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donovan-h-parks / RefineM

A toolbox for improving metagenome-assembled genomes.
GNU General Public License v3.0
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Error ktImportText missing #18

Closed palomo11 closed 6 years ago

palomo11 commented 6 years ago

Hi,

I'm running refinem scaffold_stats and I'm getting this error:

ktImportText is not on the system path.

  Controlled exit resulting from an unrecoverable error or warning.

I guess it s because I don't have Krona installed, but is Krona needed for "Removing contamination based on genomic properties"? If it is not, is there anyway to run refineM without the need of having Krona installed?

Thanks in advance.

donovan-h-parks commented 6 years ago

No. The Krona plots are only generated during the "Removing contamination based on taxonomic assignments". Thank you for bringing this to my attention. I will modify this dependency in the next release of RefineM.

palomo11 commented 6 years ago

OK, thanks, that would be great as I'm having some issues installing Krona and I will not needed it anyway as I'm just using "Removing contamination based on genomic properties"

donovan-h-parks commented 6 years ago

In the meantime, you could modify "main.py" to remove this dependency or just create a fake ktImportText executable.

palomo11 commented 6 years ago

By modifying the "main.py", it works. Thanks!