Body: <p>I have some highly contaminated ancient DNA sequences. I have adapter removed and collapsed these and run them through Kraken2. The Kraken reports show multiple levels of taxa with good numbers of reads in each.</p>
  <p>However, when I run Bracken - I keep getting an error saying it can't find any reads.</p>
  <pre><code>Error: no reads found. Please check your Kraken report
  </code></pre>
  <p>I have tried adjusting the taxonomic level (all the way up to Phylum) and get the same result. I have tried using different databases to run the Kraken analysis through and updating both packages.</p>
  <p>Any ideas what could be going wrong?</p>
  <p>Update:</p>
  <p>Here's the head of one of the report files:</p>
  <p><a href="https://i.sstatic.net/5nrA0.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/5nrA0.png" alt="enter image description here" /></a></p>
  <p>I am also using the latest version of Bracken downloaded via Bioconda. My command to run Bracken is via a bash script:</p>
  <pre><code>#SBATCH --partition=day
  #SBATCH --output=slurm_bracken_job%J.out
  #SBATCH --mem-per-cpu=10G
  #SBATCH --cpus-per-task=32
  
  # we load kraken2 and bracken into our environment:
  ml kraken2
  ml bracken
  
  NAME=$1
  
  srun bracken -d /workspaces/groups/database/nt-taxonomy-2021-02-04_braken/ -i <span class="math-container">${NAME}.kreport -o $</span>{NAME}.bracken -r 75 -l S
  </code></pre>
  <p>This is then run using:</p>
  <pre><code>for i in <span class="math-container">$(ls -1 ./*.report | sed 's/.report//'); do sbatch Test_Kraken.sh "$</span>i&quot;; done
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-14T15:21:32.443Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-14T16:06:36.123Z
Comments.Text: It would be helpful if you could give details about your Bracken installation, the structure of your Kraken2 reports (what do the first few lines look like?), and the exact command you ran that threw the error
Comments.UserDisplayName: acvill
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-14T16:50:22.377Z
Comments.Text: I've updated the main post - I have used a couple of different databases as was suggested in a github post that had the same problem but to no avail.
Comments.UserDisplayName: Andy Walton
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-14T16:51:15.447Z
Comments.Text: Thanks thats much better. My advice is one working first without the bash for loop. Bracken works, what I think is somethings not right in the run command.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-14T17:14:27.580Z
Comments.Text: I have just tried running a basic `bracken -d /workspaces/groups/database/nt-taxonomy-2021-02-04_braken/ -i Sample_1.collapsed.report -o Sample_!.report.bracken -r 75 -l S` and still the same error
Comments.UserDisplayName: Andy Walton
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-15T23:55:34.800Z
Comments.Text: I personally dunno. I do know is Bracken works and adjusts the frequency of the bacterial estimates from Kraken. I would personally try with their sample data which is here https://github.com/jenniferlu717/Bracken/commit/a6283e34c3925afe1e1bca3527e9fe0066fcae61#diff-223bc6965d2713e87fc5a41de1d0d94090ca3ea14ac92990c7191826b4e98df7
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-09T14:59:24.790Z
Comments.Text: I had the same error. Here is how I fixed it. My problem was my kraken2 file. I ran kraken2 with the report zero counts option. When I deleted that, all was fine. I also used to run kraken2 with a confidence level of 0.6. I also removed that. Os you probably want to go back to your kraken2 report file and toy with how you generate this to make bracken work. Hope this helps.
Comments.UserDisplayName: AlexThi
Tags: <sequence-analysis><metagenome>
Title: Bracken not working
ThreadText: # Bracken not working
  
  (Asked by: username_0 on 2023-07-14)
  
  I have some highly contaminated ancient DNA sequences. I have adapter removed and collapsed these and run them through Kraken2. The Kraken reports show multiple levels of taxa with good numbers of reads in each.
  
  However, when I run Bracken - I keep getting an error saying it can't find any reads.
  
  ```
  Error: no reads found. Please check your Kraken report
  
  ```
  
  I have tried adjusting the taxonomic level (all the way up to Phylum) and get the same result. I have tried using different databases to run the Kraken analysis through and updating both packages.
  
  Any ideas what could be going wrong?
  
  Update:
  
  Here's the head of one of the report files:
  
  [![enter image description here](https://i.sstatic.net/5nrA0.png)](https://i.sstatic.net/5nrA0.png)
  
  I am also using the latest version of Bracken downloaded via Bioconda. My command to run Bracken is via a bash script:
  
  ```
  #SBATCH --partition=day
  #SBATCH --output=slurm_bracken_job%J.out
  #SBATCH --mem-per-cpu=10G
  #SBATCH --cpus-per-task=32
  
  # we load kraken2 and bracken into our environment:
  ml kraken2
  ml bracken
  
  NAME=$1
  
  srun bracken -d /workspaces/groups/database/nt-taxonomy-2021-02-04_braken/ -i ${NAME}.kreport -o ${NAME}.bracken -r 75 -l S
  
  ```
  
  This is then run using:
  
  ```
  for i in $(ls -1 ./*.report | sed 's/.report//'); do sbatch Test_Kraken.sh "$i"; done
  
  ```
  
  **Tags:** sequence-analysis, metagenome
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: It would be helpful if you could give details about your Bracken installation, the structure of your Kraken2 reports (what do the first few lines look like?), and the exact command you ran that threw the error  
  > **username_0**: I've updated the main post - I have used a couple of different databases as was suggested in a github post that had the same problem but to no avail.  
  > **username_3**: Thanks thats much better. My advice is one working first without the bash for loop. Bracken works, what I think is somethings not right in the run command.  
  > **username_0**: I have just tried running a basic `bracken -d /workspaces/groups/database/nt-taxonomy-2021-02-04_braken/ -i Sample_1.collapsed.report -o Sample_!.report.bracken -r 75 -l S` and still the same error  
  > **username_3**: I personally dunno. I do know is Bracken works and adjusts the frequency of the bacterial estimates from Kraken. I would personally try with their sample data which is here https://github.com/jenniferlu717/Bracken/commit/a6283e34c3925afe1e1bca3527e9fe0066fcae61#diff-223bc6965d2713e87fc5a41de1d0d94090ca3ea14ac92990c7191826b4e98df7  
  > **username_4**: I had the same error. Here is how I fixed it. My problem was my kraken2 file. I ran kraken2 with the report zero counts option. When I deleted that, all was fine. I also used to run kraken2 with a confidence level of 0.6. I also removed that. Os you probably want to go back to your kraken2 report file and toy with how you generate this to make bracken work. Hope this helps.  
  
  ---
  
  ## 0 answers
  
  