CAPSULE EXCEPTION: Error resolving dependencies

[gigantniki]

Hi,

I'm new to nextflow and programming in general so I apologize if I might ask rather basic questions while trying to figure this problem out.

I am working on a server and have downloaded nextflow to use later with the HLA-pipeline of nfcore. However, there seems to be some problem with running nextflow. When i run /gpfs2/well/ternette/users/hiz504/installs/hiz504_nextflow/nextflow run tutorial.nf to test if it works i get the Error message "CAPSULE EXCEPTION: Error resolving dependencies"

I have sadly no idea how to solve this.

The ful output of the command is this:

(base) [hiz504@rescomp2 .nextflow]$ /gpfs2/well/ternette/users/hiz504/installs/hiz504_nextflow/nextflow run tutorial.nf
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.7
CAPSULE: Downloading dependency org.checkerframework:checker-compat-qual:jar:2.0.0
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:21.04.3
CAPSULE: Downloading dependency com.google.guava:guava:jar:24.1.1-jre
CAPSULE: Downloading dependency org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:1.7.25
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:21.04.3
CAPSULE: Downloading dependency com.beust:jcommander:jar:1.35
CAPSULE: Downloading dependency org.jsoup:jsoup:jar:1.11.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.7
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.1.11
CAPSULE: Downloading dependency ch.grengine:grengine:jar:1.3.0
CAPSULE: Downloading dependency jline:jline:jar:2.9
CAPSULE: Downloading dependency com.github.zafarkhaja:java-semver:jar:0.9.0
CAPSULE: Downloading dependency javax.mail:mail:jar:1.4.7
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.1.11
CAPSULE: Downloading dependency commons-lang:commons-lang:jar:2.6
CAPSULE: Downloading dependency org.codehaus.gpars:gpars:jar:1.2.1
CAPSULE: Downloading dependency com.google.code.findbugs:jsr305:jar:1.3.9
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:21.04.3
CAPSULE: Downloading dependency org.objenesis:objenesis:jar:2.1
CAPSULE: Downloading dependency org.yaml:snakeyaml:jar:1.18
CAPSULE: Downloading dependency com.esotericsoftware.kryo:kryo:jar:2.24.0
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:1.7.25
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.3.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.7
CAPSULE: Downloading dependency com.googlecode.javaewah:JavaEWAH:jar:1.1.6
CAPSULE: Downloading dependency javax.activation:activation:jar:1.1.1
CAPSULE: Downloading dependency com.jcraft:jsch:jar:0.1.54
CAPSULE: Downloading dependency org.pf4j:pf4j:jar:3.4.1
CAPSULE: Downloading dependency org.iq80.leveldb:leveldb:jar:0.12
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.7
CAPSULE: Downloading dependency com.jcraft:jzlib:jar:1.1.1
CAPSULE: Downloading dependency com.google.code.gson:gson:jar:2.2.4
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:5.2.1.201812262042-r
CAPSULE: Downloading dependency org.pf4j:pf4j-update:jar:2.3.0
CAPSULE: Downloading dependency commons-codec:commons-codec:jar:1.10
CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false (for stack trace, run with -Dcapsule.log=verbose)
Unable to initialize nextflow environment

Also when I downloaded nextflow I first ran curl -s https://get.nextflow.io | bash and then chmod +x nextflow . I'm not sure what the second command does. Does it just give me execution permission? I didn't see any change in the permissions bar or any other change in the terminal or console. could that be causing the error?

Thank you all and I hope it's clear from my message what the problem is.

[jz940]

Hey I noticed the issue this was sourced from was closed. I'm having the same issue downloading nextflow, did you find a way to fix it?

[pditommaso]

Try running enabling the debugging info as show below, and copy & paste the printed output

nextflow -Dcapsule.log=verbose info 

[jz940]

Not sure what's going on (Allow-Snapshots or java) but I checked and I have java11

CAPSULE: Jar: /Users/name/.nextflow/framework/21.04.3/nextflow-21.04.3-one.jar
CAPSULE: Platform: macos
CAPSULE: Loading caplet: MavenCapsule
CAPSULE: Applying caplet MavenCapsule
CAPSULE: Initializing app ID
CAPSULE: Initialized app ID: nextflow_21.04.3
CAPSULE: Launching app nextflow_21.04.3
CAPSULE: WARNING resolve [] was empty
CAPSULE: WARNING resolve [] was empty
CAPSULE: Cache directory: /Users/name/.nextflow/capsule
CAPSULE: Dependency manager repositories: [central (https://repo1.maven.org/maven2/, default, releases), seqera (seqera, default, releases)]
CAPSULE: Resolving artifact org.slf4j:log4j-over-slf4j:pom:1.7.25
CAPSULE: Downloading artifact org.slf4j:log4j-over-slf4j:pom:1.7.25 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Downloading: https://repo1.maven.org/maven2/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.pom
CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.slf4j:log4j-over-slf4j:pom:1.7.25 from/to central (https://repo1.maven.org/maven2/): repo1.maven.org: nodename nor servname provided, or not known
capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.slf4j:log4j-over-slf4j:pom:1.7.25 from/to central (https://repo1.maven.org/maven2/): repo1.maven.org: nodename nor servname provided, or not known
	at capsule.org.eclipse.aether.connector.basic.ArtifactTransportListener.transferFailed(ArtifactTransportListener.java:43)
	at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:355)
	at capsule.org.eclipse.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:67)
	at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$DirectExecutor.execute(BasicRepositoryConnector.java:581)
	at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector.get(BasicRepositoryConnector.java:249)
	at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads(DefaultArtifactResolver.java:520)
	at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:421)
	at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
	at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:223)
	at capsule.org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:267)
	at capsule.org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor(DefaultArtifactDescriptorReader.java:198)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.resolveCachedArtifactDescriptor(DefaultDependencyCollector.java:535)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.getArtifactDescriptorResult(DefaultDependencyCollector.java:519)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.processDependency(DefaultDependencyCollector.java:409)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.processDependency(DefaultDependencyCollector.java:363)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.process(DefaultDependencyCollector.java:351)
	at capsule.org.eclipse.aether.internal.impl.DefaultDependencyCollector.collectDependencies(DefaultDependencyCollector.java:254)
	at capsule.org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:341)
	at capsule.DependencyManager.resolve0(DependencyManager.java:377)
	at capsule.DependencyManager.resolveDependencies(DependencyManager.java:314)
	at MavenCapsule.resolve0(MavenCapsule.java:224)
	at Capsule.resolve(Capsule.java:3375)
	at Capsule.resolve(Capsule.java:3389)
	at Capsule.buildJavaProcess(Capsule.java:2228)
	at Capsule.buildProcess0(Capsule.java:1530)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.buildProcess(Capsule.java:1521)
	at Capsule.prelaunch0(Capsule.java:1494)
	at Capsule.prelaunch(Capsule.java:1487)
	at NextflowLoader.prelaunch(NextflowLoader.java:42)
	at Capsule.prepareForLaunch(Capsule.java:1339)
	at Capsule.launch(Capsule.java:1268)
	at Capsule.main0(Capsule.java:399)
	at Capsule.main(Capsule.java:379)
Caused by: java.net.UnknownHostException: repo1.maven.org: nodename nor servname provided, or not known
	at java.base/java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
	at java.base/java.net.InetAddress$PlatformNameService.lookupAllHostAddr(InetAddress.java:929)
	at java.base/java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1519)
	at java.base/java.net.InetAddress$NameServiceAddresses.get(InetAddress.java:848)
	at java.base/java.net.InetAddress.getAllByName0(InetAddress.java:1509)
	at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1368)
	at java.base/java.net.InetAddress.getAllByName(InetAddress.java:1302)
	at capsule.org.apache.http.impl.conn.SystemDefaultDnsResolver.resolve(SystemDefaultDnsResolver.java:44)
	at capsule.org.apache.http.impl.conn.DefaultClientConnectionOperator.resolveHostname(DefaultClientConnectionOperator.java:259)
	at capsule.org.apache.http.impl.conn.DefaultClientConnectionOperator.openConnection(DefaultClientConnectionOperator.java:159)
	at capsule.org.apache.http.impl.conn.ManagedClientConnectionImpl.open(ManagedClientConnectionImpl.java:304)
	at capsule.org.apache.http.impl.client.DefaultRequestDirector.tryConnect(DefaultRequestDirector.java:611)
	at capsule.org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:446)
	at capsule.org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
	at capsule.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:72)
	at capsule.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
	at capsule.org.apache.http.impl.client.DecompressingHttpClient.execute(DecompressingHttpClient.java:158)
	at capsule.org.eclipse.aether.transport.http.HttpTransporter.execute(HttpTransporter.java:318)
	at capsule.org.eclipse.aether.transport.http.HttpTransporter.implGet(HttpTransporter.java:274)
	at capsule.org.eclipse.aether.spi.connector.transport.AbstractTransporter.get(AbstractTransporter.java:59)
	at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask(BasicRepositoryConnector.java:447)
	at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:350)
	... 33 more
...
Unable to initialize nextflow environment

[pditommaso]

Could not transfer artifact org.slf4j:log4j-over-slf4j:pom:1.7.25 from/to central (https://repo1.maven.org/maven2/): repo1.maven.org:

This suggests you are behind a firewall that does not allow accessing public repositories.

[QuantumQualia]

I had same issue, got on another network and was good.

[timini]

anyway to pre-install capsules for offline use?

[ChadBurdyshaw]

I'd also like to know if there is a way to preinstall capsules. I am on a restricted network, and would like to bundle everything into a standalone singularity file

[colindaven]

I just directly download the binary package from releases, since I'm behind a firewall, then set JAVA_HOME etc and unset other problematic java env variables. This works well for many pipelines to avoid having to set up a local conda env for each pipeline with nextflow and java.

wget https://github.com/nextflow-io/nextflow/releases/download/v23.04.3/nextflow-23.04.3-all