Skip to content

Crash if dna_reference not provided #81

@nromashchenko

Description

@nromashchenko

Read2Tree version: 2.0.1

According to the help command, it's possible to call read2tree without dna reference:

> read2tree --help
2025-11-14 10:56:45 INFO      ------- Read2Tree version: 2.0.1 -------
...
  --dna_reference DNA_REFERENCE
                        [Default is None] Reference file that contains nucleotide sequences (fasta, hdf5). If not given it will usethe RESTapi and retrieve sequences from http://omabrowser.org directly. NOTE: internet connection
                        required!

and it is indeed possible:

> read2tree --tree --standalone_path marker_genes --reads sample_1.fastq sample_2.fastq --output_path ./output
...
    with open_(self.args.dna_reference, 'rt') as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: ''

I assume it's an artifact from earlier versions and it should be a required argument

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions