failure to reproduce Completeness data from Supplementary Table 6

[chklovski]

failure to reproduce Completeness data from Supplementary Table 6

[chklovski]

Hi,

Is the issue that you get different completeness/contamination values for the endosymbiont genomes in supplementary table 6?

After testing checkm2 on these genomes, we subsequently added them to the CheckM2 database for the subsequent release (from the paper: " incorporating the test genomes into the final models will likely substantially improve its accuracy on future endosymbiont cases". This should probably be stated in a clearer way, apologies for that).

Therefore the current version of CheckM2 will likely produce much more complete results for these endosymbionts and likely others as well.

For testing your local installation, I recommend running checkm2 testrun, which runs checkm2 on three genomes from very different lineages to ensure that results are as expected.

[azat-badretdin]

Is the issue that you get different completeness/contamination values for the endosymbiont genomes in supplementary table 6?

Yes.

I recommend running checkm2 testrun

Thanks! That was our number one test.

" incorporating the test genomes into the final models will likely substantially improve its accuracy on future endosymbiont cases".

Do you have perchance these new results? I am posting here the results from our testing for GCA and GCF genomes from that table:

With protein FASTA as input: prot_quality_report.txt

With nucleotide FASTA as input: nuc_quality_report.txt