Entering edit mode
4.6 years ago
mcs
•
0
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
Was there some other error before that message at the end?
There was no prior error message.
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.
You could retry the build and see if it completes.
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.
I repeated the 2nd build;
When I use Kraken (Biostar online workbook) I still get the error message:
I am guessing the database files are downloaded but Kraken2 can't access them.
Should I give up and use Kraken1?
Thanks,
Michael Snyderman
kraken
andkraken2
are different programs. If biostar handbook is referring tokraken v.1.0
then you can interchangeably use the directions for other version. I suggest you follow the manual forkraken2
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.Thank you. The link is for minikraken but I will be very happy to get that to work.
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