Hi all, I am running NFcore mag for my pacbio sequences and all jobs are failing at this step Caused by: Process

NFCORE_MAG:mag:DOMAIN_CLASSIFICATION:TIARA:TIARA_CLASSIFY (group-0)

terminated with an error exit status (1) Command executed: domain_classification.R --classification_file METAMDBG-group-0.tiara.txt --contig_to_bin METAMDBG-MaxBin2-group-0.tsv --join_prokaryotes --assembler METAMDBG --output_prefix METAMDBG-MaxBin2-unbins-group-0 mkdir eukarya mkdir prokarya mkdir bacteria mkdir archaea mkdir organelle mkdir unknown while IFS=$" " read bin domain; do find -L . -name "${bin}*" -exec mv {} ${domain}/ \; done < bin2classification.tsv cat <<-END_VERSIONS > versions.yml r-base: $(R --version | head -n 1 | grep -Eo '[0-9.]+ ') r-tidyverse: $(cat tidyverse_version.txt) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.4.0 ✔ purrr 1.0.1 ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.5.0 ✔ readr 2.1.3 ✔ forcats 0.5.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Warning message: Failed to locate timezone database Error: Invalid assembler provided. Execution halted

markdownhelp

Using some code formatting helps with readability and finding the issue. Here are some tips about how to format code snippets nicely in Slack: http://tiny.cc/mdcodeblocks http://tiny.cc/slacksnippets

moreinfo

To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding

.nextflow.log

file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!

this is the full log

That's not the log file @Reshma Silvester, please find the

.nextflow.log

file (will be hidden by default, so run

ls -lha

to find it, and should be wherever you executed teh

run

command

Feb-24 010340.170 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/mag -r 5.1.0 -profile apptainer -c /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/scw_MAG_wastewaterKB.conf -params-file /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/nf-params_wastewaterKB.json -work-dir /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/KBwork --skip_concoct --skip_gtdbtk --checkm_download_url 'https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz' -resume -with-report /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/logs/report.html -with-timeline /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/logs/timeline.html -with-trace /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/logs/trace.txt Feb-24 010340.221 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.3 Feb-24 010340.314 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/.nextflow/plugins; core-plugins: nf-amazon@3.4.3,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.4,nf-k8s@1.2.2,nf-tower@1.17.4,nf-wave@1.16.1 Feb-24 010340.341 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Feb-24 010340.342 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Feb-24 010340.344 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Feb-24 010340.408 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config Feb-24 010340.954 [main] INFO org.pf4j.AbstractPluginManager - No plugins Feb-24 010340.976 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/.nextflow/scm Feb-24 010341.014 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Feb-24 010341.021 [main] INFO nextflow.cli.CmdRun - Pulling nf-core/mag ... Feb-24 010341.024 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/mag/contents/nextflow.config?ref=5.1.0 Feb-24 010342.153 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/mag/contents/main.nf?ref=5.1.0 Feb-24 010342.288 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/mag Feb-24 010342.476 [main] DEBUG nextflow.scm.AssetManager - Pulling nf-core/mag -- Using remote clone url: https://github.com/nf-core/mag.git Feb-24 010348.935 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/nf-core/mag.git Feb-24 010348.979 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/.nextflow/assets/nf-core/mag/nextflow.config Feb-24 010348.981 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/scw_MAG_wastewaterKB.conf Feb-24 010348.981 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/.nextflow/assets/nf-core/mag/nextflow.config Feb-24 010348.982 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/scratch/SCWF00048/legacydata/b.rss23xrz/pacbio/KB/scw_MAG_wastewaterKB.conf Feb-24 010348.990 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:

apptainer

Feb-24 010350.108 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:

apptainer

Feb-24 010350.132 [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, icr_alma, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, iris, tes, scw, unc_longleaf, tigem, tubingen_apg, apollo, ipop_up, vsc_calcua, pdc_kth, ceci_nic5, ccga_cau, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, test_minimal, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, rki, ucl_myriad, utd_ganymede, charliecloud, fred_hutch, seattlechildrens, icr_davros, ceres, munin, rosalind, hasta, cfc, emulate_amd64, uzh, shu_bmrc, ebi_codon_slurm, test_alternatives, ebc, ccga_dx, test_hybrid, crick, ku_sund_danhead, marvin, lrz_cm4, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, eva_grace, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, arm64, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, test_assembly_input, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, test_longreadonly_alternatives, computerome, ucd_sonic, gpu, test_single_end, seg_globe, mssm, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, dirac, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, hki_genie, genouest, cbe, unsw_katana, utd_juno, phoenix, seawulf, test_longreadonly, uod_hpc, fub_curta, lovelace, uct_hpc, aws_tower, binac, fsu_draco] Feb-24 010350.136 [main] WARN nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option

-resume

is ignored Feb-24 010350.170 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.5.1] Feb-24 010350.170 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Feb-24 010350.170 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.5.1] Feb-24 010350.261 [main] DEBUG n.plugin.HttpPluginRepository - Registry request: https://registry.nextflow.io/api/v1/plugins/dependencies?plugins=nf-schema%402.5.1&amp;nextflowVersion=25.10.3 - code: 200 - body: {"plugins":[{"id":"nf-schema","releases":[{"version":"2.5.1","url":"https://registry.nextflow.io/api/v1/plugins/nf-schema/2.5.1/download/nf-schema-2.5.1.zip","date":"2025-09-02T144839.714892Z","sha512sum":"82c9c17a9f77319386e670e7b52cf79b067320001f083ccdfec77dada9fd53499506200fd10b493cf8f6fc0420f42e2314481c353ca14b3a92f354bf07ad5c13","requires":">=25.04.0","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nextflow-io/nf-schema","provider":"nextflow-io"}]} Feb-24 010350.288 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.5.1 Feb-24 010350.295 [main] INFO nextflow.plugin.PluginUpdater - Downloading plugin nf-schema@2.5.1