Meryl count crashed on something todo with genome size although it is not an input.

[MartinPippel]

Describe the bug
Meryl count crashed on something todo with genome size although it is not an input.

N E X T F L O W  ~  version 24.10.0
Launching `/cfs/klemming/projects/supr/snic2021-6-194/private/martin/prog/Earth-Biogenome-Project-pilot_MYFORK/main.nf` [pedantic_liskov] DSL2 - revision: 13e9362f94

    Running NBIS Earth Biogenome Project Assembly workflow.

WARN: There's no process matching config selector: QUARTO -- Did you mean: QUAST?
WARN: There's no process matching config selector: MULTIQC
WARN: There's no process matching config selector: BUILD_FASTK_HIFI_DATABASE
[skipping] Stored process > DECONTAMINATE:FCSGX_FETCHDB (1)
Staging foreign file: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
[skipping] Stored process > PREPARE_INPUT:UNTAR_TAXONOMY (1)
[be/0e068d] Submitted process > PREPARE_INPUT:TAXONKIT_NAME2LINEAGE (Homarus gammarus)
[93/354582] Submitted process > PREPARE_INPUT:GOAT_TAXONSEARCH (Homarus_gammarus)
[7b/546ab1] Submitted process > ASSEMBLY_REPORT:REPORT_GENOMETRAITS (Homarus gammarus)
[6b/aeafe4] Submitted process > ASSEMBLY_REPORT:TOL_SEARCH (Taxid: 6707)
ERROR ~ Error executing process > 'BUILD_MERYL_HIFI_DATABASE:MERYL_COUNT (Homarus_gammarus)'

Caused by:
  For input string: "4156500000" -- Check script '/cfs/klemming/projects/supr/snic2021-6-194/private/martin/prog/Earth-Biogenome-Project-pilot_MYFORK/modules/nf-core/meryl/count/main.nf' at line: 24


Source block:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  """
  for READ in $reads; do
      meryl count \\
          k=$kvalue \\
          threads=$task.cpus \\
          $args \\
          \$READ \\
          output read.\${READ%.f*}.meryl
  done

  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      meryl: \$( meryl --version |& sed 's/meryl //' )
  END_VERSIONS
  """

Container:
  /cfs/klemming/projects/snic/snic2021-6-194/nobackup/ebp-singularity-cache/depot.galaxyproject.org-singularity-meryl-1.4.1--h4ac6f70_0.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

            Thank you for using the NBIS Earth Biogenome Project Assembly workflow.
            The workflow completed unsuccessfully.

            Please read over the error message. If you are unable to solve it, please
            post an issue at https://github.com/NBISweden/Earth-Biogenome-Project-pilot/issues
            where we will do our best to help.

WARN: Killing running tasks (1)

To Reproduce
Can not be reproduced at the moment.

Expected behavior
A clear and concise description of what you expected to happen.

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• on PDC. Dardel

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[LucileSol]

I got a similar one on nac with FASTK:

Running on HPC=nac.
Nextflow 24.10.3 is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.04.4
Pulling NBISweden/Earth-Biogenome-Project-pilot ...
 Already-up-to-date
Launching `https://github.com/NBISweden/Earth-Biogenome-Project-pilot` [insane_kalman] DSL2 - revision: 80bec32e9c [main]

    Running NBIS Earth Biogenome Project Assembly workflow.
    
WARN: There's no process matching config selector: QUARTO -- Did you mean: QUAST?
WARN: There's no process matching config selector: MULTIQC
Staging foreign file: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
[skipping] Stored process > PREPARE_INPUT:UNTAR_TAXONOMY (1)
[76/a22707] Cached process > PREPARE_INPUT:TAXONKIT_NAME2LINEAGE (Ranunculus sceleratus)
[37/3b3d09] Cached process > PREPARE_INPUT:GOAT_TAXONSEARCH (Ranunculus_sceleratus)
[ce/2fb8dc] Cached process > ASSEMBLY_REPORT:REPORT_GENOMETRAITS (Ranunculus sceleratus)
[6b/9b33ed] Submitted process > ASSEMBLY_REPORT:TOL_SEARCH (Taxid: 147635)
ERROR ~ Error executing process > 'BUILD_FASTK_HIC_DATABASE:FASTK_FASTK (Ranunculus_sceleratus)'

Caused by:
  For input string: "3667500000" -- Check script '/home/lucso605/.nextflow/assets/NBISweden/Earth-Biogenome-Project-pilot/modules/nf-core/fastk/fastk/main.nf' at line: 28


Source block:
  if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
      error "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead."
  }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
  """
  FastK \\
      $args \\
      -T$task.cpus \\
      -M${task.memory.toGiga()} \\
      -N${prefix}_fk \\
      $reads
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      fastk: $FASTK_VERSION
  END_VERSIONS
  """

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
[9c/a4350b] Submitted process > PREPARE_INPUT:SAMTOOLS_FASTA (Ranunculus_sceleratus:m84093_240531_133307_s1.hifi_reads.bc2079)

            Thank you for using the NBIS Earth Biogenome Project Assembly workflow.
            The workflow completed unsuccessfully.

            Please read over the error message. If you are unable to solve it, please
            post an issue at https://github.com/NBISweden/Earth-Biogenome-Project-pilot/issues
            where we will do our best to help.
            
WARN: Killing running tasks (1)
WARN: Killing running tasks (1)

[MartinPippel]

@LucileSol: Could you try to specify the following 3 additional arguments in your assembly_parameters.yaml file?

# Mandatory - sample metadata
sample:
  name: 'YOUR_SPECIES_NAME'
  genome_size: 3667500000 # From Genomescope. To bypass failing GOAT
  ploidy: XX
  haploid_number: XX

This solved this issue me. Though I still have no clue why.

[LucileSol]

Yes it seems to have solved the issue for me as well! Thank you!!