pipeline crash when building references

[ReposGB]

Description of the bug

The reference building step fails before writing all reference file and seems to crash when downloading https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
Please find the content of .nextflow.log attached to this issue

Command used and terminal output

$ nextflow run nf-core/rnafusion -profile singularity  --outdir References   --build_references

Relevant files

janv.-17 16:05:54.633 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnafusion -profile docker --outdir References --build_references
janv.-17 16:05:54.676 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.2
janv.-17 16:05:54.726 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/bidaut/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
janv.-17 16:05:54.751 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
janv.-17 16:05:54.752 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
janv.-17 16:05:54.754 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
janv.-17 16:05:54.763 [main] INFO org.pf4j.AbstractPluginManager - No plugins
janv.-17 16:05:54.773 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /Users/bidaut/.nextflow/scm
janv.-17 16:05:55.274 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/rnafusion.git
janv.-17 16:05:55.291 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
janv.-17 16:05:55.297 [main] DEBUG nextflow.scm.AssetManager - Git config: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/rnafusion.git
janv.-17 16:06:03.106 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/nextflow.config
janv.-17 16:06:03.107 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/nextflow.config
janv.-17 16:06:03.113 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/bidaut/.nextflow/secrets/store.json
janv.-17 16:06:03.116 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@33f2cfda] - activable => nextflow.secret.LocalSecretsProvider@33f2cfda
janv.-17 16:06:03.123 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker
janv.-17 16:06:03.878 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, ceci_nic5, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, unity, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, debug, genouest, cbe, unsw_katana, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
janv.-17 16:06:03.909 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
janv.-17 16:06:03.910 [main] DEBUG nextflow.cli.CmdRun - Launching https://github.com/nf-core/rnafusion [extravagant_tuckerman] DSL2 - revision: f27e732 [master]
janv.-17 16:06:03.911 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[[email protected]]
janv.-17 16:06:03.911 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
janv.-17 16:06:03.911 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected]]
janv.-17 16:06:03.911 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3
janv.-17 16:06:03.920 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
janv.-17 16:06:03.920 [main] INFO org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
janv.-17 16:06:03.944 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
janv.-17 16:06:03.987 [main] DEBUG nextflow.Session - Session UUID: 638fd134-f823-403c-a18b-991a448b555e
janv.-17 16:06:03.988 [main] DEBUG nextflow.Session - Run name: extravagant_tuckerman
janv.-17 16:06:03.988 [main] DEBUG nextflow.Session - Executor pool size: 10
janv.-17 16:06:03.999 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
janv.-17 16:06:04.002 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
janv.-17 16:06:04.164 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.2 build 5932
Created: 27-11-2024 21:23 UTC (22:23 CEST)
System: Mac OS X 15.2
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 21+35
Encoding: UTF-8 (UTF-8)
Process: [email protected] [192.168.64.1]
CPUs: 10 - Mem: 32 GB (4.9 GB) - Swap: 4 GB (852.7 MB)
janv.-17 16:06:04.175 [main] DEBUG nextflow.Session - Work-dir: /Users/bidaut/data/test-nfcore/RNA-seq-fusion/work [Mac OS X]
janv.-17 16:06:04.203 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
janv.-17 16:06:04.209 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
janv.-17 16:06:04.239 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
janv.-17 16:06:04.246 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 11; maxThreads: 1000
janv.-17 16:06:04.283 [main] DEBUG nextflow.Session - Session start
janv.-17 16:06:04.284 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/bidaut/data/test-nfcore/RNA-seq-fusion/References/pipeline_info/execution_trace_2025-01-17_16-06-03.txt
janv.-17 16:06:04.367 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
janv.-17 16:06:04.513 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation
janv.-17 16:06:04.533 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation
janv.-17 16:06:04.533 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation
janv.-17 16:06:04.544 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
janv.-17 16:06:04.544 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation
janv.-17 16:06:05.442 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation
janv.-17 16:06:05.442 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation
janv.-17 16:06:05.443 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation
janv.-17 16:06:05.444 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
janv.-17 16:06:05.445 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation
janv.-17 16:06:05.497 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
janv.-17 16:06:06.780 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json
janv.-17 16:06:06.781 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
janv.-17 16:06:06.791 [main] INFO nextflow.Nextflow -

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�[1mInput/output options�[0m
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�[1mAlignment compression options�[0m
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�[0;34mgtf : �[0;32mReferences/references/ensembl/Homo_sapiens.GRCh38.102.gtf�[0m
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!! Only displaying parameters that differ from the pipeline defaults !!
-�[2m----------------------------------------------------�[0m-
If you use nf-core/rnafusion for your analysis please cite:

• The pipeline

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md
  -�[2m----------------------------------------------------�[0m-
  janv.-17 16:06:06.792 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
  janv.-17 16:06:07.063 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/bidaut/.nextflow/assets/nf-core/rnafusion/assets/schema_input.json'
  janv.-17 16:06:07.545 [main] DEBUG n.file.http.XFileSystemProvider - Remote redirect location: https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/reads_2.fq.gz
  janv.-17 16:06:08.112 [main] DEBUG n.file.http.XFileSystemProvider - Remote redirect location: https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/reads_1.fq.gz
  janv.-17 16:06:08.390 [main] DEBUG n.file.http.XFileSystemProvider - Remote redirect location: https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/reads_2.fq.gz
  janv.-17 16:06:08.536 [main] DEBUG n.file.http.XFileSystemProvider - Remote redirect location: https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/reads_1.fq.gz
  janv.-17 16:06:08.630 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/bidaut/.nextflow/assets/nf-core/rnafusion/assets/schema_input.json'
  janv.-17 16:06:08.630 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
  janv.-17 16:06:08.679 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD
  janv.-17 16:06:08.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:ENSEMBL_DOWNLOAD matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD
  janv.-17 16:06:08.687 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.687 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.691 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
  janv.-17 16:06:08.695 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=10; memory=32 GB; capacity=10; pollInterval=100ms; dumpInterval=5m
  janv.-17 16:06:08.697 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
  janv.-17 16:06:08.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD
  janv.-17 16:06:08.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:HGNC_DOWNLOAD matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD
  janv.-17 16:06:08.725 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.725 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX
  janv.-17 16:06:08.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SAMTOOLS_FAIDX matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX
  janv.-17 16:06:08.734 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.734 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY
  janv.-17 16:06:08.739 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.739 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.743 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS
  janv.-17 16:06:08.745 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.745 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.748 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED
  janv.-17 16:06:08.750 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.750 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST
  janv.-17 16:06:08.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GATK4_BEDTOINTERVALLIST matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST
  janv.-17 16:06:08.755 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.755 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.759 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT
  janv.-17 16:06:08.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GTF_TO_REFFLAT matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT
  janv.-17 16:06:08.761 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
  janv.-17 16:06:08.761 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
  janv.-17 16:06:08.766 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
  janv.-17 16:06:08.766 [main] DEBUG nextflow.Session - Igniting dataflow network (25)
  janv.-17 16:06:08.771 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST
  janv.-17 16:06:08.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT
  janv.-17 16:06:08.773 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_4e9882194484d3f6: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../modules/local/starfusion/build/main.nf
  Script_7209aa115a74352a: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../modules/local/fusionreport/download/main.nf
  Script_a3098d9767e43c91: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/../../modules/local/vcf_collect/main.nf
  Script_a6a0e0b1f39503bd: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/../../modules/local/starfusion/detect/main.nf
  Script_ade8fcbf89393501: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/../../modules/nf-core/arriba/main.nf
  Script_8401e8f29e05aaca: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/trim_workflow.nf
  Script_fe0e47917c44c873: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/qc_workflow.nf
  Script_28aa8d2d720e28a0: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/rnafusion.nf
  Script_c36e10e8147aab51: /Users/bidaut/.nextflow/assets/nf-core/rnafusion/./workflows/../subworkflows/local/../../modules/local/picard/collectrnaseqmetrics/main.nf
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  janv.-17 16:06:08.773 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
  janv.-17 16:06:08.773 [main] DEBUG nextflow.Session - Session await
  janv.-17 16:06:08.850 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
  janv.-17 16:06:08.851 [Task submitter] INFO nextflow.Session - [51/65aabb] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl)
  janv.-17 16:06:08.882 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
  janv.-17 16:06:08.882 [Task submitter] INFO nextflow.Session - [da/84aac2] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc)
  janv.-17 16:06:21.776 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc); status: COMPLETED; exit: 8; error: -; workDir: /Users/bidaut/data/test-nfcore/RNA-seq-fusion/work/da/84aac20274f174d6513859c9bfe8e7]
  janv.-17 16:06:21.776 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
  janv.-17 16:06:21.782 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc); work-dir=/Users/bidaut/data/test-nfcore/RNA-seq-fusion/work/da/84aac20274f174d6513859c9bfe8e7
  error [nextflow.exception.ProcessFailedException]: Process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) terminated with an error exit status (8)
  janv.-17 16:06:21.794 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc)'

Caused by:
Process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) terminated with an error exit status (8)

Command executed:

wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD":
wget: $(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml)
END_VERSIONS

Command exit status:
8

Command output:
(empty)

Command error:
Unable to find image 'quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5' locally
1.18--h5bf99c6_5: Pulling from biocontainers/gnu-wget
cefc4d495539: Already exists
4ca545ee6d5d: Pulling fs layer
a29258f9db8d: Pulling fs layer
a29258f9db8d: Download complete
4ca545ee6d5d: Verifying Checksum
4ca545ee6d5d: Download complete
4ca545ee6d5d: Pull complete
a29258f9db8d: Pull complete
Digest: sha256:176ab278e80632d540a60cffeaf4cd18edafdedb0eedafbb3929588ea289d463
Status: Downloaded newer image for quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
--2025-01-17 15:06:21-- https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
Resolving ftp.ebi.ac.uk... 193.62.193.165
Connecting to ftp.ebi.ac.uk|193.62.193.165|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2025-01-17 15:06:21 ERROR 404: Not Found.

Work dir:
/Users/bidaut/data/test-nfcore/RNA-seq-fusion/work/da/84aac20274f174d6513859c9bfe8e7

Container:
quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
janv.-17 16:06:21.801 [TaskFinalizer-1] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
janv.-17 16:06:21.811 [main] DEBUG nextflow.Session - Session await > all processes finished
janv.-17 16:09:32.714 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl); status: COMPLETED; exit: 0; error: -; workDir: /Users/bidaut/data/test-nfcore/RNA-seq-fusion/work/51/65aabb384a6e27494f95c8b7143c22]
janv.-17 16:09:32.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
janv.-17 16:09:32.716 [main] DEBUG nextflow.Session - Session await > all barriers passed
janv.-17 16:09:32.735 [TaskFinalizer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=30; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
janv.-17 16:09:32.741 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
janv.-17 16:09:35.171 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
janv.-17 16:09:35.185 [main] INFO nextflow.Nextflow - -�[0;35m[nf-core/rnafusion]�[0;31m Pipeline completed with errors�[0m-
janv.-17 16:09:35.194 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=6m 22s; failedDuration=25.7s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=4; peakMemory=24 GB; ]
janv.-17 16:09:35.194 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
janv.-17 16:09:35.195 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
janv.-17 16:09:36.136 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
janv.-17 16:09:36.388 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
janv.-17 16:09:36.450 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
janv.-17 16:09:36.450 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
janv.-17 16:09:36.451 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
janv.-17 16:09:36.451 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

Netxtflow version 24.10.2.5932
Hardware: Desktop
Executor: local
Container engine: docker
OS: MacOS
Version of rnafusion: v3.0.2-gf27e732

[gianfilippo]

same issue here

Netxtflow version 24.04.4
Version of rnafusion: v3.0.2

[atrigila]

Duplicate of: #506