Playing with Pan-genome parameters

[Jarrod]

Hi all, 

The last bullet point of the Running a pangenome analysis  states that anvio "Will try to utilize previous search results if there is already a directory". This is a very interesting option. Has anyone tried this? I cannot get it to work without either throwing an overwrite error (makes sense) or re-running the blast search. My impression is that one can re-run anvi-pan-genome command without re-running blast search?

here is the first command I use:

anvi-pan-genome -g woese-GENOMES.h5 -o woese --num-threads 8 --min-occurrence 1 --sensitive --mcl-inflation 2.0 --maxbit 0.5 --use-ncbi-blast -J woese

:: Anvo'o version ...

Anvi'o version ...............................: 2.0.3

Profile DB version ...........................: 16

Contigs DB version ...........................: 7

Pan DB version ...............................: 4

Samples information DB version ...............: 2

Genome data storage version ..................: 1

Auxiliary data storage version ...............: 2

Anvi'server users data storage version .......: 1

[A. Murat Eren]

Yes, it should utilize the previous search results if they are available (becomes very handy when you want to change small things, like maxbit score, or inflation, or min-occurrence). I must have introduced a bug if it is throwing an error :/ I will take a look at this. Can you please open an issue for it so we have no way of running away from it? :)

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Jarrod]

Will do! Thanks

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