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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
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Confusing error message when using `build-custom` #244

Closed jfy133 closed 1 year ago

jfy133 commented 1 year ago

Hello,

I'm testing a conda-installed ganon 1.5 on this FASTA File.

However when running with the following command I get the error:

$ ganon build-custom -i genome.fasta -d out/ --verbose
- - - - - - - - - -
   _  _  _  _  _   
  (_|(_|| |(_)| |  
   _|   v. 1.5.0
- - - - - - - - - -
Total valid files: 1

Downloading and parsing ncbi taxonomy
 - done in 20.09s.

Parsing sequences from --input (1 files)
 - 1 unique entries
 - done in 0.01s.

Retrieving sequence information from NCBI e-utils
The following command failed to run:
 -i out/_files/build/accessions.txt -k -e 
[Errno 2] No such file or directory: '-i'
Error code: 1

I'm not sure what the -i is referring to here... do you have any idea what is causing it?

jfy133 commented 1 year ago

(note I know this maybe isn't the standard way of using ganon, but I'm using it to add a ganon nextflow wrapper for nf-core/modules, with the plan to integrate it into nf-core/taxprofiler - but to get it into modules we need to have a very small CI tests for all the tools to make sure they work)

jfy133 commented 1 year ago

More information, I just tried again but after downgrading to 1.4 and that seems to work OK :), so the error happens in 1.5

pirovc commented 1 year ago

Thanks for reporting. It's indeed a very silly bug introduce by myself on 1.5.0 and strangely not properly covered by the tests. Will provide a fix still today.

Let me know if you need any help or something is unclear, glad to be included in the nf-core pipeline :)

jfy133 commented 1 year ago

Hi @pirovc

Thanks for the quick response!

I just hit another issue with 1.4, I will make a separate issue.

pirovc commented 1 year ago

Fixed with #246. Let me know if it doesn't work for you. Conda version will be up later today. Further, I'd suggest to use a name prefix, -d out/ will generate out/.ibf and out/.tax which I guess are not so desired filenames.

jfy133 commented 1 year ago

Thank you very much @pirovc ! I'll test once conda recipe is working :), and report back here.

Thanks for the advice too - don't worry I'm aware. This was just a very minimum test example for the CI test :)