mashtree error

[MonaMghi]

Describe the bug
I have approximately 10,000 genomes in .fna format that contain my Energetics population. I tried to run mashtree command in terminal with this command (mashtree was installed correctly before): mashtree --mindepth 0 --numcpus 8 /Users/mona.mahrooghi/Documents/GCF-complete-genome-Salmonella-enterica/sample-with-new-naming/*fna file path/*fna file path/*fna file path/*fna file path /*fna file path /*fna file path /*fna file path /*fna file path /*fna file path /*fna file path /*fna > Entericsmashtree.tre

To Reproduce
This is the error message: argument list too long: mashtree. To solve this problem, I mixed all the genomes at one folder to shorten the command line. Now change the command to: mashtree --mindepth 0 --numcpus 8 /Users/mona.mahrooghi/Documents/Enterobacteriacea_NCBI_Ref_edited/enterics/*fna > allentericsmashtree.tre
Again, this error message came up: argument list too long: mashtree

Expected behaviour
I expect to see the program running and see the results.

Screenshots
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Desktop (please complete the following information):

• OS: iOS
• Version [e.g. v0.57, can be obtained by running mashtree --version.]
• Which method did you install with? https://anaconda.org/bioconda/mashtree
• Command: conda install bioconda::mashtree

Additional context
Add any other context about the problem here.
If you can help me fix that, I would appreciate it.

[lskatz]

This is a shell issue. You have too many arguments. You need to make a file of files and use --file-of-files for mashtree. One way to do that is find . -name '*.fna' > assemblies.fofn and then mashtree --file-of-files assemblies.fofn ...

[MonaMghi]

Thank you so much for answering the question. That was so helpful.