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widdowquinn / pyani

Application and Python module for average nucleotide identity analyses of microbes.
http://widdowquinn.github.io/pyani/
MIT License
181 stars 54 forks source link

Running --graphics after analysis #427

Open artfet opened 3 weeks ago

artfet commented 3 weeks ago

I have run pyani, without specifying the --graphics option, which led to me not having a graphical output to my analysis. I dont want to rerun the whole analysis, but only generate the graophical output.

I have already stumbled upon this thread: https://github.com/widdowquinn/pyani/issues/15

and this response: https://github.com/widdowquinn/pyani/issues/15#issuecomment-203480553

however, if I try to perform my analysis like this: average_nucleotide_identity.py --skip_nucmer --skip_blastn -i PATH_input -o PATH_with previous_results --noclobber -g --gformat png,pdf,eps

I receive this error: ERROR: Output directory /home/[...]/Results would overwrite existing files (exiting)

If I use a new folder name for the --output location, the analysis starts completely from anew.

pyani Version:

pyani 0.2.12 Ubuntu 22.04.4 LTS

widdowquinn commented 3 weeks ago

Hi @artfet - you'll need the --force option as well, as in the example from @peterjc - pyani/average_nucleotide_identity.py -i . -o demo --graphics --skip_nucmer --force --noclobber

You might want to back up the original output before you try it, just in case ;)

L.