multiqc|get_software_versions fatal error?

[the-awesome-pawesome]

Hey there,

When attempting to the Rnaseq pipeline, I'm getting a fatal error right at the start of the pipeline

WARN: The config file defines settings for an unknown process: multiqc|get_software_versions

Anybody know a fix? I'm running via pip installation of nf-core using the nextflow run nf-core/rnaseq ... etc. command.

[drpatelh]

Hi @the-awesome-pawesome ! This is a Nextflow bug. See:
nextflow-io/nextflow#1167

It is just a warning so shouldnt be fatal. Can you post the full error message you are getting please?

[the-awesome-pawesome]

Here's the nextflow debug log. It points to an unknown error

Jul-17 18:05:18.287 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Jul-17 18:05:18.774 [main] WARN nextflow.Session - The config file defines settings for an unknown process: multiqc|get_software_versions
Jul-17 18:05:18.774 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-17 18:05:18.857 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider
Jul-17 18:05:18.863 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {}
Jul-17 18:05:19.117 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: ./; pattern: *.R{1,2}.fastq.gz; options: [:]
Jul-17 18:05:19.191 [main] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.StackOverflowError
Jul-17 18:05:19.216 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.StackOverflowError: null
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:105)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:1845)
at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:3773)
at nextflow.script.WorkflowMetadata.getProperty(WorkflowMetadata.groovy)
at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190)
at nextflow.script.WorkflowMetadata.get(WorkflowMetadata.groovy:284)
at sun.reflect.GeneratedMethodAccessor50.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)

[drpatelh]

Hi @the-awesome-pawesome! Sorry, I seemed to have missed your response here. Did you manage to fix this? If not, can you send me the full command you were using please? Seeing as it was quite a while back I will close for now but we can reopen if you are still having the same problems. Alternatively, feel free to join the #rnaseq channel on the nf-core Slack workspace where we can try and help in real-time.