Open charlottecc opened 5 years ago
Have you tried the command from directly inside the database folder?
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
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.
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)
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.
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