Question: How to use Kraken after installation?
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gravatar for shojaee.zhr
3.1 years ago by
shojaee.zhr0 wrote:

Hi everybody I'm new in bioinformatics and also new in Linux! IMy system has a 4G Ram that i have swiped it two 8G, and installed ubuntu on it. I'm tracing the Kraken's manual[1] step by step, and installed Kraken, and Jellifish 1.1.11, as the manual says, next step is downloading database; Now if I type in the shell: sudo /opt/kraken/kraken-build --standard --jellyfish-hash-size 100M --db /opt/DBKraken then I recieve the error :

/opt/kraken/check-for-jellyfish.sh:jellyfish:command not found

and if I type in the shell: sudo /opt/kraken/kraken-build --standard --jellyfish-hash-size --db /opt/DBKraken then I recieve the error :

Extra argumenys in command line

Is there anybody who can guide me and explain smoothly how can I handle this problem??I'll be appreciated.

kraken next-gen software error • 2.2k views
ADD COMMENTlink modified 3.1 years ago by h.mon30k • written 3.1 years ago by shojaee.zhr0

My system has a 4G Ram that i have swiped it two 8G, and installed ubuntu on it

Is that real 16 GB RAM? Perhaps instead of trying to make your own database you should just use the one they supply.

If you are new to Linux then it would be best to spend some time familiarizing yourself with basics of UNIX

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax87k

1) add jellyfish (and kraken, why not?) to the PATH

export PATH=/path/to/jellyfish:$PATH
export PATH=/path/to/kraken:$PATH

2) If you are the sole user of the computer, I advise you to install the software on your HOME folder, and not use sudo, either for install, but particullarly for running the software.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by h.mon30k

Thank you very much I successfully downloaded it but after 9 hours downloading!But I typed the command:

kraken --db MY_DB MYSEQ.fasta (where MY_SEQ.fasta is one sequnce which I downloaded from ncbi, and MY_DB is the downloaded database)

But I received this error: MY_DB/database.kdb does not exist!

As I read in kraken's mannual, there should be 4 part in every database : database.kdb: Contains the k-mer to taxon mappings database.idx: Contains minimizer offset locations in database.kdb taxonomy/nodes.dmp: Taxonomy tree structure + ranks taxonomy/names.dmp: Taxonomy names

But in the downloaded db, I dont have all of them, and all things that I have are: A librarary folder, containing abouat 2000 subfolders containing nodes.dmp and names.dmp

And a taxonomy folder containing names.dmp and nodes.dmp

can you help me plz??

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by shojaee.zhr0
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