nextflow error

Question

[Dan]

I installed nextflow with conda install -c bioconda nextflow on HPC, which has Singularity3.7.1 installed.

When I nextflow -Dcapsule.log=verbose There is an error:

CAPSULE: Jar: /lila/home/lid/miniconda3/envs/nf-core/share/nextflow/dist/20.10.0/nextflow-20.10.0-one.jar
CAPSULE: Platform: linux
CAPSULE: Loading caplet: MavenCapsule
CAPSULE: Applying caplet MavenCapsule
CAPSULE EXCEPTION: Could not read pom.xml while processing system property capsule.log: verbose
java.lang.RuntimeException: Could not read pom.xml
        at MavenCapsule.createPomReader(MavenCapsule.java:249)
        at MavenCapsule.createPomReader(MavenCapsule.java:242)
        at MavenCapsule.finalizeCapsule(MavenCapsule.java:70)
        at Capsule.finalizeCapsule(Capsule.java:819)
        at Capsule.<init>(Capsule.java:744)
        at NextflowLoader.<init>(NextflowLoader.java:37)
        at jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:490)
        at Capsule.newCapsule0(Capsule.java:5603)
        at Capsule.newCapsule(Capsule.java:5595)
        at Capsule.myCapsule(Capsule.java:361)
        at Capsule.main0(Capsule.java:387)
        at Capsule.main(Capsule.java:379) Caused by: java.util.zip.ZipException: invalid entry CRC (expected 0xc952da5c but got 0x7155fe57)
        at java.util.zip.ZipInputStream.readEnd(ZipInputStream.java:408)
        at java.util.zip.ZipInputStream.read(ZipInputStream.java:197)
        at java.util.jar.JarInputStream.read(JarInputStream.java:207)
        at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:141)
        at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:119)
        at java.util.jar.JarInputStream.getNextEntry(JarInputStream.java:142)
        at Capsule.getEntry(Capsule.java:3839)
        at Capsule.getEntryInputStream(Capsule.java:3835)
        at MavenCapsule.createPomReader(MavenCapsule.java:246)
        ... 14 more
Unable to initialize nextflow environment

What should I do to fix this problem? Thanks

[Arup Ghosh]

Try the Netflow standalone version.

Answer 1

[Pierre Lindenbaum]

: invalid entry CRC (expected 0xc952da5c but got 0x7155fe57)

looks like there is a problem in a zip/jar file which is badly packaged or installed.

You should try by downloading nextflow itself rather than using your conda installation.

[Matthias Zepper]

I second that. Installing nextflow via conda breaks all kinds of things and is clearly not advised...fixing that mess took me a while.

For example, it will install an own version of git and mess with the global Unicode configuation of multiple programs, such that you will get Normal-Form-Composed / Normal-Form-Decomposed errors all over the place when executing or editing scripts.

Answer 2

[ATpoint]

While conda is awesome for many things, nextflow installation is really just curl -s https://get.nextflow.io | bash and done. Try that without the unnecessary complexity of conda in that case. Install any nextflow version, you can then easily run the desired version by doing NXF_VER=XX.XX.XX nextflow run... in case the installed version is greater/smaller than the one required by the workflow.

[Dan]

Yes. This solution worked for me. Thanks