Constructing phylogeny tree based on bacterial core genes

Question

[krishna.gundawar26]

Hello there! I'm new to this forum and very glad to be part of such a vibrant community. Well, I would like to know whether anyone has ever used UBCG (up-to-date bacterial core gene), a JAVA based application developed by ChunLab (https://www.ezbiocloud.net/tools/ubcg). I tried to use it to analyze certain bacterial genomes in order to construct a phylogenomic tree based on core genes. I followed instructions as mentioned in the user's manual of this application but faced consistent errors while execution on my system (Ubuntu 18.04.4 LTS). The error message described as mentioned below.

krishna@krishna-Vostro-3480:~/Desktop/UBCG_v3/UBCG$ java -jar UBCG.jar extract -bcg_dir bcg -i /home/krishna/Desktop/UBCG_v3/UBCG fasta/CP012646_s_GCA_001281025.1_KCOM_1350.fasta -label "CP012646_s KCOM 1350" -acc "GCA_001281025.1" -taxon "CP012646_s" -strain "KCOM 1350" Exception in thread "main" java.lang.NoClassDefFoundError: org/json/simple/parser/ParseException

at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:398)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:56)

Caused by: java.lang.ClassNotFoundException: org.json.simple.parser.ParseException

at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:471)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:588)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 3 more

Why does it happen every time? any guess?

Looking forward to your kind help.

Thanks in advance.

-Krishna Gundawar

[selmavieira]

Hi! I am having the same issue. Did you ever find a solution?

[andersonlee]

+1. Let me know if you find out a way to fix this.

Answer 1

[bharatgu19]

You may not be using the correct java / version:

1. Check the java version $java - - version openjdk version "11.0.7" 2020-04-14 OpenJDK Runtime Environment (build 11.0.7+10-post-Ubuntu-2ubuntu218.04) OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Ubuntu-2ubuntu218.04, mixed mode, sharing)

2. If you see the above, which is the most recent java than you will ned to install Java Runtime Environment Version 8 which is not present

3. Download Java Runtime Environment Version 8 (jre-8): (a) https://www.oracle.com/java/technologies/javase-jre8-downloads.html#license-lightboxhttps:// (b) Click jre-8u251-linux-x64.tar.gz and download the compressed version after signing the agreement

4. Set the environment for jre-8

   $cat >> /etc/environment <<eol< p="">

   JAVA_HOME= /usr/lib/jvm/java-8-openjdk-amd64

   JRE_HOME=/usr/lib/jvm/java-8-openjdk-amd64/jre

   EOL

5. Check which java exisits in your system and select jre8: $sudo update-alternatives --config java

Selection Path Priority Status

• 0 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 auto mode

  1 /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 manual mode

  2 /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java 1081 manual mode

---

There are 2 choices for java (java8 and java10). #2 should be selected to run UBCG.jar

[andersonlee]

Thanks for the help! I'm on Mac and changing the PATH variable worked for me:

export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home