Empty custom database

[Gepiro]

Hi, I need to build a custom database for my master thesis, but the problem is that, eventually, if I check the DB with the inspect function, it has "table size" equal to 0.

I followed the documentation and I did the following commands: kraken2-build --download-taxonomy --db $DBNAME kraken2-build --download-library bacteria --db $DBNAME kraken2-build --download-library fungi --db $DBNAME kraken2-build --build --db $DBNAME

Do you have the same issue?

[AzizHN]

what do you have as output for every command ?

[Gepiro]

what do you have as output for every command ?

The results to the taxonomy download is: Downloading nucleotide gb accession to taxon map... done. Downloading nucleotide wgs accession to taxon map... done. Downloaded accession to taxon map(s) Downloading taxonomy tree data... done. Uncompressing taxonomy data... done. Untarring taxonomy tree data... done.

For the library (just for fungi, in this example): Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library... done.

Eventually, for the build: Creating sequence ID to taxonomy ID map (step 1)... Sequence ID to taxonomy ID map complete. [0.063s] Estimating required capacity (step 2)... Estimated hash table requirement: 48272 bytes Capacity estimation complete. [39.188s] Building database files (step 3)... Taxonomy parsed and converted. CHT created with 9 bits reserved for taxid. Completed processing of 2006 sequences, 2332569986 bp Writing data to disk... complete. Database files completed. [1m22.989s] Database construction complete. [Total: 2m2.276s]

If I inspect this db the table size is equal to 0