kraken2: database does not contain necessary file taxo.k2d

[charlottecc]

Hi,

I have tried run the command kraken2 --db=~/Metagenomics/kraken/krakenDB --threads 20 <( find -L ~/Metagenomics/kraken/krakenDB/library \( -name "*.fna" -o -name "*.fa" -o -name "*.fasta" \) -exec cat {} + ) > database.kraken

However I am getting the error message:
kraken2: database ("~/Metagenomics/kraken/krakenDB") does not contain necessary file taxo.k2d
find: `cat' terminated by signal 13

I get this error message despite the taxo.k2d being present. I have tried to rebuild the kraken2 database (custom database of bacteria, fungi, human, plasmid, viral) but I am still getting this error.

If anyone has any advice how to progress I'd be grateful!

Thanks in advance

[jenniferlu717]

Have you tried the command from directly inside the database folder?

[calizilla]

Hi Jennifer,

I am experiencing this also. I created a custom db and have the same error as charlottecc. I followed the custom database creation steps carefully and there were no errors. total database size is 190 GB. It contains bacteria, archaea, viral, fungi, plasmid, univec_core, human and mouse.

The error:
kraken2: database ("~/kraken2_custom") does not contain necessary file taxo.k2d

Below is the database listing and sizes:

-rw-r--r-- 54G hash.k2d
drwxr-sr-x 4.0K library
-rw-r--r-- 56 opts.k2d
-rw-r--r-- 3.4M seqid2taxid.map
-rwxr-xr-- 2.5M taxo.k2d
drwxr-sr-x 4.0K taxonomy
-rw-r--r-- 4.4K unmapped.txt

The command used:

kraken2 \ --db $database \ --threads $NCPUS \ --output $out \ --report $report \ --report-zero-counts \ --use-names \ --paired \ --minimum-base-quality 20 \ --gzip-compressed \ $reads_1 $reads_2

The exact same script was used successfully prior, just changing the $database variable. This was using the pre-built kraken2/bracken2 db from https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20201202.tar.gz

I tried your suggestion of running from within the kraken2_custom db directory and the error remained the same. I also tried making the taxo.k2d file executable which also did not help.

Your assistance much appreciated.

Kind regards,
Cali

[sanderdebacker]

Hi all,

Recently experienced the same error (no taxo.k2d file).
However, every time this error was the result of specifying the wrong directory of the database with the "--db" argument.
It may seem a banality, but they are often overlooked!

kraken2: database ("greengenes/") does not contain necessary file taxo.k2d
--> the database I need is actually called "greengenes_db/", therefore the error.

[stjacqrm]

I had the same error. I used the full path to the db and still got the error.

I tried renaming my files from *.fastq -> *.fq and was able to get Kraken on the work! (it worked)

[russellsmithies]

Not sure if anyone has found a solution, but I discovered that I get this error if there are symlinks in the database path.
If I use the full path then it works OK.