Database library does not exist

[mawa86]

Hi Just as issues #85 and #164, I'm trying to run bracken but can't get past the database building. I've previously downloaded and built the 16S_SILVA138_k2db database and using it to generate kraken .report and .kraken files works flawlessly. However, none of the

_${KRAKEN_DB} is the path to a built Kraken database which also must contain:
**the taxonomy/nodes.dmp file**
**and library sequences *.fna, *.fa, or *.fasta in the library directory._**

are present in the directory created. When I try to run

bracken-build - d PATH/TO/MY/SILVA/DB -t 12 -k 35 -l 1200

i get this error:

ERROR: Database library PATH/TO/MY/SILVA/DB/library does not exist

Also, there is no "library" directory in the built database...

Any idea? Thanks in advance for any help

Martin

[lynngao]

Did you clean the kraken2 database? If you use the clean command after the database build in kraken2, it will delete the taxonomy and library folder as well as the seqid2taxid.map file. So you need to download the taxonomy and library again into kraken2 database and build it again for generating the seqid2taxid.map file.