Execution failed when --kmerfinder_db and --ncbi_assembly_metadata are provided

[IBEXCluster]

Dear developers,
We are trying to use additional parameters --kmerfinder_db and --ncbi_assembly_metadata for bacass workflow with release 2.4.0 or development version. Both are failed with the following error:

WARN: The following invalid input values have been detected:
 
* --kmerfinder_db: DATABASES/bacteria.tar.gz
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  Kmerfinder database and NCBI assembly metadata not provided.

  Please specify the '--kmerfinderdb' and '--ncbi_assembly_metadata' parameters.

  Both are required to run Kmerfinder.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Any advise?

Here is the run script:

rm -rf ~/.nextflow/assets/nf-core/bacass ;

nextflow run nf-core/bacass -r dev -c nextflow.config -profile singularity --input samplesheet.tsv --kraken2db /ibex/ai/reference/KSL/kraken2/kraken2_dbs/scripts_download/k2_nt_20230502.tar.gz --kmerfinder_db DATABASES/bacteria.tar.gz --ncbi_assembly_metadata ASSEMBLY-REPORTS/assembly_summary_refseq.txt --outdir outputs/2024-12-04_15-KSA-samples__local-downloads__dev

Here is the complete log file:

Nextflow 24.10.2 is available - Please consider updating your version to it

 

N E X T F L O W   ~  version 24.04.4

 

Pulling nf-core/bacass ...

downloaded from [https://github.com/nf-core/bacass.git](https://urldefense.com/v3/__https://github.com/nf-core/bacass.git__;!!Nmw4Hv0!0mP0MQIUjAAB-QNxI3mFS2Dk1FPivNLfEt_5nSL8E1w47QotyFxumO7yk5_kK57CL3WLftfSsoxw9gHJmOmCgncD09XgPC-mszOd6Vy7Ht0$)

Launching `[https://github.com/nf-core/bacass](https://urldefense.com/v3/__https://github.com/nf-core/bacass__;!!Nmw4Hv0!0mP0MQIUjAAB-QNxI3mFS2Dk1FPivNLfEt_5nSL8E1w47QotyFxumO7yk5_kK57CL3WLftfSsoxw9gHJmOmCgncD09XgPC-mszOdQdoeFKY$)` [thirsty_bhabha] DSL2 - revision: ad892edcdb [dev]

 

 

------------------------------------------------------

                                        ,--./,-.

        ___     __   __   __   ___     /,-._.--~'

  |\ | |__  __ /  ` /  \ |__) |__         }  {

  | \| |       \__, \__/ |  \ |___     \`-._,-`-,

                                        `._,._,'

  nf-core/bacass 2.5.0dev

------------------------------------------------------

Input/output options

  input                 : samplesheet.tsv

  outdir                : outputs/2024-12-04_15-KSA-samples__local-downloads__dev

 

Contamination Screening

  kraken2db             : /ibex/ai/reference/KSL/kraken2/kraken2_dbs/scripts_download/k2_nt_20230502.tar.gz

  ncbi_assembly_metadata: ASSEMBLY-REPORTS/assembly_summary_refseq.txt

 

Assembly parameters

  canu_mode             : -nanopore

 

Annotation

  dfast_config          : /home/pampum/.nextflow/assets/nf-core/bacass/assets/test_config_dfast.py

 

Core Nextflow options

  revision              : dev

  runName               : thirsty_bhabha

  containerEngine       : singularity

  launchDir             : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies

  workDir               : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work

  projectDir            : /home/pampum/.nextflow/assets/nf-core/bacass

  userName              : pampum

  profile               : singularity

  configFiles           :

 

!! Only displaying parameters that differ from the pipeline defaults !!

------------------------------------------------------* The pipeline

  [https://doi.org/10.5281/zenodo.2669428](https://urldefense.com/v3/__https://doi.org/10.5281/zenodo.2669428__;!!Nmw4Hv0!0mP0MQIUjAAB-QNxI3mFS2Dk1FPivNLfEt_5nSL8E1w47QotyFxumO7yk5_kK57CL3WLftfSsoxw9gHJmOmCgncD09XgPC-mszOdfnSEiLo$)

 

* The nf-core framework

    [https://doi.org/10.1038/s41587-020-0439-x](https://urldefense.com/v3/__https://doi.org/10.1038/s41587-020-0439-x__;!!Nmw4Hv0!0mP0MQIUjAAB-QNxI3mFS2Dk1FPivNLfEt_5nSL8E1w47QotyFxumO7yk5_kK57CL3WLftfSsoxw9gHJmOmCgncD09XgPC-mszOdNw1r3WM$)

 

* Software dependencies

    [https://github.com/nf-core/bacass/blob/master/CITATIONS.md](https://urldefense.com/v3/__https://github.com/nf-core/bacass/blob/master/CITATIONS.md__;!!Nmw4Hv0!0mP0MQIUjAAB-QNxI3mFS2Dk1FPivNLfEt_5nSL8E1w47QotyFxumO7yk5_kK57CL3WLftfSsoxw9gHJmOmCgncD09XgPC-mszOdJfshqHM$)

 

WARN: The following invalid input values have been detected:

 

* --kmerfinder_db: DATABASES/bacteria.tar.gz

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  Kmerfinder database and NCBI assembly metadata not provided.

  Please specify the '--kmerfinderdb' and '--ncbi_assembly_metadata' parameters.

  Both are required to run Kmerfinder.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

We may not possible to use custom parameters.
Can you please help us to fix this error?

[m-jahn]

• try using absolute paths for the kmer db and ncbi metadata input
• possibly similar to issue FASTP module not finding input paths #187

[IBEXCluster]

Dear @m-jahn
Thanks for your recommendations.
I was downloaded the Kmerfinder database from https://zenodo.org/records/13447056.
However, this kmerfinder job step was failed to locate bacteria.tax and it's not part of the distribution.

i.e.,

Command executed:

  kmerfinder.py \
      --infile SRR10093029_1.fastp.fastq.gz SRR10093029_2.fastp.fastq.gz \
      --output_folder . \
      --db_path 20190108_kmerfinder_stable_dirs/bacteria.ATG \
      -tax 20190108_kmerfinder_stable_dirs/bacteria.tax \
      -x
  
  mv results.txt SRR10093029_results.txt
  mv data.json SRR10093029_data.json
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_BACASS:BACASS:KMERFINDER_SUBWORKFLOW:KMERFINDER":
      kmerfinder: $(echo "3.0.2")
  END_VERSIONS

Command exit status:
  1

Command output:
  # Time used to run KMA for species identifation: 0.016 s
  Cant open file: [Errno 2] No such file or directory: '20190108_kmerfinder_stable_dirs/bacteria.tax'

As you may refer this Kmerfinder database (2019/01/08 - 17GB) - stable dir, which may not have bacteria.tax.

Version: 20190108_stable_dirs
Website: ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/

Content 20190108_stable_dirs.tar.gz:

bacteria
├── bacteria.ATG.comp.b
├── bacteria.ATG.length.bp
├── bacteria.ATG.name
├── bacteria.ATG.seq.b
└── bacteria.name

Update: Same KmerFinder version, but the previous database was corrupted and resulted in untar errors. This version should fix that.

Any further suggestions?
Thanks in advance.

[m-jahn]

In your work directory for this module, rename bacteria.name to bacteria.tax. Then it will work.
This is due to a change in the kmerfinder database structure. Strange enough, the bacass pipe should actually work with both as this module looks for both .name and .tax ending, but it doesn't.

[m-jahn]

More specifically, this line in modules/local/kmerfinder/main.nf looks for both file endings:

def db_tax = file("${kmerfinderdb_path}/${tax_group}.name").exists() ? "${kmerfinderdb_path}/${tax_group}.name" : "${kmerfinderdb_path}/${tax_group}.tax"

I can not explain why it doesn't accept the .name file.

[IBEXCluster]

Many thanks @m-jahn for your recommendations.
I noticed, the taxonomy file was unavailable at ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/.
However, I was trying to install the required database fromKmerFinder : bash ~/kmerfinder/src/kmerfinder_db/INSTALL.sh $PWD bacteria latest and it's helped to create a bacteria taxonomy file bacteria.tax. Thanks for your suggestions again!