search

grp-bork / gunc

Python package for detection of chimerism and contamination in prokaryotic genomes.
GNU General Public License v3.0
66 stars 8 forks source link

gunc download_db: gunc: error: the following arguments are required: -d/--database_file #6

Closed uloeber closed 3 years ago

uloeber commented 3 years ago

Dear @fullama , I get the error gunc download_db ./ usage: gunc [-h] -d (-i | -g ) [-p] [-t] [-o] [-s] [-v] gunc: error: the following arguments are required: -d/--database_file In both cases, running gunc download_db ./ or gunc --download_db ./ What am I doing wrong? Bests, Ulrike

fullama commented 3 years ago

As far as I can tell you are doing nothing wrong, the same command you put there works fine for me: image

Could you maybe try copy paste this command: 

gunc download_db ./

Just to see what happens and maybe post a screen shot of exactly what the output is?

uloeber commented 3 years ago

Dear @fullama , sure! image

fullama commented 3 years ago

Is it version 1.0.1? 

gunc -v
uloeber commented 3 years ago

Installed via conda: gunc -v 0.1.2

image

fullama commented 3 years ago

Ah.. that version is no longer supported.. (I'll have to see if I can remove it) can you try force conda to install the latest version?

conda install -n gunc -c bioconda gunc=1.0.1

I'll update the Installation documentation to specify 1.0.1 also..

uloeber commented 3 years ago

Thanks! there seem to be a lot of conflicts. Is this due to the conda receipt? Tried to setup from scratch: conda create -n gunc -c bioconda gunc=1.0.1 May I need to specify all dependency versions on my own then? Thanks for your quick help image

fullama commented 3 years ago

Issue #5 was a very similar issue: in that case it was the order of the channels that fixed it maybe that might solve your issue here too?

https://github.com/grp-bork/gunc/issues/5#issuecomment-750512031

uloeber commented 3 years ago

Tried to solve it as suggested in #5 , but failed Then tried it with conda create -n gunc -c bioconda diamond=2.0.4 prodigal python gunc=1.0.1 with the same result image

fullama commented 3 years ago

Sorry I suddenly stopped answering.. I had to go hospital like 20 mins after my last comment.. did you check the channel order? Is it set up exactly as it is in the link? That's my current suspicion of what it could be?

uloeber commented 3 years ago

Dear Anthony, I hope you are doing better. I checked the channel order and am still getting the same error. :(

fullama commented 3 years ago

Huh.. are you able to install just diamond by itself? Maybe try install one by one until only gunc is left and see if everything else will install before gunc at the end? It can be very hard to diagnose conda installation issues, maybe this might narrow it down..

uloeber commented 3 years ago

pip3 instead of pip made it. thanks!

uloeber commented 3 years ago

Well, unfortunately running into the next problem: image

uloeber commented 3 years ago

conda create -n gunc -c bioconda -c conda-forge diamond=2.0.4 prodigal python=3.9 gunc=1.0.1 libgcc-ng=9.1.0 libstdcxx-ng=9.3.0 works! Still the db parameter seems to not be correctly recognized: image image --db_file works!

fullama commented 3 years ago

Great that we finally got there..! The last error is my fault for forgetting to update that part of the documentation.. it was supposed to be -r (for reference) not -d anymore.. I've updated it now so hopefully no one else will get tripped up by that.. thanks for noticing that though!

Im not sure why conda wouldn't work nicely for you.. I'll look into it but at least it seems to be installed now for you?

Is it working ok for you now or is there anything else I can help with?

uloeber commented 3 years ago

Maybe putting libgcc-ng=9.1.0 libstdcxx-ng=9.3.0 in the package metadata? Works, thanks!

fullama commented 3 years ago

ill have to have a look at what it might do on other systems if i also specify libgcc-ng=9.1.0 libstdcxx-ng=9.3.0 but ill take it into consideration for the next version..

Thanks for your help here!