Question: error message using Kraken: does not contain necessary file taxo.k2d
0
gravatar for mcs
6 months ago by
mcs0
mcs0 wrote:

I typed as per the manual:

kraken2-build --standard --threads 24 --db download-taxonomy

and that appeared to work as I got the message:

Database construction complete. [Total: 43m39.729s]

I don't think I was able to "clean" successfully as per the manual.

I have been trying use Kraken and keep getting the error message:

kraken2: database ("/home/mcs/refs/kraken2/standard") does not contain necessary file taxo.k2d

Is there any remedy for this?

Thank you
Michael Snyderman

software error • 609 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by mcs0

as I got the message: Database construction complete. [Total: 43m39.729s]

Was there some other error before that message at the end?

ADD REPLYlink written 6 months ago by genomax80k

There was no prior error message.

ADD REPLYlink written 6 months ago by mcs0

I'm sorry, half way through the "build" there was a (r --r --r) ? that stopped the build so I typed y and the build finished.

ADD REPLYlink written 6 months ago by mcs0

You could retry the build and see if it completes.

ADD REPLYlink written 6 months ago by genomax80k

Thank you. I am trying that now. Will it overwrite the old build or do I somehow need to delete the old build? I appreciate your help.

ADD REPLYlink written 6 months ago by mcs0

I repeated the 2nd build;

Database construction complete. [Total: 8m36.591s]
(bioinfo) 
mcs@pop-os

When I use Kraken (Biostar online workbook) I still get the error message:

does not contain necessary file taxo.k2d

I am guessing the database files are downloaded but Kraken2 can't access them.

Should I give up and use Kraken1?

Thanks,
Michael Snyderman

ADD REPLYlink modified 6 months ago by RamRS26k • written 6 months ago by mcs0

kraken and kraken2 are different programs. If biostar handbook is referring to kraken v.1.0 then you can interchangeably use the directions for other version. I suggest you follow the manual for kraken2 if that is the version you are actually using.

You can also download the preformatted databases for kraken2 from this page and make sure you don't get that error.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax80k

Thank you. The link is for minikraken but I will be very happy to get that to work.

ADD REPLYlink written 6 months ago by mcs0

I downloaded from the link minikraken2_v1_8GB and extracted it. It is seen in my downloads as a 4.0 KiB folder. However, the kraken command modified for this version of minikraken from the Biostar handbook: kraken -db ~/refs/kraken/minikraken2_v1_8GB -fastq-input subset.fq > results.out

returns: kraken: database ("/home/mcs/refs/kraken/minikraken2_v1_8GB") does not contain necessary file database.kdb (bioinfo) mcs@pop-os ~

I have Kraken2 and apparently it is unable to read the minikraken I just downloaded and extracted or for that matter any of the databases that I built or downloaded. Is there any way to overcome this? Thank you Michael Snyderman

ADD REPLYlink written 6 months ago by mcs0
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