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CAPSULE EXCEPTION: Could not read pom.xml while processing system property capsule.log: verbose

Open danli349 opened this issue 3 years ago • 0 comments

Description of the bug

I installed nextflow with conda install -c bioconda nextflow on HPC, which has Singularity3.7.1 When I nextflow -Dcapsule.log=verbose There is 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

Command used and terminal output

No response

Relevant files

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System information

No response

danli349 avatar Jul 06 '22 14:07 danli349