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kraken on nt library

Hi, I'd like to perform a kraken library on the nt library, since my fastq sequences are not human

I build a kraken nt library, as follows:

kraken2-build --download-taxonomy --db nt

Then the followng step, was to "kraken" my fastq file:

kraken2 --db nt --output ERR637906.output.txt --report ERR637906.report.txt ERR637906.fastq.gz

Here is the output error message:

kraken2: database ("./nt") does not contain necessary file taxo.k2d

Could you please explain me how to build a right kraken "nt" database?

kraken nt
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written by Francois Piumi • Francois Piumi

Here are the commands I found to download the nt database:

wget http://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz

pv nt.gz | zcat | cat -v | sed 's/\^A/\t/g' > nt.fasta

kraken2-build --download-taxonomy --db nt

the "pv" command was not working, so I used:

zcat nt.gz | cat -v | sed 's/\^A/\t/g' > nt.fasta

there were also two other command lines that I didn't use:

kraken2-build --add-to-library ./nt.fasta --db nt kraken2-build --build --threads 6 --db nt

• 0 views • link
written by Francois Piumi • Francois Piumi

Looks like you did not build the actual database. $DBNAME is whatever you want to call your database.

kraken2-build --download-library nt --db $DBNAME

kraken2-build --build --db $DBNAME

That said save yourself the trouble and download prebuilt kraken nt database indexes from here: https://benlangmead.github.io/aws-indexes/k2

As you can see they are large ~480 GB and it would be a chore to build locally and need a lot of resources.

• 0 views • link
written by GenoMax GenoMax

the first command is not working since I got the following error message:

gzip: nt: Disk quota exceeded

So it seems impossible for me to perform a kraken on nt.....

• 0 views • link
written by Francois Piumi • Francois Piumi

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