danpal96

I think that a clarification of this two behaviors in the docstring would be enough for now

I have been trying to undestand the `simulator.py` script in `metagenome` mode and when it gets stuck in an infinite loop. Let's say that I have genomes with max length...

@kmnip I made some small tests and it didnt get stuck, I will do more tests when I have more time. Sorry for the late response for some reason github...

Installed using anaconda: diamond 2.1.8 h43eeafb_0 bioconda Here are the files that I have used: [test.zip](https://github.com/bbuchfink/diamond/files/13180860/test.zip) I made a db with the next proteins: - sp|P0A9A9|FUR_ECOLI Ferric uptake regulation protein...

v9.11.0 added PR #3716 that removes temp files after all checkpoint have finished

I encountered the same error, in my case, it was because I hadn’t created the output directory. It might be helpful if hifiasm could check whether the output file is...

It's a problem with diamond v2.1.11 https://github.com/bbuchfink/diamond/issues/855 You can install v2.1.10 until a new version is released or convert to FASTA

snakemake == 9.13.7 from bioconda @dariober I created a minimal example for your issue: test.txt: ``` hello world yes ``` Snakefile: ```snakemake rule test: input: "test/aggregated.txt", "test_no_dir/aggregated.txt", rule copy: input:...

@dariober One caveat is that if the rule that has `split/` as an input (the `check` rule in this example) finishes before other rules that use the files inside that...

@dariober last hack hahaha. Instead of marking the directory as temp, you can create a rule that its only purpose is to mark the files inside that directory as temp...