jiarong

@meisiy , sorry for the late reply. You can just submit the same script. VS2 can pick up where it stopped and continue.

@wenhaoli-wenhaoli , it looks like some internet issue or bioconda server issue to install the dependencies. You can retry if the problem is at the bioconda server. Another option is...

Hi, the error shows there is no output files from prodigal (for gene prediction), which should not happen. Could you re-try to make sure this error is reproducible? I can...

Hi, sorry for the late reply. You have set the python to use the packages in your `.local` first before others. You can disable it by the command below: `export...

@gonzalezibeas The numpy installed by VS2 is being used in your case. No need to set PYTHONNOUSERSITE. Please check your VS2 version and make update to the current.

@gonzalezibeas, it looks like the db installed by you before (NOT the one in the container) is used: `/home/user01/data/brevipalpus/virsorter2/db`. You can try remove the config files in `$HOME/.virsorter`, and re-run.

Hi, thanks for report the issue. This is interesting. I do not have an answer. Can you share the three contigs involved?

That's correct. It's in the intermediate file directory, e.g., `iter-0/dsDNAphage/all.pdg.faa`. It's generated by `prodigal`. There is also a `.gff` file in the same directory.

Basically, conda could not install the packages due to conda or internet issues. Check out [installation option 3](https://github.com/jiarong/VirSorter2?tab=readme-ov-file#option-3) to avoid this issue. (It still needs internet connection..)

Hi, it's the first time I have seen this error from prodigal. The "Segmentation fault" error can sometimes caused by the system ran out of memory due to other jobs....