Java issue

[brittonstrickland]

Hi all,

Excited to get this pipeline started. The installation via Conda and the precheck worked great. I'm currently trying to run some data through the pipeline, but there seems to be an issue when pointing to my java installation.

By running:

/nextflow run TransPi.nf --all --reads '~Desktop/RNAseq/*_R[1,2].fastq.gz' --k 25,41,53 --maxReadLen 80 -profile conda

I made sure I have java set in my path: export JAVA_HOME=$(/usr/libexec/java_home)

Running the transpi command, I get the following error:

ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later is installed NOTE: Nextflow is trying to use the Java VM defined by the following environment variables: JAVA_CMD: /Library/Java/JavaVirtualMachines/jdk-16.0.2.jdk/Contents/Home/bin/java JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk-16.0.2.jdk/Contents/Home

I tried a few troubleshooting items online but no success. Any thoughts? Thanks for your help.

[rivera10]

Hello @brittonstrickland,

What do you have as output when running java -version and nextflow -version?

I am not sure what is the problem but I can help you to figure it out. Let me know

Best, Ramon

[brittonstrickland]

Java

Brittons-MBP:~ brittonstrickland$ java -version openjdk version "11.0.9.1" 2020-11-04 LTS OpenJDK Runtime Environment Zulu11.43+55-CA (build 11.0.9.1+1-LTS) OpenJDK 64-Bit Server VM Zulu11.43+55-CA (build 11.0.9.1+1-LTS, mixed mode)

Nextflow

Brittons-MBP:~ brittonstrickland$ /Users/brittonstrickland/Desktop/TransPi/nextflow -version ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later is installed NOTE: Nextflow is trying to use the Java VM defined by the following environment variables: JAVA_CMD: /Library/Java/JavaVirtualMachines/jdk-16.0.2.jdk/Contents/Home/bin/java JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk-16.0.2.jdk/Contents/Home

I have JRE installed, and the location that Nextflow points to is correct. Typing java results in running java correctly.

Thanks!

[rivera10]

I found this https://github.com/nextflow-io/nextflow/issues/2057.

You can either use JVM up to 15 or use the edge version of nextflow 21.05.0-edge. This version should work with JDK 16 (https://github.com/nextflow-io/nextflow/commit/caace1c5b26ad878091a8d4afcc6dd338fbdf985).

To use the edge version use export NXF_VER=21.05.0-edge && curl -s https://get.nextflow.io | bash

Let me know if this solves the issue

[brittonstrickland]

Yes that fixed it! Thanks for your help.

[rivera10]

No worries. Anything let us know.