[bug] (or user error) kraken2 db not found

[incoherentian]

Hi! Probably doing something wrong here, but left bug in title just-in-case :)

The Error

--------------------------------------------------------------------
ERROR ~ Required parameters are missing, please check: --kraken2_db

 -- Check '.nextflow.log' file for details
Required Parameters
  --bactopia                          [string]  The path to bactopia results to use as inputs
  --kraken2_db                        [string]  The a single tarball or path to a Kraken2 formatted database

--------------------------------------------------------------------
ERROR ~ ERROR: Validation of pipeline parameters failed!

The Execution

bactopia --wf kraken2 \
  -profile arcc_hawk \
  --cluster_opts '--account scw1234 --qos=maxjobs1500' \
  --max_cpus 8 \
  --bactopia /scratch/c.medib/bactopia/out_bactopia/d121_via_d83_COV_19122023JA1TO59_tg_c.medib_job56038718 \ 
  --kraken2_db /scratch/c.medib/.databases/k2_pluspf_08gb_20240112 \
  --max_retry 0 \
  --cleanup_workdir 

Databased exists:

[c.medib@cl2(hawk) .databases]$ tar -xvzf k2_pluspf_08gb_20240112.tar.gz -C /scratch/c.medib/.databases/k2_pluspf_08gb_20240112
hash.k2d
opts.k2d
taxo.k2d
seqid2taxid.map
inspect.txt
ktaxonomy.tsv
library_report.tsv
database100mers.kmer_distrib
database150mers.kmer_distrib
database200mers.kmer_distrib
database250mers.kmer_distrib
database300mers.kmer_distrib
database50mers.kmer_distrib
database75mers.kmer_distrib
unmapped_accessions.txt

bactopia file structure intact

/scratch/c.medib/bactopia/out_bactopia/d121_via_d83_COV_19122023JA1TO59_tg_c.medib_job56038718/COV419_tg
|-- main
|   |-- annotator
|   |   `-- prokka
|   |       |-- COV419_tg-blastdb.tar.gz
|   |       |-- COV419_tg.faa.gz
|   |       |-- COV419_tg.ffn.gz
|   |       |-- COV419_tg.fna.gz
|   |       |-- COV419_tg.fsa.gz
|   |       |-- COV419_tg.gbk.gz
|   |       |-- COV419_tg.gff.gz
|   |       |-- COV419_tg.sqn.gz
|   |       |-- COV419_tg.tbl.gz
|   |       |-- COV419_tg.tsv
|   |       |-- COV419_tg.txt
|   |       `-- logs
|   |           |-- COV419_tg.err
|   |           |-- COV419_tg.log
|   |           |-- nf-prokka.begin
|   |           |-- nf-prokka.err
|   |           |-- nf-prokka.log
|   |           |-- nf-prokka.out
|   |           |-- nf-prokka.run
|   |           |-- nf-prokka.sh
|   |           |-- nf-prokka.trace
|   |           `-- versions.yml
|   |-- assembler
|   |   |-- COV419_tg.fna.gz
|   |   |-- COV419_tg.tsv
|   |   |-- flash.hist
|   |   |-- flash.histogram
|   |   |-- logs
|   |   |   |-- nf-assembler.begin
|   |   |   |-- nf-assembler.err
|   |   |   |-- nf-assembler.log
|   |   |   |-- nf-assembler.out
|   |   |   |-- nf-assembler.run
|   |   |   |-- nf-assembler.sh
|   |   |   |-- nf-assembler.trace
|   |   |   |-- shovill.log
|   |   |   `-- versions.yml
|   |   |-- shovill.corrections
|   |   `-- spades-unpolished.gfa.gz
|   |-- gather
|   |   |-- COV419_tg-meta.tsv
|   |   |-- logs
|   |   |   |-- nf-gather.begin
|   |   |   |-- nf-gather.err
|   |   |   |-- nf-gather.log
|   |   |   |-- nf-gather.out
|   |   |   |-- nf-gather.run
|   |   |   |-- nf-gather.sh
|   |   |   |-- nf-gather.trace
|   |   |   `-- versions.yml
|   |   `-- multiple-read-sets-merged.txt
|   |-- qc
|   |   |-- COV419_tg_R1.fastq.gz
|   |   |-- COV419_tg_R2.fastq.gz
|   |   |-- extra
|   |   |   `-- EMPTY_EXTRA
|   |   |-- logs
|   |   |   |-- COV419_tg-fastp.log
|   |   |   |-- nf-qc.begin
|   |   |   |-- nf-qc.err
|   |   |   |-- nf-qc.log
|   |   |   |-- nf-qc.out
|   |   |   |-- nf-qc.run
|   |   |   |-- nf-qc.sh
|   |   |   |-- nf-qc.trace
|   |   |   `-- versions.yml
|   |   `-- summary
|   |       |-- COV419_tg.fastp.html
|   |       |-- COV419_tg.fastp.json
|   |       |-- COV419_tg_R1-final_fastqc.html
|   |       |-- COV419_tg_R1-final_fastqc.zip
|   |       |-- COV419_tg_R1-final.json
|   |       |-- COV419_tg_R1-original_fastqc.html
|   |       |-- COV419_tg_R1-original_fastqc.zip
|   |       |-- COV419_tg_R1-original.json
|   |       |-- COV419_tg_R2-final_fastqc.html
|   |       |-- COV419_tg_R2-final_fastqc.zip
|   |       |-- COV419_tg_R2-final.json
|   |       |-- COV419_tg_R2-original_fastqc.html
|   |       |-- COV419_tg_R2-original_fastqc.zip
|   |       `-- COV419_tg_R2-original.json
|   `-- sketcher
|       |-- COV419_tg-k21.msh
|       |-- COV419_tg-k31.msh
|       |-- COV419_tg-mash-refseq88-k21.txt
|       |-- COV419_tg.sig
|       |-- COV419_tg-sourmash-gtdb-rs207-k31.txt
|       `-- logs
|           |-- nf-sketcher.begin
|           |-- nf-sketcher.err
|           |-- nf-sketcher.log
|           |-- nf-sketcher.out
|           |-- nf-sketcher.run
|           |-- nf-sketcher.sh
|           |-- nf-sketcher.trace
|           `-- versions.yml
`-- tools
  |-- amrfinderplus
  |   |-- COV419_tg-genes.tsv
  |   |-- COV419_tg-proteins.tsv
  |   `-- logs
  |       |-- nf-amrfinderplus.begin
  |       |-- nf-amrfinderplus.err
  |       |-- nf-amrfinderplus.log
  |       |-- nf-amrfinderplus.out
  |       |-- nf-amrfinderplus.run
  |       |-- nf-amrfinderplus.sh
  |       |-- nf-amrfinderplus.trace
  |       `-- versions.yml
  `-- mlst
      |-- COV419_tg.tsv
      `-- logs
          |-- nf-mlst.begin
          |-- nf-mlst.err
          |-- nf-mlst.log
          |-- nf-mlst.out
          |-- nf-mlst.run
          |-- nf-mlst.sh
          |-- nf-mlst.trace
          `-- versions.yml

19 directories, 104 files

I received the same error when originally attempting to point directly to the tarball, e.g.

bactopia --wf kraken2 \
  -profile arcc_hawk \
  --cluster_opts '--account scw1773 --qos=maxjobs1500' \
  --max_cpus 8 \
  --bactopia /scratch/c.medib/bactopia/out_bactopia/d121_via_d83_COV_19122023JA1TO59_tg_c.medib_job56038718 \ 
  --kraken2_db /scratch/c.medib/.databases/k2_pluspf_08gb_20240112.tar.gz \
  --max_retry 0 \
  --cleanup_workdir 

Expected Behavior
Kraken2 executes using database specified by --kraken2_db

Execution Environment

• Bactopia Version: 3.0.1 built 202311 with some merlin and cfg edits unrelated to kraken2
• OS: RHEL or CentOS
• Environment:
  SLURM-executed conda env running on a cluster for nf,
  nf+SLURM spinning up resulting singularity jobs on same cluster

Additional Information
⚠️ I'll probably stick with mashdist but thought I'd ask about this in case I'm ever desperate for bracken

[rpetit3]

That's no bueno, and something I will look into.

Hope to update soon, hope all is well on your end!