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A DSL for data-driven computational pipelines
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CAPSULE exception: cannot transfer nextflow-23.04.1.jar #3988

Closed flass closed 1 year ago

flass commented 1 year ago

Bug report

I have a nextflow user who cannot manage to get any pipeline to run, always hitting the same bug when initiating the nextflow environment and more specifically when downloading the required dependencies. It precisely always happen when trying to download the nextflow-23.04.1.jar file, which puzzles me as it does not need it, the command being executed form that same very file to start with.
Why would nextflow try to download itself?
Annoyingly, it seems to be a user-specific issue as I can't reproduce this error with my own user, but I can't find anything specific in their environment that would cause such an issue. Disk space for downloading the artifacts does not seem to be an issue, even though I might be underestimating the size of the nextflow-23.04.1.jar file.

Can you please help me diagnose what is the issue here?

Expected behavior and actual behavior

that the pipeline runs, or at least that they could get the Nextflow usage message when doing nextflow -h

from an environment that works fine (under my own user), we should get this:

[fl4@farm5-head2 test]$ nano-rave --help
N E X T F L O W  ~  version 23.04.1
Launching `/software/pathogen/custom_installs/nano-rave/v1.0.1/nano-rave/nano-rave` [agitated_bose] DSL2 - revision: c2f00dc80c

Usage:
    nextflow run nano-rave

Options:
    --sequencing_manifest        Manifest containing paths to sequencing directories and sequencing summary files (mandatory)
    --reference_manifest         Manifest containing reference identifiers and paths to fastq reference files (mandatory)
    --results_dir                Specify results directory [default: ./nextflow_results] (optional)
    --variant_caller             Specify a variant caller to use [medaka (default), medaka_haploid, freebayes] (optional)
    --min_barcode_dir_size       Specify the expected minimum size of the barcode directories, in MB. Must be > 0. [default: 10] (optional)
    --help                       Print this help message (optional)

[fl4@farm5-head2 test]$ nano-rave -h
Execute a pipeline project
Usage: run [options] Project name or repository url
  Options:
    -E
       Exports all current system environment
       Default: false
    -ansi-log
       Enable/disable ANSI console logging
[...]

Steps to reproduce the problem

This bug is observed on the Sanger Institute LSF HPC. The command actually run is nano-rave, executing the main.nf workflow; see here https://github.com/sanger-pathogens/nano-rave#running-on-the-farm-sanger-hpc-clusters

with the following commands, we observe the respective outputs in the section below:

nano-rave -h
nano-rave -Dcapsule.log=verbose

Program output

CAPSULE: Downloading dependency io.nextflow:nextflow:jar:23.04.1
CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false (for stack trace, run with  -Dcapsule.log=verbose)
Unable to initialize nextflow environment
CAPSULE: Jar: /nfs/users/nfs_m/mb29/.nextflow/framework/23.04.1/nextflow-23.04.1-one.jar
CAPSULE: Platform: linux
CAPSULE: Loading caplet: MavenCapsule
CAPSULE: Applying caplet MavenCapsule
CAPSULE: Initializing app ID
CAPSULE: Initialized app ID: nextflow_23.04.1
CAPSULE: Launching app nextflow_23.04.1
CAPSULE: Using JVM: /software/pathogen/custom_installs/nextflow/23.04.1-5866/dependencies/jdk
CAPSULE: WARNING resolve [] was empty
CAPSULE: WARNING resolve [] was empty
CAPSULE: Cache directory: /nfs/users/nfs_m/mb29/.nextflow/capsule
CAPSULE: Adding `http` proxy: wwwcache.sanger.ac.uk:3128 [from system environment]
CAPSULE: Adding `https` proxy: wwwcache.sanger.ac.uk:3128 [from system environment]
CAPSULE: Dependency manager repositories: [central (https://repo1.maven.org/maven2/, default, releases), seqera (seqera, default, releases)]
CAPSULE: Resolving artifact org.multiverse:multiverse-core:pom:0.7.0
CAPSULE: Resolved artifact org.multiverse:multiverse-core:pom:0.7.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.multiverse:multiverse:pom:0.7.0
CAPSULE: Resolved artifact org.multiverse:multiverse:pom:0.7.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache.ivy:ivy:pom:2.5.1
CAPSULE: Resolved artifact org.apache.ivy:ivy:pom:2.5.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache:apache:pom:7
CAPSULE: Resolved artifact org.apache:apache:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:jul-to-slf4j:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:jul-to-slf4j:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-parent:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-parent:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-templates:pom:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-templates:pom:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:jcl-over-slf4j:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:jcl-over-slf4j:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-parent:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-parent:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-io:commons-io:pom:2.11.0
CAPSULE: Resolved artifact commons-io:commons-io:pom:2.11.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache.commons:commons-parent:pom:52
CAPSULE: Resolved artifact org.apache.commons:commons-parent:pom:52 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache:apache:pom:23
CAPSULE: Resolved artifact org.apache:apache:pom:23 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.junit:junit-bom:pom:5.7.2
CAPSULE: Resolved artifact org.junit:junit-bom:pom:5.7.2 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.jsr166-mirror:jsr166y:pom:1.7.0
CAPSULE: Resolved artifact org.codehaus.jsr166-mirror:jsr166y:pom:1.7.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-codec:commons-codec:pom:1.15
CAPSULE: Resolved artifact commons-codec:commons-codec:pom:1.15 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache.commons:commons-parent:pom:52
CAPSULE: Resolved artifact org.apache.commons:commons-parent:pom:52 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache:apache:pom:23
CAPSULE: Resolved artifact org.apache:apache:pom:23 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:listenablefuture:pom:9999.0-empty-to-avoid-conflict-with-guava
CAPSULE: Resolved artifact com.google.guava:listenablefuture:pom:9999.0-empty-to-avoid-conflict-with-guava from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:guava-parent:pom:26.0-android
CAPSULE: Resolved artifact com.google.guava:guava-parent:pom:26.0-android from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:9
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:9 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.artecat.grengine:grengine:pom:3.0.0
CAPSULE: Resolved artifact ch.artecat.grengine:grengine:pom:3.0.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.beust:jcommander:pom:1.35
CAPSULE: Resolved artifact com.beust:jcommander:pom:1.35 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:3
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:3 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nextflow:pom:23.04.1
CAPSULE: Resolved artifact io.nextflow:nextflow:pom:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact jline:jline:pom:2.9
CAPSULE: Resolved artifact jline:jline:pom:2.9 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-core:pom:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-core:pom:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-parent:pom:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-parent:pom:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.github.zafarkhaja:java-semver:pom:0.9.0
CAPSULE: Resolved artifact com.github.zafarkhaja:java-semver:pom:0.9.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:9
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:9 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact javax.mail:mail:pom:1.4.7
CAPSULE: Resolved artifact javax.mail:mail:pom:1.4.7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.sun.mail:all:pom:1.4.7
CAPSULE: Resolved artifact com.sun.mail:all:pom:1.4.7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact net.java:jvnet-parent:pom:1
CAPSULE: Resolved artifact net.java:jvnet-parent:pom:1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-json:pom:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-json:pom:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.eclipse.jgit:org.eclipse.jgit:pom:6.2.0.202206071550-r
CAPSULE: Resolved artifact org.eclipse.jgit:org.eclipse.jgit:pom:6.2.0.202206071550-r from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.eclipse.jgit:org.eclipse.jgit-parent:pom:6.2.0.202206071550-r
CAPSULE: Resolved artifact org.eclipse.jgit:org.eclipse.jgit-parent:pom:6.2.0.202206071550-r from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.code.findbugs:jsr305:pom:3.0.2
CAPSULE: Resolved artifact com.google.code.findbugs:jsr305:pom:3.0.2 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy:pom:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy:pom:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-lang:commons-lang:pom:2.6
CAPSULE: Resolved artifact commons-lang:commons-lang:pom:2.6 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache.commons:commons-parent:pom:17
CAPSULE: Resolved artifact org.apache.commons:commons-parent:pom:17 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache:apache:pom:7
CAPSULE: Resolved artifact org.apache:apache:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb-api:pom:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb-api:pom:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb-project:pom:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb-project:pom:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.airlift:airbase:pom:77
CAPSULE: Resolved artifact io.airlift:airbase:pom:77 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.gpars:gpars:pom:1.2.1
CAPSULE: Resolved artifact org.codehaus.gpars:gpars:pom:1.2.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-classic:pom:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-classic:pom:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-parent:pom:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-parent:pom:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.jsoup:jsoup:pom:1.15.4
CAPSULE: Resolved artifact org.jsoup:jsoup:pom:1.15.4 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:log4j-over-slf4j:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:log4j-over-slf4j:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-parent:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-parent:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:guava:pom:31.1-jre
CAPSULE: Resolved artifact com.google.guava:guava:pom:31.1-jre from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:guava-parent:pom:31.1-jre
CAPSULE: Resolved artifact com.google.guava:guava-parent:pom:31.1-jre from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.objenesis:objenesis:pom:2.1
CAPSULE: Resolved artifact org.objenesis:objenesis:pom:2.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.objenesis:objenesis-parent:pom:2.1
CAPSULE: Resolved artifact org.objenesis:objenesis-parent:pom:2.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.esotericsoftware.kryo:kryo:pom:2.24.0
CAPSULE: Resolved artifact com.esotericsoftware.kryo:kryo:pom:2.24.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-api:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-api:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-parent:pom:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-parent:pom:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.yaml:snakeyaml:pom:2.0
CAPSULE: Resolved artifact org.yaml:snakeyaml:pom:2.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.code.gson:gson:pom:2.10.1
CAPSULE: Resolved artifact com.google.code.gson:gson:pom:2.10.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.code.gson:gson-parent:pom:2.10.1
CAPSULE: Resolved artifact com.google.code.gson:gson-parent:pom:2.10.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.errorprone:error_prone_annotations:pom:2.11.0
CAPSULE: Resolved artifact com.google.errorprone:error_prone_annotations:pom:2.11.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.errorprone:error_prone_parent:pom:2.11.0
CAPSULE: Resolved artifact com.google.errorprone:error_prone_parent:pom:2.11.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-nio:pom:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-nio:pom:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nf-httpfs:pom:23.04.1
CAPSULE: Resolved artifact io.nextflow:nf-httpfs:pom:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact dev.failsafe:failsafe:pom:3.1.0
CAPSULE: Resolved artifact dev.failsafe:failsafe:pom:3.1.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.j2objc:j2objc-annotations:pom:1.3
CAPSULE: Resolved artifact com.google.j2objc:j2objc-annotations:pom:1.3 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact javax.activation:activation:pom:1.1.1
CAPSULE: Resolved artifact javax.activation:activation:pom:1.1.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-xml:pom:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-xml:pom:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.pf4j:pf4j:pom:3.4.1
CAPSULE: Resolved artifact org.pf4j:pf4j:pom:3.4.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.pf4j:pf4j-parent:pom:3.4.1
CAPSULE: Resolved artifact org.pf4j:pf4j-parent:pom:3.4.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb:pom:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb:pom:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb-project:pom:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb-project:pom:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.airlift:airbase:pom:77
CAPSULE: Resolved artifact io.airlift:airbase:pom:77 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:failureaccess:pom:1.0.1
CAPSULE: Resolved artifact com.google.guava:failureaccess:pom:1.0.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:guava-parent:pom:26.0-android
CAPSULE: Resolved artifact com.google.guava:guava-parent:pom:26.0-android from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:9
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:9 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.googlecode.javaewah:JavaEWAH:pom:1.1.13
CAPSULE: Resolved artifact com.googlecode.javaewah:JavaEWAH:pom:1.1.13 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:5
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:5 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.checkerframework:checker-qual:pom:3.12.0
CAPSULE: Resolved artifact org.checkerframework:checker-qual:pom:3.12.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nf-commons:pom:23.04.1
CAPSULE: Resolved artifact io.nextflow:nf-commons:pom:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.pf4j:pf4j-update:pom:2.3.0
CAPSULE: Resolved artifact org.pf4j:pf4j-update:pom:2.3.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.sonatype.oss:oss-parent:pom:7
CAPSULE: Resolved artifact org.sonatype.oss:oss-parent:pom:7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Resolved artifact org.multiverse:multiverse-core:jar:0.7.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.apache.ivy:ivy:jar:2.5.1
CAPSULE: Resolved artifact org.apache.ivy:ivy:jar:2.5.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:jul-to-slf4j:jar:1.7.36
CAPSULE: Resolved artifact org.slf4j:jul-to-slf4j:jar:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-templates:jar:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-templates:jar:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:jcl-over-slf4j:jar:1.7.36
CAPSULE: Resolved artifact org.slf4j:jcl-over-slf4j:jar:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-io:commons-io:jar:2.11.0
CAPSULE: Resolved artifact commons-io:commons-io:jar:2.11.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0
CAPSULE: Resolved artifact org.codehaus.jsr166-mirror:jsr166y:jar:1.7.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-codec:commons-codec:jar:1.15
CAPSULE: Resolved artifact commons-codec:commons-codec:jar:1.15 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava
CAPSULE: Resolved artifact com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.artecat.grengine:grengine:jar:3.0.0
CAPSULE: Resolved artifact ch.artecat.grengine:grengine:jar:3.0.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.beust:jcommander:jar:1.35
CAPSULE: Resolved artifact com.beust:jcommander:jar:1.35 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nextflow:jar:23.04.1
CAPSULE: Resolving artifact jline:jline:jar:2.9
CAPSULE: Resolved artifact jline:jline:jar:2.9 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-core:jar:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-core:jar:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.github.zafarkhaja:java-semver:jar:0.9.0
CAPSULE: Resolved artifact com.github.zafarkhaja:java-semver:jar:0.9.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact javax.mail:mail:jar:1.4.7
CAPSULE: Resolved artifact javax.mail:mail:jar:1.4.7 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-json:jar:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-json:jar:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.eclipse.jgit:org.eclipse.jgit:jar:6.2.0.202206071550-r
CAPSULE: Resolved artifact org.eclipse.jgit:org.eclipse.jgit:jar:6.2.0.202206071550-r from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.code.findbugs:jsr305:jar:3.0.2
CAPSULE: Resolved artifact com.google.code.findbugs:jsr305:jar:3.0.2 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy:jar:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy:jar:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact commons-lang:commons-lang:jar:2.6
CAPSULE: Resolved artifact commons-lang:commons-lang:jar:2.6 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb-api:jar:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb-api:jar:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.gpars:gpars:jar:1.2.1
CAPSULE: Resolved artifact org.codehaus.gpars:gpars:jar:1.2.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact ch.qos.logback:logback-classic:jar:1.2.11
CAPSULE: Resolved artifact ch.qos.logback:logback-classic:jar:1.2.11 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.jsoup:jsoup:jar:1.15.4
CAPSULE: Resolved artifact org.jsoup:jsoup:jar:1.15.4 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:log4j-over-slf4j:jar:1.7.36
CAPSULE: Resolved artifact org.slf4j:log4j-over-slf4j:jar:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:guava:jar:31.1-jre
CAPSULE: Resolved artifact com.google.guava:guava:jar:31.1-jre from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.objenesis:objenesis:jar:2.1
CAPSULE: Resolved artifact org.objenesis:objenesis:jar:2.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.esotericsoftware.kryo:kryo:jar:2.24.0
CAPSULE: Resolved artifact com.esotericsoftware.kryo:kryo:jar:2.24.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.slf4j:slf4j-api:jar:1.7.36
CAPSULE: Resolved artifact org.slf4j:slf4j-api:jar:1.7.36 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.yaml:snakeyaml:jar:2.0
CAPSULE: Resolved artifact org.yaml:snakeyaml:jar:2.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.code.gson:gson:jar:2.10.1
CAPSULE: Resolved artifact com.google.code.gson:gson:jar:2.10.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.errorprone:error_prone_annotations:jar:2.11.0
CAPSULE: Resolved artifact com.google.errorprone:error_prone_annotations:jar:2.11.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-nio:jar:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-nio:jar:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nf-httpfs:jar:23.04.1
CAPSULE: Resolved artifact io.nextflow:nf-httpfs:jar:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact dev.failsafe:failsafe:jar:3.1.0
CAPSULE: Resolved artifact dev.failsafe:failsafe:jar:3.1.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.j2objc:j2objc-annotations:jar:1.3
CAPSULE: Resolved artifact com.google.j2objc:j2objc-annotations:jar:1.3 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact javax.activation:activation:jar:1.1.1
CAPSULE: Resolved artifact javax.activation:activation:jar:1.1.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.codehaus.groovy:groovy-xml:jar:3.0.16
CAPSULE: Resolved artifact org.codehaus.groovy:groovy-xml:jar:3.0.16 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.pf4j:pf4j:jar:3.4.1
CAPSULE: Resolved artifact org.pf4j:pf4j:jar:3.4.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.iq80.leveldb:leveldb:jar:0.12
CAPSULE: Resolved artifact org.iq80.leveldb:leveldb:jar:0.12 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.google.guava:failureaccess:jar:1.0.1
CAPSULE: Resolved artifact com.google.guava:failureaccess:jar:1.0.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact com.googlecode.javaewah:JavaEWAH:jar:1.1.13
CAPSULE: Resolved artifact com.googlecode.javaewah:JavaEWAH:jar:1.1.13 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.checkerframework:checker-qual:jar:3.12.0
CAPSULE: Resolved artifact org.checkerframework:checker-qual:jar:3.12.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact io.nextflow:nf-commons:jar:23.04.1
CAPSULE: Resolved artifact io.nextflow:nf-commons:jar:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Resolving artifact org.pf4j:pf4j-update:jar:2.3.0
CAPSULE: Resolved artifact org.pf4j:pf4j-update:jar:2.3.0 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Downloading artifact io.nextflow:nextflow:jar:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Downloading: https://repo1.maven.org/maven2/io/nextflow/nextflow/23.04.1/nextflow-23.04.1.jar

CAPSULE: Transfer failed: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact io.nextflow:nextflow:jar:23.04.1 from/to central (https://repo1.maven.org/maven2/): Range Not Satisfiable (416)
capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact io.nextflow:nextflow:jar:23.04.1 from/to central (https://repo1.maven.org/maven2/): Range Not Satisfiable (416)
    at capsule.org.eclipse.aether.connector.basic.ArtifactTransportListener.transferFailed(ArtifactTransportListener.java:43)
    at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:355)
    at capsule.org.eclipse.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:67)
    at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$DirectExecutor.execute(BasicRepositoryConnector.java:581)
    at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector.get(BasicRepositoryConnector.java:249)
    at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads(DefaultArtifactResolver.java:520)
    at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:421)
    at capsule.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
    at capsule.org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:373)
    at capsule.DependencyManager.resolve0(DependencyManager.java:377)
    at capsule.DependencyManager.resolveDependencies(DependencyManager.java:314)
    at MavenCapsule.resolve0(MavenCapsule.java:224)
    at Capsule.resolve(Capsule.java:3375)
    at Capsule.resolve(Capsule.java:3389)
    at Capsule.buildJavaProcess(Capsule.java:2228)
    at Capsule.buildProcess0(Capsule.java:1530)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.prelaunch0(Capsule.java:1494)
    at Capsule.prelaunch(Capsule.java:1487)
    at NextflowLoader.prelaunch(NextflowLoader.java:42)
    at Capsule.prepareForLaunch(Capsule.java:1339)
    at Capsule.launch(Capsule.java:1268)
    at Capsule.main0(Capsule.java:399)
    at Capsule.main(Capsule.java:379)
Caused by: capsule.org.apache.http.client.HttpResponseException: Range Not Satisfiable (416)
    at capsule.org.eclipse.aether.transport.http.HttpTransporter.handleStatus(HttpTransporter.java:519)
    at capsule.org.eclipse.aether.transport.http.HttpTransporter.execute(HttpTransporter.java:322)
    at capsule.org.eclipse.aether.transport.http.HttpTransporter.implGet(HttpTransporter.java:274)
    at capsule.org.eclipse.aether.spi.connector.transport.AbstractTransporter.get(AbstractTransporter.java:59)
    at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask(BasicRepositoryConnector.java:447)
    at capsule.org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:350)
    ... 24 more
CAPSULE: Downloaded artifact io.nextflow:nextflow:jar:23.04.1 from central (https://repo1.maven.org/maven2/, default, releases)
CAPSULE: Downloading artifact io.nextflow:nextflow:jar:23.04.1 from seqera (seqera, default, releases)
CAPSULE: Downloaded artifact io.nextflow:nextflow:jar:23.04.1 from seqera (seqera, default, releases)
CAPSULE: Resolved artifact io.nextflow:nextflow:jar:23.04.1 from null
CAPSULE: Cleanup
CAPSULE EXCEPTION: Error resolving dependencies. while processing attribute Allow-Snapshots: false
java.lang.RuntimeException: Error resolving dependencies.
    at capsule.DependencyManager.resolve0(DependencyManager.java:382)
    at capsule.DependencyManager.resolveDependencies(DependencyManager.java:314)
    at MavenCapsule.resolve0(MavenCapsule.java:224)
    at Capsule.resolve(Capsule.java:3375)
    at Capsule.resolve(Capsule.java:3389)
    at Capsule.buildJavaProcess(Capsule.java:2228)
    at Capsule.buildProcess0(Capsule.java:1530)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.buildProcess(Capsule.java:1521)
    at Capsule.prelaunch0(Capsule.java:1494)
    at Capsule.prelaunch(Capsule.java:1487)
    at NextflowLoader.prelaunch(NextflowLoader.java:42)
    at Capsule.prepareForLaunch(Capsule.java:1339)
    at Capsule.launch(Capsule.java:1268)
    at Capsule.main0(Capsule.java:399)
    at Capsule.main(Capsule.java:379)
Caused by: capsule.org.eclipse.aether.resolution.DependencyResolutionException: Could not transfer artifact io.nextflow:nextflow:jar:23.04.1 from/to central (https://repo1.maven.org/maven2/): Range Not Satisfiable (416)
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:391)
    at capsule.DependencyManager.resolve0(DependencyManager.java:377)
    ... 16 more
Caused by: capsule.org.eclipse.aether.resolution.ArtifactResolutionException: Could not transfer artifact io.nextflow:nextflow:jar:23.04.1 from/to central (https://repo1.maven.org/maven2/): Range Not Satisfiable (416)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:444)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:373)
    ... 17 more
Caused by: capsule.org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact io.nextflow:nextflow:jar:23.04.1 from/to central (https://repo1.maven.org/maven2/): Range Not Satisfiable (416)
    at org.eclipse.aether.connector.basic.ArtifactTransportListener.transferFailed(ArtifactTransportListener.java:43)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:355)
    at org.eclipse.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:67)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$DirectExecutor.execute(BasicRepositoryConnector.java:581)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get(BasicRepositoryConnector.java:249)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads(DefaultArtifactResolver.java:520)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:421)
    ... 19 more
Caused by: capsule.org.apache.http.client.HttpResponseException: Range Not Satisfiable (416)
    at org.eclipse.aether.transport.http.HttpTransporter.handleStatus(HttpTransporter.java:519)
    at org.eclipse.aether.transport.http.HttpTransporter.execute(HttpTransporter.java:322)
    at org.eclipse.aether.transport.http.HttpTransporter.implGet(HttpTransporter.java:274)
    at org.eclipse.aether.spi.connector.transport.AbstractTransporter.get(AbstractTransporter.java:59)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask(BasicRepositoryConnector.java:447)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run(BasicRepositoryConnector.java:350)
    ... 24 more
Unable to initialize nextflow environment

Environment

Additional context

(Add any other context about the problem here)

flass commented 1 year ago

user deleting their .nextflow folder seem to have solved the issue. Previous content of folder might have been corrupted or held artifacts from runs with previous versions of Nextflow?