Hej hej, I have been trying to run phyloplace within ampliseq (2.16.1) and it terminates giving the following comments: -[nf-core/ampliseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:EPANG_PLACE (bac120.r10rs226)' Caused by: Process

NFCORE_AMPLISEQ:AMPLISEQ:FASTA_NEWICK_EPANG_GAPPA:EPANG_PLACE (bac120.r10rs226)

terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: epa-ng \ --model GTR+F+I+G4 \ --threads 10 \ --query bac120.r10rs226.query.hmmalign.masked.afa.gz \ --ref-msa bac120.r10rs226.ref.hmmalign.masked.afa.gz \ --tree sbdi-gtdb-sativa.r10rs226-2.bac120.sprepr.brlenopt.newick \ \ if [ -e epa_result.jplace ]; then gzip epa_result.jplace cp epa_result.jplace.gz bac120.r10rs226.epa_result.jplace.gz fi [ -e epa_info.log ] && cp epa_info.log bac120.r10rs226.epa_info.log cat <<-END_VERSIONS > versions.yml "NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:EPANG_PLACE": epang: $(echo $(epa-ng --version 2>&1) | sed 's/^EPA-ng v//') END_VERSIONS Command exit status: - Command output: INFO Selected: Output dir: ./ INFO Selected: Query file: bac120.r10rs226.query.hmmalign.masked.afa.gz INFO Selected: Tree file: sbdi-gtdb-sativa.r10rs226-2.bac120.sprepr.brlenopt.newick INFO Selected: Reference MSA: bac120.r10rs226.ref.hmmalign.masked.afa.gz INFO Selected: Automatic switching of use of per rate scalers INFO Selected: Preserving the root of the input tree INFO Selected: Specified model: GTR+F+I+G4 INFO Selected: Using threads: 10 INFO ______ __ _ _ __ ______ / ____// __ \ / | / | / // ____/ / __/ / /_/ // /| | ______ / |/ // / __ / /___ / ____// _ |/_____// /| // /_/ / /_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.8) INFO Using model parameters: INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1 (ML), weights&rates: (0.25,0.136954) (0.25,0.476752) (0.25,1) (0.25,2.38629) P-inv (ML): 0 Base frequencies (empirical): 0.254302 0.200097 0.338562 0.207039 Substitution rates (ML): 0.5 0.5 0.5 0.5 0.5 1 INFO Output file: ./epa_result.jplace Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: fuse2fs not found, will not be able to mount EXT3 filesystems INFO: gocryptfs not found, will not be able to use gocryptfs Work dir: /cfs/klemming/projects/supr/naiss2025-22-1066/ampliseq/work/f8/5d7a34040c5551fd0a55eb9b7a8a89 Container: /cfs/klemming/projects/supr/naiss2025-22-1066/ampliseq/work/singularity/depot.galaxyproject.org-singularity-epa-ng-0.3.8--h9a82719_1.img Tip: when you have fixed the problem you can continue the execution adding the option

-resume

to the run command line -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details My params-file looks like this: { "input": "manifest_BS.tsv", "skip_cutadapt": true, "outdir": "results_new", "pplace_tree": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/SBDI_GTDB_v11/sbdi-gtdb-sativa.r10rs226-2.bac120.sprepr.brlenopt.newick", "pplace_aln": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/SBDI_GTDB_v11/sbdi-gtdb-sativa.r10rs226-2.bac120.sprepr.alnfna", "pplace_taxonomy": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/SBDI_GTDB_v11/sbdi-gtdb-sativa.r10rs226-2.bac120.sprepr.taxonomy.tsv", "pplace_model": "GTR+F+I+G4", "pplace_name": "bac120.r10rs226", "skip_qiime_downstream": true, "skip_barplot": true, "skip_abundance_tables": true, "skip_alpha_rarefaction": true, "skip_ancom": true, "picrust": false } Can you please help me with this? Thank you!

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

But

Process `NFCORE_AMPLISEQ:AMPLISEQ:FASTA_NEWICK_EPANG_GAPPA:EPANG_PLACE (bac120.r10rs226)` terminated for an unknown reason -- Likely it has been terminated by the external system

Is your issue, yuor cluster has killed the job, maybe the job used too much memory??

You likely need to configure the pipeline to your available computational resources to you machine or infrastructure. Please see the following two(!) sections: - https://nf-co.re/docs/usage/getting_started/configuration#tuning-workflow-resources - https://nf-co.re/docs/usage/getting_started/configuration#max-resources of the documentation for more information.

Thanks!