<p>I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
<a href="https://i.sstatic.net/X0i7W.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/X0i7W.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2023-08-01T21:35:20.973Z
Thanks for your question. As a general point it's always good to write out the error in asci rather than have an image. It makes it difficult to read and remember at least on my browser. The context of the question is processing mass-spec and I don't know if anyone here knows (maybe someone does). Is there a file format issue per chance?
M__
CC BY-SA 4.0
2023-08-02T16:32:35.547Z
the file format that I use as input is control.raw and treated.raw for fragpipe and affter running it i got the following log which is below:
Mahendra Singh
CC BY-SA 4.0
2023-08-02T16:35:37.090Z
Checking database...
Failed in checking /home/ms/MS/Control_1.raw. Will ignore it.
Failed in checking /home/ms/MS/Treated_1.raw. Will ignore it.
Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
There are corrupted files. Please remove those files and re-start the task.
Checking spectral files...
/home/ms/MS/Control_1.raw: Scans = 0
/home/ms/MS/Treated_1.raw: Scans = 0
Process 'MSFragger' finished, exit code: 1
Process returned non-zero exit code, stopping
Mahendra Singh
CC BY-SA 4.0
2023-08-02T19:11:24.277Z
Edit your post and add the plain text content there with proper formatting.
Ram RS
CC BY-SA 4.0
2023-08-25T05:26:45.443Z
Thanks for your valuable time, well my error has been resolved through Fragpipe support Here I am adding the discussion link below: 
https://github.com/Nesvilab/FragPipe/issues/1207
Mahendra Singh
<genomics><proteomics><systems-biology>
running fragpipe
# running fragpipe

(Asked by: username_0 on 2023-08-01)

I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
[![enter image description here](https://i.sstatic.net/X0i7W.png)](https://i.sstatic.net/X0i7W.png)

**Tags:** genomics, proteomics, systems-biology
> **Comments:**
> **username_1**: Thanks for your question. As a general point it's always good to write out the error in asci rather than have an image. It makes it difficult to read and remember at least on my browser. The context of the question is processing mass-spec and I don't know if anyone here knows (maybe someone does). Is there a file format issue per chance?  
> **username_0**: the file format that I use as input is control.raw and treated.raw for fragpipe and affter running it i got the following log which is below:  
> **username_0**: Checking database... Failed in checking /home/ms/MS/Control_1.raw. Will ignore it. Failed in checking /home/ms/MS/Treated_1.raw. Will ignore it. Batmass-IO binaries for Thermo support and/or Thermo native libraries not found Batmass-IO binaries for Thermo support and/or Thermo native libraries not found There are corrupted files. Please remove those files and re-start the task. Checking spectral files... /home/ms/MS/Control_1.raw: Scans = 0 /home/ms/MS/Treated_1.raw: Scans = 0 Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping  
> **username_2**: Edit your post and add the plain text content there with proper formatting.  
> **username_0**: Thanks for your valuable time, well my error has been resolved through Fragpipe support Here I am adding the discussion link below:  https://github.com/Nesvilab/FragPipe/issues/1207  

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## 0 answers

