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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
sinamajidian
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