Jul-27 14:54:58.752 [main] DEBUG nextflow.cli.Launcher - $> nextflow run . -profile test,docker --outdir results Jul-27 14:54:58.933 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 26.04.6 Jul-27 14:54:59.023 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@3.9.2,nf-azure@1.22.6,nf-cloudcache@0.6.0,nf-codecommit@0.5.3,nf-console@1.3.0,nf-google@1.27.3,nf-k8s@1.5.4,nf-seqera@0.21.1,nf-tower@1.28.2,nf-wave@1.21.0 Jul-27 14:54:59.108 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jul-27 14:54:59.111 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jul-27 14:54:59.123 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.14.1 in 'deployment' mode Jul-27 14:54:59.178 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config Jul-27 14:54:59.505 [main] DEBUG nextflow.plugin.PluginUpdater - Using plugin repository: HttpPluginRepository [registry]; url=https://registry.nextflow.io/api Jul-27 14:54:59.512 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jul-27 14:54:59.592 [main] DEBUG nextflow.scm.AssetManager - Selecting multi-revision strategy Jul-27 14:54:59.626 [main] DEBUG nextflow.config.ConfigParserFactory - Using config parser v2 Jul-27 14:55:01.139 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /workspaces/reportho/nextflow.config Jul-27 14:55:01.145 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workspaces/reportho/nextflow.config Jul-27 14:55:01.150 [main] DEBUG nextflow.config.ConfigParserFactory - Using config parser v2 Jul-27 14:55:01.174 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` Jul-27 14:55:02.878 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [debug, conda, mamba, docker, arm64, emulate_amd64, singularity, podman, shifter, charliecloud, apptainer, wave, gpu, test, test_fasta, test_full, test_offline, array, abims, adcra, alice, alliance_canada, apollo, arcc, aws_tower, awsbatch, azurebatch, bi, bigpurple, bih, binac2, biohpc_gen, biowulf, bluebear, cambridge, cannon, cbe, ccga_dx, ccga_cau, ceci_dragon2, ceci_nic5, cedars, ceres, cfc, cfc_dev, cheaha, computerome, create, crg, crick, cropdiversityhpc, crukmi, csiro_petrichor, czbiohub_aws, daisybio, denbi_qbic, dkfz, dirac, ebc, eddie, ebi_codon, ebi_codon_slurm, einstein, embl_hd, engaging, ethz_euler, eva, eva_grace, fgcz, fred_hutch, fsu_draco, fub_curta, genotoul, genouest, giga, gis, googlebatch, hasta, hazel, hki_genie, hypatia, humantechnopole, icr_alma, ifb_core, imb, imperial, incliva, ipop_up, iris, janelia, jax, jex, unsw_katana, ku_sund_danhead, kaust, kelvin2, ki_luria, leicester, lovelace, lrz_cm4, lugh, m3c, maestro, mahuika, mana, marjorie, marvin, mccleary, mcw_rcc, medair, mjolnir_globe, mpcdf, mpcdf_viper, mssm, munin, nci_gadi, nu_genomics, nygc, nyu_hpc, oist, pasteur, pawsey_setonix, pdc_kth, phoenix, psmn, purdue_bell, purdue_gautschi, purdue_negishi, qmul_apocrita, rki, rosalind, rosalind_uge, roslin, sage, sahmri, sanger, ilifu, seadragon, seattlechildrens, seawulf, seg_globe, self_hosted_runner, shu_bmrc, stjude, tes, tigem, tubingen_apg, tufts, tuos_stanage, ucd_sonic, ucl_cscluster, ucl_myriad, uct_hpc, uge, unc_lccc, unc_longleaf, unibe_ibu, unity, uod_hpc, uppmax, utd_juno, uw_hyak_pedslabs, uzh, uzl_omics, vai, vsc_calcua, vsc_kul_uhasselt, vsc_ugent, wehi, xanadu, york_viking] Jul-27 14:55:02.949 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.5.1] Jul-27 14:55:02.950 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jul-27 14:55:02.951 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.5.1] Jul-27 14:55:02.954 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.5.1 Jul-27 14:55:02.965 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.5.1' resolved Jul-27 14:55:02.965 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.5.1' Jul-27 14:55:02.971 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.5.1 Jul-27 14:55:02.978 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json Jul-27 14:55:02.982 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@23121d14] - activable => nextflow.secret.LocalSecretsProvider@23121d14 Jul-27 14:55:02.999 [main] DEBUG nextflow.cli.CmdRun - Launching `./main.nf` [voluminous_allen] - revision: 9d988b1e86 Jul-27 14:55:03.003 [main] ERROR org.pf4j.AbstractExtensionFinder - Different class loaders: 'org.pf4j.PluginClassLoader@b06d46d' (E) and 'jdk.internal.loader.ClassLoaders$AppClassLoader@c387f44' (EP) Jul-27 14:55:03.034 [main] WARN nextflow.config.ConfigValidator - Unrecognized config option 'validation.defaultIgnoreParams' Jul-27 14:55:03.034 [main] WARN nextflow.config.ConfigValidator - Unrecognized config option 'validation.monochromeLogs' Jul-27 14:55:03.088 [main] DEBUG nextflow.Session - Session UUID: 1ec92b53-3d10-4ce2-b3fd-c8e70a5d3a88 Jul-27 14:55:03.088 [main] DEBUG nextflow.Session - Run name: voluminous_allen Jul-27 14:55:03.089 [main] DEBUG nextflow.Session - Executor pool size: 4 Jul-27 14:55:03.118 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Jul-27 14:55:03.126 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Jul-27 14:55:03.152 [main] DEBUG nextflow.cli.CmdRun - Version: 26.04.6 build 12646 Created: 09-07-2026 18:49 UTC System: Linux 6.8.0-1052-azure Runtime: Groovy 4.0.31 on OpenJDK 64-Bit Server VM 21.0.6+9-b895.97 Encoding: UTF-8 (UTF-8) Process: 7475@codespaces-a735a0 [127.0.0.1] CPUs: 4 - Mem: 15.6 GB (264.3 MB) - Swap: 0 (0) Jul-27 14:55:03.205 [main] DEBUG nextflow.Session - Work-dir: /workspaces/reportho/work [ext2/ext3] Jul-27 14:55:03.261 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jul-27 14:55:03.276 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Jul-27 14:55:03.278 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory Jul-27 14:55:03.315 [main] DEBUG nextflow.Session - Observer factory (v2): ValidationObserverFactory Jul-27 14:55:03.357 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jul-27 14:55:03.370 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000 Jul-27 14:55:03.442 [main] DEBUG nextflow.Session - Session start Jul-27 14:55:03.451 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/pipeline_info/execution_trace_2026-07-27_14-55-01.txt Jul-27 14:55:03.455 [main] DEBUG nextflow.script.ScriptLoaderFactory - Using script parser v2 Jul-27 14:55:07.431 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jul-27 14:55:07.542 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jul-27 14:55:07.551 [main] DEBUG n.validation.config.ValidationConfig - Set `validation.monochromeLogs` to false Jul-27 14:55:07.554 [main] DEBUG n.validation.config.ValidationConfig - Added the following parameters to the ignored parameters: [genomes] Jul-27 14:55:07.585 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Jul-27 14:55:07.586 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Jul-27 14:55:07.587 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Jul-27 14:55:07.590 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jul-27 14:55:07.591 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jul-27 14:55:07.592 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Jul-27 14:55:07.976 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jul-27 14:55:07.977 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jul-27 14:55:07.978 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Jul-27 14:55:08.120 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/reportho 1.2.0dev ------------------------------------------------------ Jul-27 14:55:08.162 [main] INFO nextflow.Nextflow - Input/output options input : /nf-core/test-datasets/reportho/testdata/samplesheet/samplesheet.csv outdir : results Ortholog search options skip_eggnog : true Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function Generic options max_multiqc_email_size : 25 MB trace_report_suffix : 2026-07-27_14-55-01 Core Nextflow options runName : voluminous_allen containerEngine : docker launchDir : /workspaces/reportho workDir : /workspaces/reportho/work projectDir : /workspaces/reportho userName : root profile : test,docker configFiles : /workspaces/reportho/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ Jul-27 14:55:08.163 [main] INFO nextflow.Nextflow - * The pipeline https://doi.org/10.5281/zenodo.11574565 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/reportho/blob/main/CITATIONS.md Jul-27 14:55:08.171 [main] DEBUG n.v.parameters.ParameterValidator - Starting parameters validation Jul-27 14:55:08.233 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: _nf_script_e09e37251d3c38e0: /workspaces/reportho/modules/nf-core/csvtk/join/main.nf _nf_script_bc1cd314db9f34be: /workspaces/reportho/modules/local/identify_seq_online/main.nf _nf_script_38157c4de16214cd: /workspaces/reportho/modules/nf-core/multiqc/main.nf _nf_script_68ed5ad688ea68a4: /workspaces/reportho/modules/local/fetch_oma_sequences/main.nf _nf_script_244eefe28709dc87: /workspaces/reportho/subworkflows/local/report/main.nf _nf_script_c36843ad79cfbf10: /workspaces/reportho/modules/local/make_score_table/main.nf _nf_script_9fffb764e0aa0e3c: /workspaces/reportho/subworkflows/local/get_orthologs/main.nf _nf_script_40a805da74aa4992: /workspaces/reportho/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf _nf_script_8a7b9c88afc00aa7: /workspaces/reportho/subworkflows/nf-core/utils_nfschema_plugin/main.nf _nf_script_8418975232238408: /workspaces/reportho/modules/local/dump_params/main.nf _nf_script_8286af3d40027adf: /workspaces/reportho/modules/nf-core/csvtk/concat/main.nf _nf_script_d1be2dc5c53c2694: /workspaces/reportho/modules/local/write_seqinfo/main.nf _nf_script_0ff38d40bc43bdb2: /workspaces/reportho/modules/local/fetch_refseq_sequences/main.nf _nf_script_775682920dc6a7e6: /workspaces/reportho/modules/local/fetch_eggnog_group_local/main.nf _nf_script_afcde862a5e6516b: /workspaces/reportho/modules/local/stats2csv/main.nf _nf_script_b8b60e23213a74c5: /workspaces/reportho/modules/nf-core/diamond/cluster/main.nf _nf_script_b879f8513c290bbb: /workspaces/reportho/modules/local/plot_orthologs/main.nf _nf_script_368d63ba82f9fbb9: /workspaces/reportho/modules/local/fetch_ensembl_idmap/main.nf _nf_script_106dfab9b856ad4f: /workspaces/reportho/modules/local/make_stats/main.nf _nf_script_3f39a9bec679715e: /workspaces/reportho/modules/local/make_report/main.nf _nf_script_851e1884e6d1941a: /workspaces/reportho/subworkflows/local/generate_msa_samplesheet/main.nf _nf_script_fd2657f2fdb1beeb: /workspaces/reportho/workflows/reportho.nf _nf_script_759a7c996e1e534c: /workspaces/reportho/modules/local/filter_fasta/main.nf _nf_script_ca10e4f90f098128: /workspaces/reportho/subworkflows/local/score_orthologs/main.nf _nf_script_82fc936b060c618f: /workspaces/reportho/modules/local/fetch_oma_group_local/main.nf _nf_script_6aecf58ec13666e5: /workspaces/reportho/modules/local/split_id_format/main.nf _nf_script_33f1db20499294b7: /workspaces/reportho/subworkflows/nf-core/utils_nfcore_pipeline/main.nf _nf_script_23a202cf1bb257e4: /workspaces/reportho/modules/local/fetch_ensembl_sequences/main.nf _nf_script_f5c9aaa65cacb639: /workspaces/reportho/subworkflows/nf-core/utils_nextflow_pipeline/main.nf _nf_script_7aeaa2e07d94ff30: /workspaces/reportho/modules/local/fetch_panther_group_online/main.nf _nf_script_b1e5850648257084: /workspaces/reportho/modules/local/make_hits_table/main.nf _nf_script_e5be9185c84d8153: /workspaces/reportho/modules/nf-core/gawk/main.nf _nf_script_c839f6fc5cacae2a: /workspaces/reportho/modules/local/filter_hits/main.nf _nf_script_bbd0410ac78825cf: /workspaces/reportho/subworkflows/local/merge_ids/main.nf _nf_script_b303f9fa6f514223: /workspaces/reportho/modules/local/split_taxids/main.nf _nf_script_6b0994a35c8be7f8: /workspaces/reportho/modules/local/fetch_inspector_group_online/main.nf _nf_script_813d773879086ca4: /workspaces/reportho/subworkflows/local/get_sequences/main.nf _nf_script_6832cbd7596c3ed1: /workspaces/reportho/modules/local/make_merge_table/main.nf _nf_script_f9bf037e6ac6ae24: /workspaces/reportho/modules/local/fetch_oma_group_online/main.nf _nf_script_3af4972ffc7f1571: /workspaces/reportho/modules/local/fetch_uniprot_sequences/main.nf Main: /workspaces/reportho/main.nf _nf_script_edfa1ab7a0dfb97b: /workspaces/reportho/modules/nf-core/find/concatenate/main.nf _nf_script_2e571b43ee628c8c: /workspaces/reportho/modules/local/fetch_panther_group_local/main.nf Jul-27 14:55:08.235 [main] DEBUG nextflow.Session - Session aborted -- Cause: java.lang.StackOverflowError Jul-27 14:55:08.246 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] Jul-27 14:55:08.276 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jul-27 14:55:08.953 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jul-27 14:55:09.082 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jul-27 14:55:09.107 [main] ERROR nextflow.cli.Launcher - @unknown java.lang.StackOverflowError at groovy.lang.MetaClassImpl.getMethodWithCaching(MetaClassImpl.java:1447) at groovy.lang.MetaClassImpl.getMetaMethod(MetaClassImpl.java:1353) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1205) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1096) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1009) at groovy.runtime.metaclass.NumberDelegatingMetaClass.invokeMethod(NumberDelegatingMetaClass.java:59) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.file.http.XPath$1.(XPath.groovy:244) at nextflow.file.http.XPath.iterator(XPath.groovy:242) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:206) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:168) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:416) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:206) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:168) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:416) [and so forth until crash]