Unable to run 25.10 offline on RHEL 9 - Conversion = '4' #6610
Description
Bug report
Expected behavior and actual behavior
I've copied $HOME/.nextflow and the nextflow binary from a Mac computer with internet access to a RHEL 9 cluster without access. I can't run nextflow on the cluster and get the error below.
Steps to reproduce the problem
export NXF_OFFLINE=true
~/bin/nextflow run <PIPELINE_PATH>
Program output
[paalmbj@tregul nf-core-sarek_3.6.1]$ cat .nextflow.log
Nov-25 11:31:39.132 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 3_6_1/ -c example/custom.conf -c /data/runScratch.boston/analysis/pipelines/nsc_slurm.conf -profile test --outdir test
Nov-25 11:31:39.230 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.0
Nov-25 11:31:40.395 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /data/nbcs/tools/nf-core-sarek_3.6.1/3_6_1/nextflow.config
Nov-25 11:31:40.400 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /data/nbcs/tools/nf-core-sarek_3.6.1/example/custom.conf
Nov-25 11:31:40.400 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /data/runScratch.boston/analysis/pipelines/nsc_slurm.conf
Nov-25 11:31:40.401 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/nbcs/tools/nf-core-sarek_3.6.1/3_6_1/nextflow.config
Nov-25 11:31:40.402 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/nbcs/tools/nf-core-sarek_3.6.1/example/custom.conf
Nov-25 11:31:40.402 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/runScratch.boston/analysis/pipelines/nsc_slurm.conf
Nov-25 11:31:40.418 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test`
Nov-25 11:31:43.166 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test`
Nov-25 11:31:43.189 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test`
Nov-25 11:31:43.217 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [apptainer, skip_markduplicates, tools, wave, test_full_germline_aws, docker, test_azure, test_full_azure, spark, charliecloud, conda, targeted, trimming, singularity, test_full_germline, sentieon_dedup_bam, tools_tumoronly, save_bam_mapped, arm, podman, sentieon_dedup_cram, annotation, test_full_aws, split_fastq, debug, test, tools_somatic, variantcalling_channels, recalibrate_cram, no_intervals, tools_germline, gpu, mutect, recalibrate_bam, pair, gitpod, shifter, tools_somatic_ascat, mamba, test_aws, test_full_germline_ncbench_agilent, test_full, test_full_germline_azure, skip_bqsr]
Nov-25 11:31:43.309 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/paalmbj/.nextflow/plugins; core-plugins: nf-amazon@3.4.1,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.3,nf-k8s@1.2.2,nf-tower@1.17.1,nf-wave@1.16.1
Nov-25 11:31:43.321 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Nov-25 11:31:43.323 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Nov-25 11:31:43.326 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Nov-25 11:31:43.340 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config
Nov-25 11:31:43.487 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Nov-25 11:31:43.488 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.4.2, nf-prov@1.2.2, nf-fgbio@1.0.0]
Nov-25 11:31:43.489 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Nov-25 11:31:43.489 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.4.2, nf-prov@1.2.2, nf-fgbio@1.0.0]
Nov-25 11:31:43.912 [main] DEBUG io.seqera.http.HxClient - HTTP request retry attempt 1: null
Nov-25 11:31:44.488 [main] DEBUG io.seqera.http.HxClient - HTTP request retry attempt 2: null
Nov-25 11:31:46.170 [main] DEBUG io.seqera.http.HxClient - HTTP request retry attempt 3: null
Nov-25 11:31:49.037 [main] DEBUG io.seqera.http.HxClient - HTTP request retry attempt 4: null
Nov-25 11:31:49.039 [main] DEBUG io.seqera.http.HxClient - HTTP request retry attempt 5: null
Nov-25 11:31:49.040 [main] ERROR nextflow.cli.Launcher - Conversion = '4'
java.util.UnknownFormatConversionException: Conversion = '4'
at java.base/java.util.Formatter.parse(Formatter.java:2750)
at java.base/java.util.Formatter.format(Formatter.java:2671)
at java.base/java.util.Formatter.format(Formatter.java:2625)
at java.base/java.lang.String.format(String.java:4145)
at org.pf4j.util.StringUtils.format(StringUtils.java:39)
at org.pf4j.PluginRuntimeException.<init>(PluginRuntimeException.java:41)
at nextflow.plugin.HttpPluginRepository.fetchMetadata0(HttpPluginRepository.groovy:140)
at nextflow.plugin.HttpPluginRepository.fetchMetadata(HttpPluginRepository.groovy:123)
at nextflow.plugin.HttpPluginRepository.prefetch(HttpPluginRepository.groovy:70)
at nextflow.plugin.PluginUpdater.prefetchMetadata(PluginUpdater.groovy:154)
at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:398)
at nextflow.plugin.PluginsFacade.load(PluginsFacade.groovy:291)
at nextflow.plugin.Plugins.load(Plugins.groovy:50)
at nextflow.cli.CmdRun.run(CmdRun.groovy:363)
at nextflow.cli.Launcher.run(Launcher.groovy:515)
at nextflow.cli.Launcher.main(Launcher.groovy:675)
Environment
- Nextflow version: 25.10
- Java version: 17
- Operating system: RHEL 9
-
- Bash version: 5.1.8