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tgvaughan / TransmissionChainAnalyses

Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.
GNU General Public License v3.0
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no main manifest attribute, in ./beast.jar #1

Closed liamxg closed 4 months ago

liamxg commented 6 months ago

Dear @tgvaughan,

When I run the ./run_analysis.sh script: it print: no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar no main manifest attribute, in ./beast.jar

tgvaughan commented 6 months ago

Hi Liam, the script is just running beast (2.6) from the command line. This should be possible if you have beast (2.6) installed and the command-line executable (found in the bin/ subdirectory of the directory BEAST is installed in) is in your path.

liamxg commented 6 months ago

Dear @tgvaughan,

When I use bin/beast, it prints:

sh run_analysis.sh bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory bin/beast: line 58: bin/../jre1.8.0_292/bin/java: No such file or directory

tgvaughan commented 6 months ago

Hi Liam,

This looks to be a problem with your beast 2 installation, and is quite apart from the transmission tree analysis. If I were you I'd first try to make it possible to run beast on the command line (perhaps asking the beast users group for help) before trying to attempt further to get the transmission tree analysis to run.

All the best, Tim

liamxg commented 6 months ago

Hi @tgvaughan, Some packages should be run first, thanks.

BEAST v2.6.7, 2002-2022 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

               Centre for Computational Evolution
                     University of Auckland
                   r.bouckaert@auckland.ac.nz
                    alexei@cs.auckland.ac.nz

               Institute of Evolutionary Biology
                    University of Edinburgh
                       a.rambaut@ed.ac.uk

                David Geffen School of Medicine
             University of California, Los Angeles
                       msuchard@ucla.edu

                  Downloads, Help & Resources:
                       http://beast2.org/

Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2

                       BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

                           Thanks to:
      Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 5

File: Re_skyline.xml seed: 5 threads: 1 Loading package BEAST v2.6.7

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.alignment.Alignment? Perhaps a package required for this class is not installed?

Error detected about here:

tgvaughan commented 6 months ago

Hi Liam, it looks like you haven't installed the package feast, which is listed under the required packages in the readme. Please install that first.

Tim

liamxg commented 6 months ago

Dear Tim,

Thanks. I have installed feast, and then it print to me:

java.lang.UnsupportedClassVersionError: beast/base/core/BEASTInterface$1 has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at beast.util.BEASTClassLoader.forName(Unknown Source) at beast.util.PackageManager.find(Unknown Source) at beast.util.PackageManager.find(Unknown Source) at beast.util.XMLParserUtils.(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) java.lang.UnsupportedClassVersionError: beast/base/CudaDetector has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at beast.util.BEASTClassLoader.forName(Unknown Source) at beast.util.PackageManager.find(Unknown Source) at beast.util.PackageManager.find(Unknown Source) at beast.util.XMLParserUtils.(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) java.lang.reflect.InvocationTargetException 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) Caused by: java.lang.UnsupportedClassVersionError: beast/base/evolution/alignment/Alignment has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at beast.util.BEASTClassLoader.forName(Unknown Source) at beast.util.XMLParserUtils.resolveClass(Unknown Source) at beast.util.XMLParser.createObject(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) ... 6 more

tgvaughan commented 6 months ago

Hi Liam, the classes referenced here (beast.base.* etc) are BEAST 2.7 classes, not BEAST 2.6. Are you sure that you only have BEAST 2.6 installed?

liamxg commented 6 months ago

Dear @tgvaughan,

I installed all the packages, it still prints Perhaps a package required for this class is not installed?, details see below:

BEAST v2.6.7, 2002-2022 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

               Centre for Computational Evolution
                     University of Auckland
                   r.bouckaert@auckland.ac.nz
                    alexei@cs.auckland.ac.nz

               Institute of Evolutionary Biology
                    University of Edinburgh
                       a.rambaut@ed.ac.uk

                David Geffen School of Medicine
             University of California, Los Angeles
                       msuchard@ucla.edu

                  Downloads, Help & Resources:
                       http://beast2.org/

Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2

                       BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

                           Thanks to:
      Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 2

File: Re_skyline.xml seed: 2 threads: 1 Loading package BEAST v2.6.7 Loading package feast v8.4.0 Loading package SA v2.0.2 Loading package BEASTLabs v1.9.7 Loading package BDSKY v1.4.8 Loading package EpiInf v7.5.2

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.math.distributions.MarkovChainDistribution? Perhaps a package required for this class is not installed?

Error detected about here:

tgvaughan commented 6 months ago

Hi Liam, I don't think you've got a beast 2.6-compatible bdmm-prime installed. This one should work:

https://github.com/tgvaughan/BDMM-Prime/releases/tag/v0.0.24

To install, download the .zip file and extract into a directory named bdmm-prime in your BEAST 2.6 package directory. Exactly where this directory is can be found by clicking the "?" button in the BEAUti package manager dialog:

Screenshot 2024-03-11 at 15 37 46
liamxg commented 6 months ago

Dear @tgvaughan,

Thanks again, but still have problem. Please see below:

Random number seed: 1

File: Re_skyline.xml seed: 1 threads: 1 Loading package BEAST v2.6.7 Loading package feast v8.4.0 Loading package BDMM-Prime v0.0.24 Loading package SA v2.0.2 Loading package BEASTLabs v1.9.7 Loading package BDSKY v1.4.8 Loading package EpiInf v7.5.2 TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: ......

........

TypeSet null:

Error 170 parsing the xml input file

Could not find object associated with idref tree_

Error detected about here:

tgvaughan commented 6 months ago

Hi Liam, no problem - this last issue is to do with a more recent change in beast 2.6 which prevents the script from running when no trees are logged. Commenting out the surrounding lines from the XML should fix this. (I've just committed a new version of this XML with the relevant lines commented out, so just try replacing the older XML with the new one.)

liamxg commented 6 months ago

Dear Tim,

Thanks, please help me check it again:

BEAST v2.6.7, 2002-2022 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard

               Centre for Computational Evolution
                     University of Auckland
                   r.bouckaert@auckland.ac.nz
                    alexei@cs.auckland.ac.nz

               Institute of Evolutionary Biology
                    University of Edinburgh
                       a.rambaut@ed.ac.uk

                David Geffen School of Medicine
             University of California, Los Angeles
                       msuchard@ucla.edu

                  Downloads, Help & Resources:
                       http://beast2.org/

Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2

                       BEAST developers:

Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie

                           Thanks to:
      Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 1

File: Re_skyline.xml seed: 1 threads: 1 Loading package BEAST v2.6.7 Loading package feast v8.4.0 Loading package BDMM-Prime v0.0.24 Loading package SA v2.0.2 Loading package BEASTLabs v1.9.7 Loading package BDSKY v1.4.8 Loading package EpiInf v7.5.2 TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: ...... .......

TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: TypeSet null: hCoV-19/Switzerland/BE-ETHZ-140022/2020|EPI_ISL_1129613|2020-05-19|1: 29624 4 AlignmentFromFasta(align_1) 1 taxa 29624 sites 5 patterns

Using format 'yyyy-MM-dd' to parse '2020-05-19' as: 2020.379781420765 hCoV-19/Switzerland/BE-ETHZ-140022/2020|EPI_ISL_1129613|2020-05-19|1 = 2020-05-19 (0.0) hCoV-19/Switzerland/LU-ETHZ-180054/2020|EPI_ISL_1130149|2020-06-29|2: 29705 4 AlignmentFromFasta(align_2) 1 taxa 29705 sites 5 patterns

Using format 'yyyy-MM-dd' to parse '2020-06-29' as: 2020.4918032786886 hCoV-19/Switzerland/LU-ETHZ-180054/2020|EPI_ISL_1130149|2020-06-29|2 = 2020-06-29 (0.0) hCoV-19/Switzerland/VD-ETHZ-200041/2020|EPI_ISL_1130704|2020-07-16|3: 29836 4 AlignmentFromFasta(align_3) 1 taxa 29836 sites 5 patterns

tgvaughan commented 6 months ago

Hi Liam, these look like standard initialisation messages to me: is there an error?

liamxg commented 6 months ago

Dear Tim,

Please see below:

Using format 'yyyy-MM-dd' to parse '2020-11-09' as: 2020.8551912568305 hCoV-19/Switzerland/BE-ETHZ-500085/2020|EPI_ISL_1119042|2020-11-09|1729 = 2020-11-09 (0.0) hCoV-19/Switzerland/ZH-ETHZ-500087/2020|EPI_ISL_1119045|2020-11-09|1730: 29805 4 AlignmentFromFasta(align_1730) 1 taxa 29805 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-09' as: 2020.8551912568305 hCoV-19/Switzerland/ZH-ETHZ-500087/2020|EPI_ISL_1119045|2020-11-09|1730 = 2020-11-09 (0.0) hCoV-19/Switzerland/TI-ETHZ-380308/2020|EPI_ISL_721911|2020-11-24|1731: 29836 4 AlignmentFromFasta(align_1731) 1 taxa 29836 sites 5 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-24' as: 2020.896174863388 hCoV-19/Switzerland/TI-ETHZ-380308/2020|EPI_ISL_721911|2020-11-24|1731 = 2020-11-24 (0.0) hCoV-19/Switzerland/BL-ETHZ-380349/2020|EPI_ISL_721792|2020-11-21|1733: 29836 4 AlignmentFromFasta(align_1733) 1 taxa 29836 sites 6 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-21' as: 2020.8879781420765 hCoV-19/Switzerland/BL-ETHZ-380349/2020|EPI_ISL_721792|2020-11-21|1733 = 2020-11-21 (0.0) hCoV-19/Switzerland/BE-ETHZ-500060/2020|EPI_ISL_1119041|2020-11-09|1734: 29800 4 AlignmentFromFasta(align_1734) 1 taxa 29800 sites 5 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-09' as: 2020.8551912568305 hCoV-19/Switzerland/BE-ETHZ-500060/2020|EPI_ISL_1119041|2020-11-09|1734 = 2020-11-09 (0.0) hCoV-19/Switzerland/NE-ETHZ-500068/2020|EPI_ISL_1119044|2020-11-09|1735: 29803 4 AlignmentFromFasta(align_1735) 1 taxa 29803 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-09' as: 2020.8551912568305 hCoV-19/Switzerland/NE-ETHZ-500068/2020|EPI_ISL_1119044|2020-11-09|1735 = 2020-11-09 (0.0) hCoV-19/Switzerland/ZH-ETHZ-500086/2020|EPI_ISL_1119047|2020-11-09|1736: 29825 4 AlignmentFromFasta(align_1736) 1 taxa 29825 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-09' as: 2020.8551912568305 hCoV-19/Switzerland/ZH-ETHZ-500086/2020|EPI_ISL_1119047|2020-11-09|1736 = 2020-11-09 (0.0) hCoV-19/Switzerland/BE-ETHZ-500089/2020|EPI_ISL_1119050|2020-11-12|1737: 29804 4 AlignmentFromFasta(align_1737) 1 taxa 29804 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-12' as: 2020.863387978142 hCoV-19/Switzerland/BE-ETHZ-500089/2020|EPI_ISL_1119050|2020-11-12|1737 = 2020-11-12 (0.0) hCoV-19/Switzerland/BL-ETHZ-520169/2020|EPI_ISL_1260161|2020-11-25|1738: 29840 4 AlignmentFromFasta(align_1738) 1 taxa 29840 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-25' as: 2020.8989071038252 hCoV-19/Switzerland/BL-ETHZ-520169/2020|EPI_ISL_1260161|2020-11-25|1738 = 2020-11-25 (0.0) hCoV-19/Switzerland/BL-ETHZ-520725/2020|EPI_ISL_1408627|2020-11-29|1739: 29782 4 AlignmentFromFasta(align_1739) 1 taxa 29782 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-29' as: 2020.9098360655737 hCoV-19/Switzerland/BL-ETHZ-520725/2020|EPI_ISL_1408627|2020-11-29|1739 = 2020-11-29 (0.0) hCoV-19/Switzerland/GE-ETHZ-410908/2020|EPI_ISL_737758|2020-11-30|1740: 29849 4 AlignmentFromFasta(align_1740) 1 taxa 29849 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-30' as: 2020.9125683060108 hCoV-19/Switzerland/GE-ETHZ-410908/2020|EPI_ISL_737758|2020-11-30|1740 = 2020-11-30 (0.0) hCoV-19/Switzerland/BE-ETHZ-500102/2020|EPI_ISL_1119049|2020-11-12|1741: 29806 4 AlignmentFromFasta(align_1741) 1 taxa 29806 sites 4 patterns

Using format 'yyyy-MM-dd' to parse '2020-11-12' as: 2020.863387978142 hCoV-19/Switzerland/BE-ETHZ-500102/2020|EPI_ISL_1119049|2020-11-12|1741 = 2020-11-12 (0.0) java.lang.RuntimeException: Two sequences with different length found: 29704 != 29819 at beast.evolution.alignment.Alignment.sanityCheckCalcPatternsSetUpAscertainment(Unknown Source) at beast.evolution.alignment.Alignment.initializeWithSequenceList(Unknown Source) at beast.evolution.alignment.Alignment.initAndValidate(Unknown Source) at feast.fileio.AlignmentFromFasta.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: Two sequences with different length found: 29704 != 29819

Error detected about here:

tgvaughan commented 6 months ago

It looks like you haven't aligned the sequences - you'll need to do this first.

liamxg commented 6 months ago

Dear Tim,

Is this normal? Warning: state contains a node tree_257 for which there is no operator. Warning: state contains a node tree_267 for which there is no operator. Warning: state contains a node tree_268 for which there is no operator. Warning: state contains a node tree_272 for which there is no operator. Warning: state contains a node tree_277 for which there is no operator. Warning: state contains a node tree_278 for which there is no operator. Warning: state contains a node tree_283 for which there is no operator. Warning: state contains a node tree_285 for which there is no operator. Warning: state contains a node tree_288 for which there is no operator. Warning: state contains a node tree_292 for which there is no operator. Warning: state contains a node tree_321 for which there is no operator. Warning: state contains a node tree_322 for which there is no operator. Warning: state contains a node tree_324 for which there is no operator. Warning: state contains a node tree_326 for which there is no operator. Warning: state contains a node tree_327 for which there is no operator. Warning: state contains a node tree_338 for which there is no operator. Warning: state contains a node tree_354 for which there is no operator. Warning: state contains a node tree_370 for which there is no operator. Warning: state contains a node tree_457 for which there is no operator. Start likelihood: -1.291859556995482E7 Writing file results/Re_skyline.min_chains.sampUB0.05.1.1.log Sample posterior ReSGPrior ReTheta 0 -1.291859556E7 26.8414 0.095 -- 1000000 -1.258495154E7 -62.2078 0.5913 -- 2000000 -1.258050271E7 -71.3244 0.6160 --

liamxg commented 6 months ago

Dear Tim,

This run is very slow in my personal MacBook Pro, how should I do? Thanks.

tgvaughan commented 6 months ago

Hi Liam, yes that's normal. And you definitely don't want to run this on a laptop. We ran all of these calculations in parallel on a large cluster.

liamxg commented 6 months ago

Hi Tim,

Right now I do not have large cluster, could you please share the results from BEAST run, so I can go on, thanks.

tgvaughan commented 6 months ago

Hi Liam, there are 80 distinct runs which constitute these analyses, and the logs are about 10 GB. Exactly what do you want? I can share one or two, but the whole lot is a bit difficult. It might be easier for you to just run one or two of the analyses on your side which shouldn't take so long.

On Thu, 14 Mar 2024, at 9:42 AM, Liam wrote:

Hi Tim,

Right now I do not have large cluster, could you please share the results from BEAST run, so I can go on, thanks.

-- Reply to this email directly or view it on GitHub: https://github.com/tgvaughan/TransmissionChainAnalyses/issues/1#issuecomment-1996879281 You are receiving this because you were mentioned.

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liamxg commented 6 months ago

Dear Tim,

That's really a good idea. l just want to use them for the postprocessing steps. Could you please share one or two of the analyses to me, thanks.

liamxg commented 6 months ago

BTW, Could I know to maximize the computing power of GPU, so I can run it more fast, thanks.

tgvaughan commented 6 months ago

Here's one of the logs: Re_skyline_2deme.max_chains.sampUB0.05.1.1.log.zip

tgvaughan commented 6 months ago

For help with general beast performance, please visit www.beast2.org.

liamxg commented 6 months ago

Here's one of the logs: Re_skyline_2deme.max_chains.sampUB0.05.1.1.log.zip

Thanks Tim.

liamxg commented 6 months ago

Dear Tim,

I found that some of ESS values for the log file that you attached is very low, does that matter?

image
tgvaughan commented 6 months ago

These analyses were repeated 10 times each, convergence checked, then logs combined.

On Thu, 14 Mar 2024, at 10:39 AM, Liam wrote:

Dear Tim,

I found that some of ESS values for the log file that you attached is very low, does that matter?

<img width="344" alt="image" src="https://github.com/tgvaughan/TransmissionChainAnalyses/assets/46078579/0ecdbe1a-b5b9-4430-8133-02d193806257">

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liamxg commented 6 months ago

Dear Tim,

Thanks for let me know this. I changed the chain length to 1000 and every 100, and run it again.