Dongwook Kim

Hello again, This is a weird behavior of `augustus` that I also witnessed before. I eventually failed to find the main cause or to determine the situation in which such...

Now the same problem won't happen with the newest version, but will handle the 5-minute timeouts with messages something like this: ``` WARN |: Command timed out: augustus --optCfgFile=... --predictionStart=14960...

Ideally such parallel execution should run without an error, as each of them use randomly generated headers. Still, running multiple processes with writing/deleting operations on the same working directory is...

I got the point now. Thank you for the detailed description. As you mentioned this won't be too difficult to fix. I will try to deal with this soon.

@Sebastien-Raguideau Could you please reproduce the error with the newest version?

Dear Eddie, Thank you for using our pipeline! Based on your description of your aim, it sounds like you are trying to identify marker genes for _`Candida auris`_ _de novo_...

Hi, thank you for pointing this out! This is indeed unexpected, I've never tested with symbolic files as an input. I don't think it will be too difficult to write...

Hello, If you want to use nucleotide sequences of the core genes, you can run `tree` module with `-a nucleotide` option given. Your `.ucg` profiles generated with `PRO` mode should...

That can be done by providing a strict gap filtering threshold to the `tree` module, such as `ufcg tree ... -f 10`. This will remove the alignment columns with more...

Hello, Sorry for the inconvenience, seems like my help messages were misleading. The output of `-o` flag is not a directory but a file, so your attempt to write `./output/Matrix`...