pirovc

Hi @oliverdrechsel, that's quite awkward. `download` is the name of a function inside the script and somehow the reference is being lost, maybe something related the way the script is...

I found an issue very similar to what is happening with you (parallel calling an function returning "command not found") https://stackoverflow.com/a/27833407 The problem may be multiple bash versions which are...

You can also try to use the newest release (v0.3.0) where the shebang is now `#!/usr/bin/env bash` which should be more generalized

Hi, thanks for the suggestion. genome_updater selects and filters data based on the `assembly_summary.txt` file provided by NCBI (more info https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt). Besides the filter parameters, the `-F` option allow custom...

Partial matching should be doable, will mark it as enhancement. For now one can download the full assembly_summary.txt from [genbank](https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt) or [refseq](https://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt) and apply the filter/grep manually and use the...

Hi Jason, There's currently no way to do that with genome_updater. I believe you could parse the `assembly_summary.txt` file of the current version and get the information you need to...

You are right on those points, thanks for the suggestions @oliverdrechsel, will try to implement for the next release

It is actually planned for the next release to have a log file option. For now you can use bash redirection `ganon classify ... > out.log 2>&1` to get everything...

The file that would be the closest is either the lca (`--output-lca`) or complete output (`--output-all`). Those files report [3 fields](https://github.com/pirovc/ganon#classify-1): read id, target (taxid), k-mer/minimizer count. You could use...

@rjsorr any success running recentrifuge with ganon? I'll leave this open as a possible enhancement