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CAPSULE EXCEPTION: Error resolving dependencies #2280

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gigantniki opened this issue Aug 27, 2021 · 0 comments
Closed

CAPSULE EXCEPTION: Error resolving dependencies #2280

gigantniki opened this issue Aug 27, 2021 · 0 comments

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@gigantniki
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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.

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