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Hello, I've been trying to create a phylogenetic t...
# phyloplace
n
Hello, I've been trying to create a phylogenetic tree using the ampliseq pipeline. When I use the following code, it works: "pplace_tree": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprepr.brlenopt.newick", "pplace_aln":"/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprepr.alnfna", "pplace_taxonomy":"/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprep.taxonomy.tsv", "pplace_model": "GTR+F+I+G4", "pplace_name": "bac120.r09rs220" But when I want to use the newest version of these files, the "r10rs226" version, I get the following error message: ERROR ~ Error executing process > 'NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:GAPPA_ASSIGN (bac120.r10rs226)' Caused by: Process 
NFCORE_AMPLISEQ:AMPLISEQ:FASTA_NEWICK_EPANG_GAPPA:GAPPA_ASSIGN (bac120.r10rs226)
terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: gappa \ examine assign \ --per-query-results --krona --sativa \ --threads 6 \ --jplace-path bac120.r10rs226.epa_result.jplace.gz \ --taxon-file sbdi-gtdb-sativa.r10rs226.bac120.sprep.taxonomy.tsv \ --file-prefix bac120.r10rs226.taxonomy. cat <<-END_VERSIONS > versions.yml "NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:GAPPA_ASSIGN": gappa: $(echo $(gappa --version 2>&1 | sed 's/v//' )) END_VERSIONS Command exit status: - Command output: ...' .... ... ... ... ... .... .|'|. | || '' .|| ||' || ||' || '' .|| .|' || |'' .|' || || | || | .|' || .|'|. || '.... '|..'|'. ||...' ||...' '|..'|. '||' ||:. '....' || || '''' '''' v0.8.0 (c) 2017-2022 by Lucas Czech and Pierre Barbera Invocation: gappa examine assign --per-query-results --krona --sativa --threads 6 --jplace-path bac120.r10rs226.epa_result.jplace.gz --taxon-file sbdi-gtdb-sativa.r10rs226.bac120.sprep.taxonomy.tsv --file-prefix bac120.r10rs226.taxonomy. Command: gappa examine assign Input: --jplace-path bac120.r10rs226.epa_result.jplace.gz --taxon-file sbdi-gtdb-sativa.r10rs226.bac120.sprep.taxonomy.tsv --root-outgroup --taxonomy --ranks-string superkingdom|phylum|class|order|family|genus|species Settings: --sub-taxopath --max-level 0 --distribution-ratio -1 --consensus-thresh 1 --resolve-missing-paths false --distant-label false Output: --out-dir . --file-prefix bac120.r10rs226.taxonomy. --file-suffix --cami false --sample-id --krona true --sativa true --per-query-results true --best-hit false Global Options: --allow-file-overwriting false --verbose false --threads 6 --log-file Run the following command to get the references that need to be cited: 
gappa tools citation Czech2020-genesis-and-gappa
Started 2025-09-21 143340 Found 1 jplace file Running the assignment 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/9f/08e866f71ac92b3d080d803f8261d7 Container: /cfs/klemming/projects/supr/naiss2025-22-1066/ampliseq/work/singularity/depot.galaxyproject.org-singularity-gappa-0.8.0--h9a82719_0.img Tip: you can replicate the issue by changing to the process work dir and entering the command 
bash .command.run
-- 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 ERROR ~ Failed to invoke 
workflow.onComplete
event handler -- Check script '/cfs/klemming/home/n/nicolai2/.nextflow/assets/nf-core/ampliseq/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf' at line: 123 or see '.nextflow.log' file for more details Can you help me with that?
d
I think this part of the message is key: 
Likely it has been terminated by the external system
. In most cases this means you ran out of memory. To increase the amount of memory given to a process, you need to specify the new memory in a config file. Nf-core has general documentation for this here: https://nf-co.re/docs/usage/getting_started/configuration. For your specific case, you can create a 
nextflow.config
file in the directory where you run the pipeline looking like the below.
Copy code
process {
  withName: GAPPA_ASSIGN {
    memory: 72.GB
  }
}
This will double the amount of memory assigned to process from the default 36 GiB.
BTW1: Since you actually ran #CEA7TBJGJ and not #C04NLA7QHH9, the best channel to post is the former.
BTW2: I'm working on an update of r226 dealing with some misassigned sequences. This will be available in a week or so. I'll announce that in this channel, so keep your eyes open.
n
Thank you very much! I will try that!
Hej hej, I've created a nextflow.config file with vim and entered your code above as content. I then tried running ampliseq like this "nextflow run nf-core/ampliseq -r 2.14.0 -resume -c nextflow.config -name Nicolai52 -profile pdc_kth -params-file nf-params.json --project naiss2025-22-1066" and got the following error: "ERROR ~ Unknown config attribute 
process.withName:GAPPA_ASSIGN
-- check config file: /cfs/klemming/projects/supr/naiss2025-22-1066/ampliseq/nextflow.config" I also tried to use this: process { withName: NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:GAPPA_ASSIGN (bac120.r10rs226) { memory: 72.GB } } Or this: process { withName: NFCORE_AMPLISEQAMPLISEQFASTA_NEWICK_EPANG_GAPPA:GAPPA_ASSIGN { memory: 72.GB } } in the nextflow.config file but I get the same error
d
Can you paste the exact file (or upload) you tried first?
Never mind, I can replicate your error. Back in a moment.
It might have been that my indentation was off -- weird! Try this instead:
Copy code
process {
    withName: GAPPA_ASSIGN {
        memory = 72.GB
    }
}
n
Thanks! It is running now!
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