanks for reporting it! The script > prepares the SNAPP and SNAPPER XMLs in almost exactly the same way, the > only difference being: > <taxa id="data" spec="snap.Data" dataType="integerdata"> > vs. > <taxa id="data" spec="snapper.Data" dataType="integerdata"> > , > <distribution spec="snap.likelihood.SnAPTreeLikelihood" > id="SnAPTreeLikelihood" ***@***.***" non-polymorphic="false" > pattern="coalescenceRate" ***@***.***"> > vs. > <distribution spec="snapper.SnapperTreeLikelihood" > id="SnapperTreeLikelihood" ***@***.***" initFromTree="false" > pattern="theta" useBetaRootPrior="true" ***@***.***"> > , and the exact point in the XML where <coalescentRate > idref="coalescenceRate"/> is defined. None of this has to do with the > definition of any input with name "rawdata". But perhaps SNAPPER is just a > bit scricter about the format and in principle SNAPP should also throw an > error, but doesn't. > "rawdata" occurs twice in the XML (both SNAPP and SNAPPER), namely before > the sequences are defined in <data id="snps" dataType="integer" > name="rawdata"> and later as part of the taxa definitions: > <taxa id="data" spec="snapper.Data" dataType="integerdata"> <rawdata > idref="snps"/> > Curiously, when I remove the second line with "rawdata" on it from the > XML, the error message remains the same. So I think it lies not with my > script but with the implementation of SNAPPER. > > — > Reply to this email directly, view it on GitHub > <#6 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ADJ6ZI4TU6I3RDHL5PEKOFDVUFMUXANCNFSM53S672RQ> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- Anna Tigano, Ph.D. Postdoctoral Associate The Ecological and Conservation Genomics Lab University of British Columbia - Okanagan annatigano.weebly.com — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABW5S7RGZTLNFXDSHB4FNS3VUHEILANCNFSM53S672RQ>. You are receiving this because you commented.

[rbouckaert]

The message "multiple inputs with name rawdata found" suggest that there is an XML entry that has two attributes or elements with the name rawdata where only a single entry is expected.

If you can upload the XML I can have a look and perhaps find out more closely where things went wrong.

When I generate an XML with BEAUti, this does not happen, so perhaps converting the data in a format that BEAUti can import may be a work-around.

[rbouckaert]

This should be fixed in snapper v1.0.3.

@atigano, could you upgrade to v1.0.3 and give it another try to see if the problem persists?