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jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
http://ccb.jhu.edu/software/bracken/index.shtml
GNU General Public License v3.0
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Database library does not exist #167

Open mawa86 opened 2 years ago

mawa86 commented 2 years ago

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 commented 2 years ago

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.