Answers.Body: <p>This indeed looks like some sort of binary file. I have seen bunch of those when people renamed <code>.fastq.gz</code> to <code>.fastq</code> without actually uncompressing them. However, as you say, this is not your case, as <code>file pair1.fastq</code> would identify the file as <code>gzip compressed data</code>.</p>
  <p>Looking at possible return values of <code>file</code> comments <a href="https://unix.stackexchange.com/questions/151008/linux-file-command-classifying-files">here</a>, <code>data</code> basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-13T13:06:37.947Z
Answers.Text: thanks again for the quick response. I was afraid that that might be the case. unfortunately the file came from a collaborator not a public database. I will have to bring that to their attention.
Answers.UserDisplayName: iichelhadi
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Answers.CreationDate: 2021-05-13T13:03:34.673Z
Answers.LastActivityDate: 2021-05-13T13:03:34.673Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I <code>cat</code> the file I get what seem to me to be binary syntax but not sure?</p>
  <p><a href="https://i.sstatic.net/CvKUz.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CvKUz.png" alt="weird output" /></a></p>
  <p>However when I <code>cat</code> into the other pair-end the output seems fine</p>
  <p><a href="https://i.sstatic.net/N9ouH.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/N9ouH.png" alt="correct output" /></a></p>
  <p>Any help/suggestion/solution would be greatly appreciated.</p>
  <p>It does seem to be compressed with a missing suffix:</p>
  <pre><code>file pair1.fastq
     pair1.fastq: data.
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-13T12:52:07.110Z
Comments.Text: When I run `file pair1.fastq` on the problem fastq file I get the following output: `pair1.fastq: data`. When I run it on the other pair-end file which doesn't have any issues I get `pair2.fastq: gzip compressed data, extra field`
Comments.UserDisplayName: iichelhadi
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-14T18:14:47.683Z
Comments.Text: `gzip compressed data, extra field` is probably produced using `bgzip`. If it were simple `gzip`, the `extra field` part wouldn't be there.
Comments.UserDisplayName: Ram RS
Tags: <phylogenetics><ngs><trimming><bowtie2>
Title: fastq file format unknown
ThreadText: # fastq file format unknown
  
  (Asked by: username_0 on 2021-05-13)
  
  I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I `cat` the file I get what seem to me to be binary syntax but not sure?
  
  [![weird output](https://i.sstatic.net/CvKUz.png)](https://i.sstatic.net/CvKUz.png)
  
  However when I `cat` into the other pair-end the output seems fine
  
  [![correct output](https://i.sstatic.net/N9ouH.png)](https://i.sstatic.net/N9ouH.png)
  
  Any help/suggestion/solution would be greatly appreciated.
  
  It does seem to be compressed with a missing suffix:
  
  ```
  file pair1.fastq
     pair1.fastq: data.
  
  ```
  
  **Tags:** phylogenetics, ngs, trimming, bowtie2
  
  > **Comments:**
  > **username_0**: When I run `file pair1.fastq` on the problem fastq file I get the following output: `pair1.fastq: data`. When I run it on the other pair-end file which doesn't have any issues I get `pair2.fastq: gzip compressed data, extra field`  
  > **username_1**: `gzip compressed data, extra field` is probably produced using `bgzip`. If it were simple `gzip`, the `extra field` part wouldn't be there.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-05-13. Score: 3
  
  This indeed looks like some sort of binary file. I have seen bunch of those when people renamed `.fastq.gz` to `.fastq` without actually uncompressing them. However, as you say, this is not your case, as `file pair1.fastq` would identify the file as `gzip compressed data`.
  
  Looking at possible return values of `file` comments [here](https://unix.stackexchange.com/questions/151008/linux-file-command-classifying-files), `data` basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).
  
  > **Comments:**
  > **username_0**: thanks again for the quick response. I was afraid that that might be the case. unfortunately the file came from a collaborator not a public database. I will have to bring that to their attention.  
  
  ---
  
  