Missing output for last part of the roary step-by-step exercise (pangenoma.gene = 'tetC')

[pomidorku]

Sir,

I am running the roary step-by-step tutorial. I am stuck in the last part of the exercise. After running the following:

"select '>'|| cod || '|' || locus_sequence.locus || '|' || pangenoma.gene || x'0a' || sequence from locus_sequence inner join pangenoma_locus on locus_sequence.locus = pangenoma_locus.locus inner join pangenoma on pangenoma_locus.gene = pangenoma.gene inner join genomas_locus on locus_sequence.locus = genomas_locus.locus where pangenoma.gene = 'tetC';"

I do not see in the prompt any tectC gene output. I checked for fasta files named either "pangenoma.gene" or 'tetC, and I do not see any of them.

After running "roary -a" I can see that the only missing tool is kraken (although I installed kraken2).

Sqlite does not produce any warning. Can you help me with this issue?

Regards,

[tseemann]

Roary only supports kraken (version 1)

Where is the link to the tutorial you are doing?

[pomidorku]

Hello, The link to the tutorial is:

https://github.com/microgenomics/tutorials/blob/master/pangenome.md

The part that is not working for me is the last part of the "Pangenome sequence analysis", right before the "Citation:" section.

Regards,