I am trying to clone a git repo locally through the java code that I have. And this is how it looks like:

class Scratch {
  public static void main(String[] args) {
    String repoName = "https://github.somedomain.co/AppPipelines/some-project.git";
    String username = "username";
    String personalAccessToken = "some_personal_access_token";
    String repoUrl = "https://github.somedomain.co/AppPipelines/some_repo";
    String cloneDirectoryPath = "/Users/username/DSS/1223";

    try {
      // Create credentials provider with username and token
      UsernamePasswordCredentialsProvider credentialsProvider =
        new UsernamePasswordCredentialsProvider("token", personalAccessToken);

      Git.cloneRepository()
        .setURI(repoUrl)
        .setDirectory(new File(cloneDirectoryPath))
        .setBranch("main")
        .setCredentialsProvider(credentialsProvider)
        .call();

    } catch (GitAPIException e) {
      System.err.println("Error cloning repository: " + e.getMessage());
      e.printStackTrace();
    }
  }
}

When I try to run this code, I get this exception:

Error cloning repository: git@github.bamtech.co:AppPipelines/nexus-rm: remote hung up unexpectedly
org.eclipse.jgit.api.errors.TransportException: git@github.bamtech.co:AppPipelines/nexus-rm: remote hung up unexpectedly
    at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:249)
    at org.eclipse.jgit.api.CloneCommand.fetch(CloneCommand.java:319)
    at org.eclipse.jgit.api.CloneCommand.call(CloneCommand.java:189)
    at Scratch.main(scratch_1.java:27)
Caused by: org.eclipse.jgit.errors.TransportException: git@github.bamtech.co:AppPipelines/nexus-rm: remote hung up unexpectedly
    at org.eclipse.jgit.transport.TransportGitSsh$SshFetchConnection.<init>(TransportGitSsh.java:317)
    at org.eclipse.jgit.transport.TransportGitSsh.openFetch(TransportGitSsh.java:152)
    at org.eclipse.jgit.transport.FetchProcess.executeImp(FetchProcess.java:153)
    at org.eclipse.jgit.transport.FetchProcess.execute(FetchProcess.java:105)
    at org.eclipse.jgit.transport.Transport.fetch(Transport.java:1458)
    at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:238)
    ... 3 more
Caused by: java.lang.NullPointerException: Cannot invoke "org.eclipse.jgit.transport.SshSessionFactory.getSession(org.eclipse.jgit.transport.URIish, org.eclipse.jgit.transport.CredentialsProvider, org.eclipse.jgit.util.FS, int)" because "this.sch" is null
    at org.eclipse.jgit.transport.SshTransport.getSession(SshTransport.java:107)
    at org.eclipse.jgit.transport.TransportGitSsh$SshFetchConnection.<init>(TransportGitSsh.java:285)
    ... 8 more

Here are the Gradle plugins and dependencies:

plugins {
    id 'org.springframework.boot' version '3.4.1'
    id 'io.spring.dependency-management' version '1.1.0'
    id 'java'
    id 'jacoco'
    id 'com.diffplug.spotless' version '6.20.0'
}

dependencies {
    implementation "org.springframework.boot:spring-boot-starter-web"
    implementation "org.springdoc:springdoc-openapi-starter-webmvc-ui:${swaggerVersion}"
    testImplementation "org.springframework.boot:spring-boot-starter-test"
    compileOnly "org.projectlombok:lombok:${lombokVersion}"
    annotationProcessor "org.projectlombok:lombok:${lombokVersion}"
    implementation "org.springframework.boot:spring-boot-starter-validation"
    implementation "org.eclipse.jgit:org.eclipse.jgit:${eclipseJgitVersion}"
    implementation "org.eclipse.jgit.ssh.jsch:${eclipseJgitVersion}"
    implementation group: 'com.jcraft.jsch', name: 'com.jcraft.jsch', version: '0.1.37-20081006'
    implementation "com.google.code.gson:gson:${gsonVersion}"
    implementation platform("software.amazon.awssdk:bom:${awsSdk}")
    implementation 'software.amazon.awssdk:dynamodb'
    implementation 'software.amazon.awssdk:dynamodb-enhanced'
    implementation "com.github.derjust:spring-data-dynamodb:${springDataDynamoDB}"
    implementation "com.amazonaws:aws-java-sdk-sts:${awsSdk1Sts}"
    implementation "com.datadoghq:datadog-api-client:${ddClient}"
    implementation 'software.amazon.awssdk:sts'
    implementation 'software.amazon.awssdk:eks'
    implementation "software.amazon.awssdk:batch:${awsSdk}"
    implementation "software.amazon.awssdk:autoscaling:${awsSdk}"
    implementation "software.amazon.awssdk:netty-nio-client:${awsSdk}"
    implementation "software.amazon.awssdk:ec2:${awsSdk}"
    implementation "software.amazon.awssdk:ecs:${awsSdk}"
    implementation "com.datadoghq:java-dogstatsd-client:${dataDogStatSd}"
    implementation "org.springframework.boot:spring-boot-starter-actuator"
    implementation 'org.springframework.boot:spring-boot-starter-aop'
    implementation 'io.micrometer:micrometer-registry-datadog:1.14.3'
    implementation "org.springframework.security:spring-security-web:${springSecurityWebVersion}"
    implementation "com.disneystreaming.nexus:common-java-libs:0.0.2"
}

And the version is eclipseJgitVersion=7.1.0.202411261347-r.

I am not sure if I am missing anything here. This happens only with a certain domain because, I am able to clone repositories from other domains without any issue with corresponding usernames and tokens. Let me know if this is missing anything. Thanks in advance.

In your case, the error is actually caused by the CredentialsProvider not being configured correctly. To properly authenticate, you could either follow GitHub guidelines, or a use a JGit workaround. In fact, as of March 2025, JGit still does not support OAuth 2.0 authentication (see issue 94).

GitHub Guidelines

According to GitHub docs, to authenticate via HTTPS with a personal access token, the PAT should be passed in place of the password. Therefore, your authentication should look like this:

UsernamePasswordCredentialsProvider credentialsProvider =
    new UsernamePasswordCredentialsProvider(username, personalAccessToken);

JGit Workaround

When authenticating to GitHub specifically via JGit, since there is no support for bearer tokens, the personal access token should be passed in place of the username, while the password should be empty.

UsernamePasswordCredentialsProvider credentialsProvider =
    new UsernamePasswordCredentialsProvider(personalAccessToken, "");

Other Possible Issues

When using an SSH connection (and properly configured credentials), the same error might be caused by the default SSH factory. In fact, according to this Eclipse Wiki, since version 5.8.x, the default SSH factory jsch has been moved from jgit to org.eclipse.jgit:org.eclipse.jgit.ssh.jsch. Therefore, you need to add the corresponding dependency to make it work.

Gradle Dependency

implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit.ssh.jsch', version: '(version)'

Maven Dependency

<dependency>
    <groupId>org.eclipse.jgit</groupId>
    <artifactId>org.eclipse.jgit.ssh.jsch</artifactId>
    <version>${jgit.version}</version>
</dependency>

The issue was also reported in the following GitHub repositories: issue 20 and issue 540. Keep in mind that org.eclipse.jgit.ssh.jsch also relies on com.jcraft.jsch, and, as of the time when this answer was written, the only version still maintained seems to be this fork under com.github.mwiede.