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A DSL for data-driven computational pipelines
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java.lang.IllegalStateException: Capsule not extracted with nextflow-21.10.4-all #3643

Closed aubinthomas closed 1 year ago

aubinthomas commented 1 year ago

Bug report

Expected behavior and actual behavior

Hello, on HPC I'm tryong to run nextflow-22.10.6-all. Previously I was running nextflow-21.10.4-all perfectly, but now I have an error at start: java.lang.IllegalStateException: Capsule not extracted

Steps to reproduce the problem

./nextflow-22.10.6-all -Dcapsule.log=verbose

Program output

NOTE: Nextflow is not tested with Java 1.8.0_112 -- It's recommended the use of version 11 up to 18

CAPSULE: Jar: /lustre/thomasa/nextflow-22.10.6-all CAPSULE: Platform: linux CAPSULE: Initializing app ID CAPSULE: Initialized app ID: nextflow-all_22.10.6 CAPSULE: Launching app nextflow-all_22.10.6 CAPSULE: WARNING resolve [] was empty CAPSULE: Cache directory: /home/thomasa/.nextflow/capsule CAPSULE: Creating temp file/dir /home/thomasa/.nextflow/capsule/apps/nextflow-all_22.10.6/.lock CAPSULE: Locking /home/thomasa/.nextflow/capsule/apps/nextflow-all_22.10.6/.lock CAPSULE: IOException while creating app cache: Function not implemented java.io.IOException: Function not implemented at sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:90) at sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1073) at java.nio.channels.FileChannel.lock(FileChannel.java:1053) at Capsule.lockAppCache(Capsule.java:2167) at Capsule.isAppCacheUpToDate1(Capsule.java:2104) at Capsule.buildAppCacheDir0(Capsule.java:2070) at Capsule.buildAppCacheDir(Capsule.java:2056) at Capsule.getOrCreateAppDir(Capsule.java:2004) at Capsule.appDir(Capsule.java:2016) at Capsule.simpleResolve(Capsule.java:3501) at Capsule.resolve00(Capsule.java:3490) at Capsule.resolve0(Capsule.java:3402) at Capsule.resolve(Capsule.java:3375) at Capsule.resolve00(Capsule.java:3421) at Capsule.resolve0(Capsule.java:3402) 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.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) CAPSULE: Cleanup CAPSULE EXCEPTION: Capsule not extracted. while processing attribute App-Class-Path: [/lustre/thomasa/nextflow-22.10.6-all, [nf-amazon-1.11.3.jar, nextflow-22.10.6.jar, ivy-2.3.0.jar, nf-httpfs-22.10.6.jar, jaxb-api-2.3.1.jar, aws-java-sdk-s3-1.12.129.jar, aws-java-sdk-ec2-1.12.129.jar, aws-java-sdk-batch-1.12.129.jar, aws-java-sdk-iam-1.12.129.jar, aws-java-sdk-ecs-1.12.129.jar, aws-java-sdk-logs-1.12.129.jar, aws-java-sdk-codecommit-1.12.129.jar, aws-java-sdk-sts-1.12.129.jar, nf-commons-22.10.6.jar, groovy-nio-3.0.13.jar, groovy-templates-3.0.13.jar, groovy-xml-3.0.13.jar, groovy-json-3.0.13.jar, groovy-3.0.13.jar, aws-java-sdk-kms-1.12.129.jar, aws-java-sdk-core-1.12.129.jar, httpclient-4.5.13.jar, jcl-over-slf4j-1.7.36.jar, jul-to-slf4j-1.7.36.jar, log4j-over-slf4j-1.7.36.jar, logback-classic-1.2.11.jar, logback-core-1.2.11.jar, gpars-1.2.1.jar, grengine-1.3.0.jar, commons-lang-2.6.jar, pf4j-update-2.3.0.jar, commons-codec-1.15.jar, commons-io-2.11.0.jar, jcommander-1.35.jar, kryo-2.24.0.jar, leveldb-0.12.jar, org.eclipse.jgit-6.2.0.202206071550-r.jar, mail-1.4.7.jar, activation-1.1.1.jar, snakeyaml-1.30.jar, jsoup-1.14.3.jar, jline-2.9.jar, pf4j-3.4.1.jar, failsafe-3.1.0.jar, javax.activation-api-1.2.0.jar, jmespath-java-1.12.129.jar, guava-31.1-jre.jar, slf4j-api-1.7.36.jar, multiverse-core-0.7.0.jar, jsr166y-1.7.0.jar, objenesis-2.1.jar, leveldb-api-0.12.jar, JavaEWAH-1.1.13.jar, java-semver-0.9.0.jar, ion-java-1.0.2.jar, jackson-annotations-2.12.3.jar, jackson-core-2.12.3.jar, jackson-dataformat-cbor-2.12.3.jar, jackson-databind-2.12.3.jar, joda-time-2.8.1.jar, failureaccess-1.0.1.jar, listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar, jsr305-3.0.2.jar, checker-qual-3.12.0.jar, error_prone_annotations-2.11.0.jar, j2objc-annotations-1.3.jar, gson-2.2.4.jar, httpcore-4.4.13.jar, nf-google-1.4.5.jar, google-cloud-batch-0.5.0.jar, google-cloud-logging-3.8.0.jar, google-cloud-nio-0.124.8.jar, google-cloud-storage-2.9.3.jar, google-cloud-core-2.8.0.jar, gax-2.19.4.jar, google-auth-library-oauth2-http-1.12.1.jar, google-api-services-lifesciences-v2beta-rev20210527-1.31.5.jar, google-api-services-storage-v1-rev20220705-1.32.1.jar, google-api-client-1.35.1.jar, google-oauth-client-1.34.1.jar, google-http-client-gson-1.42.2.jar, google-http-client-apache-v2-1.42.0.jar, google-http-client-1.42.2.jar, opencensus-contrib-http-util-0.31.1.jar, api-common-2.2.1.jar, protobuf-java-util-3.21.8.jar, proto-google-cloud-batch-v1alpha-0.5.0.jar, proto-google-cloud-batch-v1-0.5.0.jar, proto-google-cloud-logging-v2-0.97.0.jar, auto-value-annotations-1.10.jar, google-auth-library-credentials-1.12.1.jar, google-http-client-jackson2-1.42.0.jar, grpc-api-1.50.1.jar, opencensus-api-0.31.1.jar, grpc-context-1.50.1.jar, error_prone_annotations-2.16.jar, grpc-stub-1.50.1.jar, grpc-protobuf-1.50.1.jar, grpc-protobuf-lite-1.50.1.jar, javax.annotation-api-1.3.2.jar, proto-google-iam-v1-1.6.4.jar, proto-google-common-protos-2.9.6.jar, protobuf-java-3.21.8.jar, grpc-google-iam-v1-1.6.4.jar, checker-qual-3.26.0.jar, gax-grpc-2.19.4.jar, grpc-alts-1.50.1.jar, grpc-grpclb-1.50.1.jar, conscrypt-openjdk-uber-2.5.2.jar, grpc-auth-1.50.1.jar, grpc-netty-shaded-1.50.1.jar, perfmark-api-0.25.0.jar, grpc-core-1.50.1.jar, annotations-4.1.1.4.jar, animal-sniffer-annotations-1.22.jar, grpc-googleapis-1.50.1.jar, grpc-xds-1.50.1.jar, opencensus-proto-0.2.0.jar, grpc-services-1.50.1.jar, re2j-1.6.jar, gax-httpjson-0.104.4.jar, gson-2.9.1.jar, httpcore-4.4.15.jar, threetenbp-1.6.3.jar, bcpkix-jdk15on-1.67.jar, bcprov-jdk15on-1.67.jar, google-cloud-core-grpc-2.6.0.jar, javax.inject-1.jar, google-cloud-core-http-2.8.0.jar, google-http-client-appengine-1.42.0.jar, jackson-core-2.13.3.jar, nf-tower-1.5.6.jar, jackson-databind-2.12.5.jar, jackson-core-2.12.5.jar, jackson-annotations-2.12.5.jar, jackson-dataformat-yaml-2.12.5.jar, groovy-yaml-3.0.13.jar]] java.lang.IllegalStateException: Capsule not extracted. at Capsule.appDir(Capsule.java:2025) at Capsule.simpleResolve(Capsule.java:3501) at Capsule.resolve00(Capsule.java:3490) at Capsule.resolve0(Capsule.java:3402) at Capsule.resolve(Capsule.java:3375) at Capsule.resolve00(Capsule.java:3421) at Capsule.resolve0(Capsule.java:3402) 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.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) Unable to initialize nextflow environment

Environment

Additional context

bentsherman commented 1 year ago

I think Java 8 support was dropped somewhere between those two versions. You can use Java 11 or newer.

aubinthomas commented 1 year ago

Yes I tested with Java 11.0.15 and it works now Thank you