Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-18T09:59:44.693Z
Comments.Text: What is the output when you run `which kraken2` in your command line?
Comments.UserDisplayName: Pallie
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-18T10:24:18.707Z
Comments.Text: Simply nothing happens
Comments.UserDisplayName: Irma
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-18T12:48:20.977Z
Comments.Text: 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>`
Comments.UserDisplayName: Pallie
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-18T16:17:49.967Z
Comments.Text: I think that I am already using the absolute path. you can see it in the picture I added to my post
Comments.UserDisplayName: Irma
Tags: <database>
Title: Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error
ThreadText: # 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  
  
  ---
  
  ## 0 answers
  
  