<p>I am running kraken 2.0.8 beta to do taxonomic classification of micorbiota data coming from a MinION run based on the 16S gene. To do so I am using the pre-bult kraken SILVA  database. I managed to get the standard kraken output format but now I would like to replace the taxonomic ID column with  scientific names. According to the manual (<a href="https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual" rel="nofollow noreferrer">https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual</a>) I should run the command: </p>

<p>kraken2 --use-names</p>

<p>but it gives the error: </p>

<p>command kraken2 not found</p>

<p>I also tried variants such as: </p>

<p>./kraken 2 --use-names</p>

<p>but still it gives an error.  </p>

<p>I also tried without kraken2 and thus, </p>

<p>--use-names </p>

<p>but it gives this error: </p>

<p>--use-names command not found </p>

<p>Do you have any idea how I can proceed? </p>

<p>In the picture you can see that everything works to obtain the standard kraken output for barcode 76. But if I try to implement the --use-names command then it does not work  </p>

<p><a href="https://i.sstatic.net/hWvgY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/hWvgY.png" alt="ERROR THAT I GET IF I TRY TO USE THE --USE-NAMES COMMAND"></a>  </p>

<p>I solved the problem: it was a matter of the position of the --use-names command. By changing position (see picture) it worked.
<a href="https://i.sstatic.net/vnCGH.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/vnCGH.png" alt="problem solved picture"></a></p>

CC BY-SA 4.0
2020-02-18T09:59:44.693Z
What is the output when you run `which kraken2` in your command line?
Pallie
CC BY-SA 4.0
2020-02-18T10:24:18.707Z
Simply nothing happens
Irma
CC BY-SA 4.0
2020-02-18T12:48:20.977Z
Install kraken2 and add the executable to your path as per https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#installation , or use a complete absolute path to your kraken binary when running it e.g.: `/path/to/your/kraken/install/bin/kraken2 --use-names <rest of your command>`
Pallie
CC BY-SA 4.0
2020-02-18T16:17:49.967Z
I think that I am already using the absolute path. you can see it in the picture I added to my post
Irma
<database>
Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error
# Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error

(Asked by: username_0 on 2020-02-18)

I am running kraken 2.0.8 beta to do taxonomic classification of micorbiota data coming from a MinION run based on the 16S gene. To do so I am using the pre-bult kraken SILVA database. I managed to get the standard kraken output format but now I would like to replace the taxonomic ID column with scientific names. According to the manual (<https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual>) I should run the command:

kraken2 --use-names

but it gives the error:

command kraken2 not found

I also tried variants such as:

./kraken 2 --use-names

but still it gives an error.

I also tried without kraken2 and thus,

--use-names

but it gives this error:

--use-names command not found

Do you have any idea how I can proceed?

In the picture you can see that everything works to obtain the standard kraken output for barcode 76. But if I try to implement the --use-names command then it does not work

[![ERROR THAT I GET IF I TRY TO USE THE --USE-NAMES COMMAND](https://i.sstatic.net/hWvgY.png)](https://i.sstatic.net/hWvgY.png)

I solved the problem: it was a matter of the position of the --use-names command. By changing position (see picture) it worked.
[![problem solved picture](https://i.sstatic.net/vnCGH.png)](https://i.sstatic.net/vnCGH.png)

**Tags:** database
> **Comments:**
> **username_1**: What is the output when you run `which kraken2` in your command line?  
> **username_0**: Simply nothing happens  
> **username_1**: Install kraken2 and add the executable to your path as per https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#installation , or use a complete absolute path to your kraken binary when running it e.g.: `/path/to/your/kraken/install/bin/kraken2 --use-names <rest of your command>`  
> **username_0**: I think that I am already using the absolute path. you can see it in the picture I added to my post  

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## 0 answers

