Assembly sequence analysis

[lingbingzeng1985]

Description of the bug

Hello, when I used bactopia to analyze the assembled sequence with bactopia --samples Genomes-K-N.txt, there occurs mistake like this:
ERROR ~ Argument of file function cannot be null

-- Check script '/home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/./workflows/../lib/nf/bactopia.nf' at line: 150 or see '.nextflow.log' file for more details
How can I solve the problem? Thanks.

Command used and terminal output

bactopia --samples Genomes-K-N.txt
2025-09-30 15:52:04 INFO     2025-09-30 15:52:04:root:INFO -     download.py:544
                             Checking if environment pre-builds                 
                             are needed (this may take a while                  
                             if building for the first time)                    
Nextflow 25.04.7 is available - Please consider updating your version to it
N E X T F L O W  ~  version 23.10.1
Launching `/home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/main.nf` [nasty_brattain] DSL2 - revision: 0cd9f79ba7


---------------------------------------------
   _                _              _             
  | |__   __ _  ___| |_ ___  _ __ (_) __ _       
  | '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` |   
  | |_) | (_| | (__| || (_) | |_) | | (_| |      
  |_.__/ \__,_|\___|\__\___/| .__/|_|\__,_| 
                            |_|                  
  bactopia v3.2.0
  Bactopia is a flexible pipeline for complete analysis of bacterial genomes 
---------------------------------------------
Core Nextflow options
  runName          : nasty_brattain
  container        : quay.io/bactopia/bactopia:3.2.0
  launchDir        : /home/lzb/桌面/XR-KP/Genomes
  workDir          : /home/lzb/桌面/XR-KP/Genomes/work
  projectDir       : /home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0
  userName         : lzb
  profile          : standard
  configFiles      : /home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/nextflow.config

Required Parameters
  samples          : Genomes-K-N.txt

Dataset Parameters
  genome_size      : 0

QC Parameters
  adapters         : /home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/data/EMPTY_ADAPTERS
  phix             : /home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/data/EMPTY_PHIX

Prokka Parameters
  proteins         : /home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/data/proteins.faa

Max Job Request Parameters
  max_memory       : 61 GB (Original request (64 GB) adjusted to fit your system)
  max_time         : 2h

Nextflow Profile Parameters
  condadir         : /home/lzb/.bactopia/conda
  datasets_cache   : /home/lzb/.bactopia/datasets
  singularity_cache: /home/lzb/.bactopia/singularity

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------
If you use bactopia for your analysis please cite:

* Bactopia
  https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://bactopia.github.io/acknowledgements/
--------------------------------------------------------------------
WARN: 
WARN: Conda Disclaimer
WARN: 
WARN: If you have access to Docker or Singularity, please consider
WARN: running Bactopia using containers. The containers are less
WARN: susceptible to Conda environment related issues (e.g. version
WARN: conflicts) and errors caused by creation of conda environments
WARN: in parallel (use '--max_cpus 1' to over come this error).
WARN: 
WARN: To use containers, you can use the profile parameter
WARN:     Docker: -profile docker
WARN:     Singularity: -profile singularity
WARN: 
--------------------------------------------------------------------
[-        ] process > BACTOPIA:DATASETS              -
[-        ] process > BACTOPIA:GATHER:GATHER_MODULE  -
[-        ] process > BACTOPIA:GATHER:CSVTK_CONCAT   -
[-        ] process > BACTOPIA:QC:QC_MODULE          -
[-        ] process > BACTOPIA:ASSEMBLER:ASSEMBLE... -
[-        ] process > BACTOPIA:ASSEMBLER:CSVTK_CO... -
[-        ] process > BACTOPIA:SKETCHER:SKETCHER_... -
[-        ] process > BACTOPIA:ANNOTATOR:PROKKA_M... -
[-        ] process > BACTOPIA:AMRFINDERPLUS:AMRF... -
[-        ] process > BACTOPIA:AMRFINDERPLUS:CSVT... -
[-        ] process > BACTOPIA:MLST:MLST_MODULE      -
[-        ] process > BACTOPIA:MLST:CSVTK_CONCAT     -
[-        ] process > BACTOPIA:DUMPSOFTWAREVERSIONS  -
ERROR ~ Argument of `file` function cannot be null

 -- Check script '/home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/./workflows/../lib/nf/bactopia.nf' at line: 150 or see '.nextflow.log' file for more details

    Bactopia Execution Summary
    ------------------------------
    Workflow         : bactopia
    Bactopia Version : 3.2.0
    Nextflow Version : 23.10.1
    Command Line     : nextflow run /home/lzb/miniconda3/envs/bactopia//share/bactopia-3.2.0/main.nf -w /home/lzb/桌面/XR-KP/Genomes/work/ --samples Genomes-K-N.txt
    Profile          : standard
    Resumed          : false
    Completed At     : 2025-09-30T15:52:09.504445505+08:00
    Duration         : 2.5s
    Success          : false
    Exit Code        : null
    Error Report     : Argument of `file` function cannot be null
    Launch Dir       : /home/lzb/桌面/XR-KP/Genomes
[skipped  ] process > BACTOPIA:DATASETS              [100%] 1 of 1, stored: 1 ✔
[-        ] process > BACTOPIA:GATHER:GATHER_MODULE  [  0%] 0 of 24
[-        ] process > BACTOPIA:GATHER:CSVTK_CONCAT   -
[-        ] process > BACTOPIA:QC:QC_MODULE          -
[-        ] process > BACTOPIA:ASSEMBLER:ASSEMBLE... -
[-        ] process > BACTOPIA:ASSEMBLER:CSVTK_CO... -
[-        ] process > BACTOPIA:SKETCHER:SKETCHER_... -
[-        ] process > BACTOPIA:ANNOTATOR:PROKKA_M... -
[-        ] process > BACTOPIA:AMRFINDERPLUS:AMRF... -
[-        ] process > BACTOPIA:AMRFINDERPLUS:CSVT... -
[-        ] process > BACTOPIA:MLST:MLST_MODULE      -
[-        ] process > BACTOPIA:MLST:CSVTK_CONCAT     -
[-        ] process > BACTOPIA:DUMPSOFTWAREVERSIONS  -
[skipping] Stored process > BACTOPIA:DATASETS
ERROR ~ Argument of `file` function cannot be null

 -- Check script '/home/lzb/miniconda3/envs/bactopia/share/bactopia-3.2.0/./workflows/../lib/nf/bactopia.nf' at line: 150 or see '.nextflow.log' file for more details
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.

Relevant files

No response

System information

No response