kraken2 database does not contain necessary file taxo.k2d
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3 months ago
10mz1 • 0

Hello everyone,

I am trying to install use Kraken2 locally and am getting the error:

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

The database was built with the standard command:

kraken2-build --standard --db mydb

I don't understand why this database would not contain the necessary files, I am not trying to build a custom database. Thank you to whoever mentioned in my other thread that the way this program works is by loading the entire database into memory. Per the system specs, this requires slightly more than 29GB of RAM (thank goodness I have 32).

shotgun metagenomics kraken kraken2 • 931 views
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kraken2-build --standard --db $DBNAME

Manual says the following

This will download NCBI taxonomic information, as well as the complete genomes in RefSeq for the bacterial, archaeal, and viral domains, along with the human genome and a collection of known vectors (UniVec_Core)

If you are not seeing the taxo.k2d file then that information was not perhaps downloaded. Check the log file for kraken2-build to see if something went wrong. Manual says that the process requires 100GB of disk space (you have only talked about RAM).

A side note. Please consider validating answers for your past threads. Up-voting useful comments/accepting answers (use green check mark) is way to show appreciation for help you receive from the volunteer community on biostars.

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Thank you for your input. This has occurred multiple times now. I have plenty of disk space, around 600GB on the disk I am working on. This same issue has also occurred while trying to install just the bacterial database they offer as well. Not sure where I am going wrong..

Re: side note: yes. You are right. I cannot visit past threads unfortunately but I will do this going forward including in this thread.

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Not sure where I am going wrong..

You need to diligently check log files for all operations to make sure there were no errors. Warnings, at times, may be acceptable to move forward.

Did you check log file for kraken build process? If you did not capture that information (and kraken did not write a log file) then do so when you repeat the process. You may need to capture STDOUT/STDIN streams to file for that ( https://stackoverflow.com/questions/7526971/how-to-redirect-both-stdout-and-stderr-to-a-file )


You can visit all of your past posts at this link (copy paste the link Biostars code is parsing the link otherwise) : https://www.biostars.org/u/138413/?active=posts

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seems this has been an open issue for 4 years:

https://github.com/jenniferlu717/Bracken/issues/76

side conversation: where is this green check you speak of? I see where to upvote with the thumbs up.

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That may be a slightly different issue. There a file is present but not detected. And there is also wrong db name.

Did you check the build log? If you don't have it re-do the database build and capture the log.


Check mark is only present for answers below the bookmark button.

accept

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interesting, i do not see it in this thread. perhaps some minimum amount of time must pass.

i believe i may have found the answer. after installing a database, you must build it with: kraken2-build --build --db <database_name>

even for the standard database, and this is not shown in the instructions for building the standard database.

now we'll see if my 32GB of RAM can handle the test :)

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interesting, i do not see it in this thread.

That is because there is no answer in this thread. All of the back and forth so far is comments.

believe i may have found the answer.

Post that as answer. You can then accept it to provide closure to this thread.

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done! thanks

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3 months ago
10mz1 • 0

i believe i may have found the answer. after installing a database, you must build it with: kraken2-build --build --db <database_name>

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